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revision 1.1469 by ifenty, Wed Jun 29 21:44:26 2011 UTC revision 1.1662 by jmc, Fri Jun 1 12:56:13 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      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
9        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
10      - use h0FacW & S to compute hFac_surfW & S in calc_surf_dr.F (more similar
11        to calc_r_star.F); update results of experiment internal_wave and
12        tutorial_global_oce_in_p (affected @ truncation level).
13    o pkg/shelfice:
14      - add parameterisation of advective-diffusive flux into the ice shelf
15        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
16      - simply eps3/3a computation
17    o eesupp:
18     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
19       between tiles, just fill-in edges assuming locally periodic subdomain) and
20       add corresponding exchange subroutines (EXCH0);
21     - new CG-solver version (_EX0) for disconnected-tiles special case.
22    o model/src (CG-solvers):
23     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
24       (similar final residual output and max-Iter number as with standard version);
25     - allows to store and use lowest-residual solution (standard & _SR versions);
26     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
27     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
28    o eesup/src:
29     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
30       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
31    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
32    
33    checkpoint63m (2012/04/27)
34    o pkg/shelfice:
35     - account for partical cells in surface level below ice-shelf for hydrostatic
36       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
37    o ad test experiments:
38     - update and rename to "ad_optfile.local" local AD-optfile specific to a
39       particular adjoint verification experiment (in verification/*/code_ad/)
40    o pkg/seaice & pkg/exf:
41     - Part two of ECCO-CLIVAR code merges.
42       Completes merge of seaice area relax. code.
43       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
44       to be set in EXF_OPTIONS.h since this pkg controls its I/O
45       (and avoids second CPP option in SEAICE_OPTIONS.h)
46     - change default value of costIceStart & costIceEnd to a valid date.
47     - add snowPrecip to HSNOW in seaice_growth
48    o pkg/ptracers:
49     - move ptracers summary and setup check into separated S/R ; add a check for
50       valid PTRACERS_Iter0 value (error+stop or just warning).
51    o pkg/cal (+ pkg/ecco):
52     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
53       as input; and for AD, unless both are not differentiable (e.g., k index)).
54    o model/src:
55     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
56       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
57       temporary set to usingZCoords value (to be changed to F when using shelfice).
58     - hydrostatic pressure: implement partial cell near the surface also for
59       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
60       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
61    o pkg/ctrl/ctrl_init.F:
62     - add a formal parameter to s/r ctrl_init_rec to print
63       xx_$(ctrl_valiable)_file for easier debugging
64     - move call of cal_* routines into the if-block where they are really
65       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
66       to specify a startdate
67    o pkg/seaice:
68     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
69       global_ocean.cs32x15/code versions).
70     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
71       verification experiment global_ocean.cs32x15.seaice and update results.
72    o pkg/exf:
73     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
74       (according to useExfYearlyFields).
75    o pkg/cal:
76     - move calendar setting & summary (previously in cal_readparams.F) into new
77       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
78       length of the simulation is set (after SET_PARMS call); This is an attempt
79       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
80     - For safety: keep a record of pkg/cal parameter settings status
81               to allow to STOP if one pkg/cal S/R is called too early.
82     - add a stop in all basic pkg/cal subroutines if called before setting is done.
83     - modify cal_getdate.F: stop when nothing was returned;
84       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
85       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
86    
87    checkpoint63l (2012/04/04)
88    o pkg/bbl:
89      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
90        update global_with_exf output.yearly.txt file.
91    o pkg/cal:
92      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
93      - remove 2 unsused and very short (1 line only) functions ;
94      - remove unsused subroutines from AD-Diff list.
95    o model/src:
96      - start to implement clean wait to stop in initialization S/R (config_check.F,
97         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
98    o folowing PRINT_MESSAGE changes:
99      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
100    o pkg/bbl:
101      - modification so it can work with z*
102      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
103      - global_with_exf/input.yearly verification; changes output.yearly.txt
104    o eesupp/src:
105      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
106        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
107      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
108        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
109      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
110      - when using MPI, always set usingMPI=T ; set default accordingly and stop
111        if not consistent.
112      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
113        argument is zero (in case called within single-thread section).
114    o pkg/fizhi:
115        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
116        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
117    o pkg/exch2:
118      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
119        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
120      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
121        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
122        with bad ones coming from a not-yet-updated halo.
123        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
124    o pkg/frazil:
125        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
126        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
127    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
128    o verification/lab_sea
129      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
130      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
131      * nTimeSteps 3 -> 4
132      * changed reference output accordingly
133    o pkg/ctrl:
134      * fix ctrl_get_gen for xx_sst, xx_sss
135    o pkg/fizhi:
136      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
137        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
138      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
139        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
140        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
141    o pkg/gmredi:
142      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
143    o pkg/fizhi:
144      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
145        (old)aces open64 tuv test.
146    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
147    o pkg/mom_vecinv:
148      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
149        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
150        with non-lin free-surf).
151    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
152      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
153      some compilers (gfortran 4.6.0 on MacOS)
154    o momentum:
155      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
156        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
157        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
158    
159    checkpoint63k (2012/03/17)
160    o model/src:
161       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
162         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
163       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
164         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
165    o model/src: solve_*diagonal.F
166       - replace division with multiplication by inverse (similar to original version)
167         update output of AD exp. global_ocean.90x40x15.
168       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
169         to enable the use of the vectorized & differentiable solve_tridiagonal.F
170       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
171         vertical advection (to get solve_tridiagonal tested in AD mode).
172    o pkg/seaice: ECCO-CLIVAR merge:
173      1. seaice AREA relaxation
174         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
175         * runtime flag: SEAICE_tauAreaObsRelax
176      2. modified global mean cost imbalance code: CPP option
177          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
178    o another iteration on solve_*diagonal.F
179       Make choices independent of AUTODIFF
180       Default will be the adjoinable vectorized version.
181       Alternative choices are:
182       * non-adjoinable original version with low memory footprint:
183         #define SOLVE_DIAGONAL_LOWMEMORY
184       * still adjoinable but does not vectorize (k as inner-most loop):
185         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
186    o testreport
187     - add option to use a home made wrapper around "make"
188     - remove MITGCM_IEEE env. variable (no longer active)
189    o pkg/shelfice
190     - improve computation of friction velocity for velocity dependent
191       exchange coefficients: include velocities into SHELFICEBoundaryLayer
192       block to average velocities vertically
193     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
194    o Modify diagonal solvers, now three versions (upon request):
195      #ifndef SOLVE_DIAGONAL_AUTODIFF
196        1. default version (dating back a while ago)
197      #else /* def SOLVE_DIAGONAL_AUTODIFF */
198      # ifdef SOLVE_DIAGONAL_KINNER
199        2. adjoinable version with k-innermost loop (G. Forget)
200      # else
201        3. adjoinable vectorized version of 2.
202      # endif
203      #endif /* SOLVE_DIAGONAL_AUTODIFF */
204      All flags are currently set within routines, but could/should be moved to CPP-options.
205      Array bounds for 1. are as before, for 2.,3. cover the entire domain
206      (could be changed for 1. too).
207    o verification/lab_sea (fwd):
208      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
209        use 7 categories (except hb87), new solve4temp params (except salt_plume),
210        constant salinity (=4) or variable salinity (salt_plume) done through
211        SItracer.
212    o pkg/seaice:
213      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
214      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
215         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
216        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
217        SEAICE_freeze got retired) but already better than previously with
218        SEAICE_freeze=123456.7 deg.C;
219      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
220        (safer multi-threaded setting); always set SEAICEuseEVP;
221      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
222        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
223        stop if multiple specifications for the same coeff; make sure default
224        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
225    o pkg/obcs:
226      - allow to switch to upwind 1rst order advection scheme for the advective
227        flux computation at the open-boundary; disabled for adjoint built.
228    o pkg/ptracers:
229      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
230      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
231      - add parameter to decide when to start a tracer; use internal flag to
232        know which tracer to step-forward; switch this internal flag at the top
233        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
234        for adjoint built.
235    o pkg/seaice:
236      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
237      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
238      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
239    o pkg/ecco:
240      - fix writing of output file DiagnosCost_ClimSalt/Theta
241        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
242    o pkg/seaice:
243      - add missing initialisation of COR_ICE array in dynsolver.F
244      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
245        compiled either way, and is tested in all exps (multidim was only tested
246        in lab_sea ad before).
247      - cosmetic change to prepare for future addition of ITD. no change to results.
248        no defaults change.
249      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
250      - by lack of adequate verification experiments, I further used custom versions
251        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
252        should be correct.
253      - avoid recomputations in ad.
254    o array initialisation in adjoint mode:
255      1) pkg/mom_common/mom_calc_ke.F:
256        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
257        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
258        part this initialisation is gone, resulting in Floating Point Exception
259        (caught by open64 compiler with debug option).
260      2) model/src/convective_weights.F
261        set output convectCount over the full array range (instead of doing
262        an update): this fix a similar issue when called within recomputation (adjoint)
263        which could by-pass the initialisation (normally done in the caller S/R).
264    o pkg/seaice:
265      - final version of turbulent flux params, as agreed at MIT ice meet:
266           SEAICE_mcPheePiston (default is ~ 0.000875)
267           SEAICE_mcPheeTaper (default is 0.)
268           SEAICE_frazilFrac (defualt is 1.)
269           SEAICE_mcPheeStepFunc (default is false)
270      - changes results at trunction error level
271      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
272    o added pkg/frazil:
273      - see frazil_description.tex for details
274      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
275    o pkg/shelfice/shelfice_thermodynamics.F
276      - fix exponents for velocity dependent exchange coefficients: change
277        from 2/3(=0) to 0.66666666666666667
278      - move computation of velocity dependent exchange coefficients into
279        separate loop, so that it applies to both thermodynamics
280      - move some divisions by constants out of loops
281    
282    checkpoint63j (2012/02/16)
283    o pkg/seaice:
284      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
285      - SItracer:  added run time params, and allow coupling to ocn salinity.
286    o pkg/seaice: remove (almost) all divisions by constants within loops
287      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
288      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
289      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
290      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
291    o pkg/seaice :
292      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
293        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
294      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
295      - add permanent SItflux diag that corresponds to TFLUX but includes
296        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
297      - allow activation/testing of a fix for suspected missing term in
298        ocn-ice heat budget (to be confirmed). To test this, you want to
299        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
300        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
301      - no change in results, fwd or ad.
302    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
303      - switch to variable freezing point.
304           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
305      - bug fix : the sublimation term that was missing is now activated.
306           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
307      - bug fix : flooding sign term for SIsal0.NE.0.
308           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
309    o pkg/seaice:
310      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
311        is now the default, and the old default constant freezing point is recovered
312        with SEAICE_tempFrz0    = -1.96,
313             SEAICE_dTempFrz_dS = 0.,
314      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
315      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
316      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
317        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
318      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
319        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
320      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
321        seaice_growth r149 for legacy branch (no results change).
322      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
323        from I. Fenty).
324      - results did not change except for global_ocean.cs32x15, mostly due to the
325        switch to variable freezing point (see above item for detail).
326    o pkg/thsice:
327      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
328        seawater freezing in thsice_calc_thickn (not used).
329    o pkg/seaice: turbulent flux term specification via run time params.
330      - replace CPP switches with run time switches to facilitate testing
331      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
332                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
333      - added runtime parameter : SEAICEturbFluxFormula
334      - move Mcphee constants to SEAICE_PARAMS.h
335      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
336                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
337                 remove seaice_summary call (moved to seaice_init_fixed)
338      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
339        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
340      - seaice_summary.F : add missing report of read turbulent flux term set up
341                           and SITRACER.
342      - seaice_check.F : check range; inform and stop if retired CPPs are used
343                         (incl. SEAICE_AGE).
344      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
345             CPP switch, same computation as before for the different options.
346      - change results at the truncation level.
347    o pkg/seaice:
348      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
349        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
350        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
351      - update verification/*/input*/data.seaice:
352        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
353        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
354        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
355        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
356    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
357      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
358        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
359        difference in results only due to machine truncation.
360      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
361        MaykutPolySatVap; keep MIN_LWDOWN.
362      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
363      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
364        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
365    o pkg/salt_plume:
366      - isolate saltPlumeFlux array exch into a specific S/R called from
367        do_oceanic_phys.F
368      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
369    o verification:
370      - move untested set-up to MITgcm_contrib/verification_other.
371    o pkg/seaice:
372      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
373    o pkg/seaice:
374      - seaice_solve4temp.F (keeping results unchanged):
375        * add 2 future run-time params to select which saturation vapor pressure
376          formula is used and how post-iteration fluxes are set.
377          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
378        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
379          the linearized expression to stay consistent with tsurf finding.
380      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
381        can be < 0.
382    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
383      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
384        conductive heat flux F_c , and add it explicitly when updating tsurf as
385        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
386        so that now F_ia has a consistent meaning through the entire routine.
387        This causes differences at truncation level: update output of fwd exp.
388        global_ocean.cs32x15.seaice.
389    o pkg/seaice:
390      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
391        of arrays, sign/direction of fluxes; no effect on results.
392      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
393        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
394        note: this should have been done before changing celsius2K default.
395      - to keep results unchanged, add back old value of celsius2K in verification
396        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
397      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
398        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
399        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
400        freezing temp is consistent with value in seaice_growth.F ; this causes
401        differences at machine truncation level: update lab_sea AD output (3/4).
402    o pkg/seaice:
403      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
404        and climsst/sss even when using seaice (to prevent calculation that might
405        use SST on land); does not affect any verification exp.
406      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
407        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
408    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
409      over land (non-legacy code)
410    o vectorize salt_plume package:
411      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
412      - this code computes plumebk everywhere (also over land), thus requires
413        code to avoid divisions by zero and catch the case of kLev=Nr.
414      - efficiency of salt_plume_frac is still sub-optimal
415    o tools (genmake2):
416      - fix makefile NAME specification (option: -makefile NAME) by adding
417        "-f $MAKEFILE" in few places where it was missing including makedepend
418        command (contribution from Paul).
419    
420    checkpoint63i (2012/01/24)
421    o model/src:
422      - add factorized versions of some EOS code to find_rho.F,
423        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
424    o model/src:
425      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
426      - change default celsius2K from 273.16 to 273.15
427      - to keep results unchanged, add back old value of celsius2K in verification
428        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
429         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
430    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
431      to make TAF generate vectorizable code
432    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
433       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
434       have flags that do this more efficiently.
435    o pkg/diagnostics/diagstats_calc.F
436      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
437    o pkg/obcs (with exch2):
438      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
439        and remove code (in obcs_readparms.F) which was based on EXCH of indices
440        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
441    o pkg/exf and seaice exp:
442      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
443        so that switching off area & heff advection flags does not affect results.
444      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
445      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
446        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
447        results of verification experiments: 1D_ocean_ice_column(fwd),
448        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
449        and offline_exf_seaice (all 4).
450    o pkg/seaice:
451      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
452        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
453      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
454        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
455        not multi-dim advection;
456      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
457        SHORTWAVE_HEATING #undef.
458    o optim: make Makefile more robust (?)
459    o pkg/obcs:
460      * fix treatment of obcs_read_pickup for TAF
461    o pkg/shelfice:
462      * add missing initialisation of num_shifwflx
463      * new adjoint verification exp. for isomip
464      * change Prandtl and Schmidt numbers from generic formulations
465        (in terms of model diffus. and visc.) to separate runtime
466        parameters, with Holland and Jenkins (1999) default values.
467    o pkg/exf (interpolation):
468      - extended input field (2 rows) near the N & S poles:
469        * fill in with the symetric value (when even Nb of data in longitude)
470        * add average value at the poles only for scalar quantities ; for vector
471          component interpolation, skip the averaging and keep duplicated values,
472          unless the 2 components have same location (uvInterp=T) in which case
473          interpolate the 2 components together using S/R EXF_INTERP_UV.
474      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
475        together: this allows to account properly for local orientation when
476        averaging at N & S pole.
477      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
478        exf-interpolation near N & S poles. Undef by default.
479      - add debug check/print on 1rst iter if debugLevel >=2.
480    o pkg/exf:
481      - change masking flags definition (no longer "parameter"), put them in
482        common block and set them in S/R EXF_INIT_FIXED.
483      - change recognized masking flag from s,u,v to c,w,s since the mask
484        to use (maskC,W,S) depends on position on model grid and has little to
485        do with scalar/vector difference; fix masking if using P-coordinates.
486      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
487        and update results of exp. global_with_exf (x2).
488      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
489    o pkg/obcs
490      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
491    o pkg/exf (interpolation):
492      - assume periodicity in X only if input field cover full longitude range.
493      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
494        and should vectorise).
495      - fix input lat of the 2 added row (in case we provide N.pole data).
496    
497    checkpoint63h (2011/12/30)
498    o pkg/seaice:
499      - change declaration of UVM from _RL to _RS in order to get B-grid
500        uIce,vIce monitor when _RS = real*4
501    o pkg/offline:
502      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
503      - compute vertical velocity if not read from file (switch on exactConserv
504        & staggerTimeStep);
505      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
506    o verification:
507      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
508        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
509        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
510      - update output of exp. global_ocean.cs32x15.viscA4 after changing
511        grid-file angles (used here for coriolis-3d);
512      - remove (or gzip) few files not needed to run fizhi-cs experiments.
513    o pkg/exf (vector interpolation):
514      - rotate vector component toward local grid-axis orientation using grid-angles
515        (stored in GRID.h) instead of locally computed rotation angle; keep old code
516        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
517    o pkg/seaice:
518      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
519        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
520    o pkg/PKG_OPTIONS.h files:
521      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
522        outside of the #ifdef ALLOW_THISPKG / #endif block.
523      - update verification/*/code/PKG_OPTIONS.h files.
524    o add a verification experiment (offline_exf_seaice/input.seaice) that test
525      the B-grid LSOR solver
526    o pkg/seaice: sort out emissivity and long wave radiation step 2:
527      - add emissivity for snow and ice as new run-time parameters
528        (unfortunately) that default to the corresponding exf values; this
529        changes results in most verification experiments so that for backward
530        compatibility these parameter have to be set explicitly to inconsistent
531        values (ugly);
532      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
533        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
534        until we agree how to handle this bug properly
535    o pkg/exf (interpolation):
536      - add a set of run-time param ({inputfield}_interpMethod), one for
537        each interpolated input field, to select the interpolation method
538        with a value of zero switching off the interpolation;
539      - print interpolation parameters to standard output;
540      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
541        (to use instead runoff_interpMethod=0 in data.exf).
542      - simplify default setting of interpolation parameters (for all fields,
543        set position to match model grid cell-center position, leading to trivial
544        interpolation in case of regular Lat-Lon grid) and fix for the case of
545        non-uniform delY.
546    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
547       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
548       this factor is absolutely required, because the lw exitance (= out-going
549       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
550       where the reflectivity rho = 1-emissivity for conservation reasons. Once
551       this is established, we can remove the CPP-Flag (if we want to).
552    o pkg/seaice:
553      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
554        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
555      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
556        what the name implies (and not emissivity*BoltzmannConstant), this means
557        the old default value of 5.5e-8 now means
558        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
559        S/R exf_readparms
560      - FV-discretization of the B-grid LSOR solver, turn on with
561        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
562        of the calling routine dynsolver, so that B and C-grid code look a
563        little more alike.
564      - fix index bugs in ostres.F (B-grid code)
565    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
566    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
567      default for SEAICE_emissivity, if useEXF; requires setting a wrong
568      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
569      backward compatiblity
570    o model/src: use sigmaR in calc_ivdc
571    
572    checkpoint63g (2011/12/16)
573    o pkg/seaice/seaice_growth.F:
574      fix heat conservation of the coupled ocean-seaice system.
575      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
576      solid vs liquid water treatment is resolved via QNET.
577    o pkg/seaice/seaice_growth.F:
578      add missing term for sublimation in saltFlux, which was breaking conservation.
579    o pkg/seaice/seaice_model.F:
580      Remove this patholigical case treatment in evolution branch,
581      where it is un-necessary and breaks conservation.
582      Update global_ocean.cs32x15/results accordingly for
583      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
584    o model/src:
585      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
586      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
587    o pkg/obcs:
588      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
589      tendency for temperature and salinity that is then applied to update
590      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
591      horizontal advection and diffusion contributions on the boundary (in
592      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
593      removing the mask in S/R timestep_tracer. The advantage of this approach is
594      that the updated tracer values include contributions from the surface
595      forcing and vertical diffusion.
596      This modification changes exp4.stevens because of vertical diffusion.
597    o model/src:
598      change non-curvilinear grid setting to also work with exch2 + blank tiles:
599      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
600        face dimensions.
601      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
602        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
603        and INI_SPHERICAL_POLAR_GRID.
604      change test-experiment global_ocean.90x40x15:
605      - split the domain in many more tiles (9x4 tiles of 10x10 each);
606      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
607      - update results of both test (std & dwnslp).
608    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
609       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
610    o model/src:
611      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
612        and fix initialisation when using sigma-coords.
613    o model/src:
614     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
615       to their current value at the beginning of forward_step.F": add a new run-time
616       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
617     - set doResetHFactors=T in the following test exp:
618        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
619        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
620        and tutorial_global_oce_in_p (nonLinFS in p)
621    o pkg/ecco
622      - added IES cost term
623    o verification/advect_xz
624      - scale down the depth by 1/100 (from 200 km to just 2.km)
625      - add secondary test using divergent flow, r-star and implicit vertical advection.
626      - add note (check_conserve_TS.txt) and matlab script to check global
627        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
628    o pkg/rbcs:
629      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
630    o pkg/obcs (Stevens BCs):
631      - fix various problems in the phase speed computations of the Stevens
632        boundary conditions:
633        - sign error for western and southern boundaries,
634        - time tendencies were underestimated by factor of dTracerLev and some just
635          zero (for multidim advection schemes) -> now estimate time tendencies
636          from difference between previous (n) time level and the one before (n-1);
637          this requires storing a field per tracer per boundary, also in the pickup
638          files.
639        - replace deltaTmom in cflMer/Zon computation with dTracerLev
640        - set default phase velocity to cflMer/Zon
641      - update verification experiment exp4.stevens
642    o pkg/generic_advdiff (implicit_r):
643      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
644        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
645      - fix implicit vertical diffusion or advection with NonLin FreeSurf
646        (was using current recip_hFacC instead of future recip_hFacC): set future
647        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
648        solver S/R ;
649      - fill diagnostics of vertical advective fluxes (computed from tendency)
650        when using implicit vert. advection;
651      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
652         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
653         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
654         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
655    o pkg/diagnostics:
656      - add diags for T & S tendency which goes through Adams-Bashforth.
657    
658    checkpoint63f (2011/11/30)
659    o pkg/obcs/obcs_calc_stevens.F:
660      - join some loops to reduce number of if-statements
661      - fix a bug in code for northern and southern boundaries.
662    o pkg/seaice/seaice_init_varia.F
663      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
664        caused zero ice-velocities for the B-grid code
665    o pkg/seaice/seaice_init_fixed.F
666      - fix a bug in the initialisation of the second metric terms
667        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
668      - this affects all seaice configurations with useCurviLinearGrid = .true.
669        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
670        = .true. (default)
671      - the only verification experiment affected is global_ocean.cs32x15:
672        icedyn, seaice, and seaice_dynmix (AD)
673    o pkg/thsice/thsice_diagnostics_state.F
674      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
675        not contain garbage that can lead to surprises in diagstats_calc.F
676    o model/src:
677      - move bi,bj loops inside INTEGR_CONTINUITY ;
678      - call INTEGR_CONTINUITY directly from forward_step.F
679        (previously called from momentum_correction_step.F)
680      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
681        forward_step.F and pkg/ecco/the_main_loop.F
682    o model/src/do_oceanic_phys.F:
683      - reset addMass to zero only if useICEFRONT ;
684      - separated k-loop for rhoInSitu calculation ;
685      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
686        and at constant T,S (= WdRHOdP);
687      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
688        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
689        transport of locally-referenced potential density);
690        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
691    o gluemnc:
692      - replace ncrcat with ncks when adding variables to *.glob.nc
693      - change the way variables without record dimensions are handled so that
694        files that have variables with and without record variables can be glued:
695        add a record dimension with a new unique name to be able to differentiate
696        between variable with and without a-prior record dimensions. Remove
697        this record dimension before adding the variable to the *.glob.nc file.
698        This procedure automatically works also for grid.*.nc files that do not
699        have any record dimension.
700    o verification/cpl_aim+ocn:
701      - generate new reference output on baudelaire (gfortran, mpich2) (previously
702        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
703    o pkg/obcs/obcs_calc_stevens.F:
704      - add code for northern and southern boundaries.
705      - reorder some loops to save some operations and so that drFBar can be scalar
706    o model/src:
707      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
708        truncation) and add diagnostics for Adams-Bashforth tendency increment.
709      - update test-exp. AD output:
710        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
711      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
712        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
713        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
714        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
715        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
716        tutorial_plume_on_slope.
717    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
718      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
719      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
720      does not even come with an F77 compiler anymore, this should not be
721      a limitation
722    
723    checkpoint63e (2011/11/06)
724    o pkg/seaice adjoint of LSR:
725      - substantially rework STORE dirs.
726      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
727        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
728        and only perform SOLV_MAX_FIXED adjoint iters.
729        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
730        always goes to same record, meaning that the last forward field will be
731        the one used in the adjoint - an approximation.
732      - now produces non-zero LSR-related gradients, and acceptable gradients for
733        An's zonal (x-z) test case (to be checked in)
734      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
735        (but these are screwed up by the thermodynamics in the first place);
736        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
737        output_adm.txt also reflects changes to seaice_lsr
738      - global_ocean.cs32x15:
739        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
740          (output_adm.seaice.txt was updated)
741        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
742          (output_adm.seaice_dynmix.txt)
743    o test-exp. exp4+stevens:
744      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
745    o pkg/seaice (lsr solver):
746      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
747        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
748      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
749      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
750        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
751      - compute (with new S/R) and print initial (+ free-driff sol. if available)
752        and final residual of linearised system.
753    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
754      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
755    o pkg/obcs: Stevens BCs (still only for east and west)
756      - fix Stevens BCs by using intermediate velocities of previous
757        time step as "baroclinic" contribution rather velocity of one grid cell
758        inside the boundaries; more consistent but makes the entire treatment
759        more complicated, requires new pickup files and two new S/Rs:
760        obcs_copy_uv_n and obcs_save_uv_n
761        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
762        (undefined by default)
763      - silently move computation of some grid factors into separate loops to
764        save some recomputations
765      - add a hack for non-linear free surface
766      - add a verification experiment to exp4 that tests this code
767    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
768    
769    checkpoint63d (2011/10/25)
770    o pkg/obcs + seaice-dynamics:
771      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
772        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
773        values (consistent with an implicit method).
774      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
775        return to older implementation (same results as before); note that none of
776        the "experimental" OBCS_SEAICE options are implemented in the new version.
777      - switch test exp. seaice_obcs to use new version (update output).
778    o pkg/seaice:
779      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
780      - add parenthesis in Water-Ice drag calculations (evp & lsr);
781      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
782        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
783      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
784        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
785    o pkg/layers:
786      - Include potential density as new coordinate (Thanks to David Munday)
787    o pkg/dic:
788      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
789        carbonate computation/output to CALC_PCO2_APPROX
790    o pkg/generic_advdiff
791      - make TAF generate code that vectorizes:
792        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
793    o model/src:
794      - improve vectorization also for adjoint code of
795        solve_tridiagonal and solve_pentadiagonal. As this requires up to
796        5 new 3D-fields, this code is only turned on for the combination of
797        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
798        for singular matrix check (only for TARGET_NEC_SX).
799      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
800        ALLOW_AUTODIFF. This flag now needs to be set outside of
801        solve_tri/pentadiagonal.F
802    o pkg/exf:
803      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
804        optional namelist EXF_NML_OBCS).
805      - add many debug-print (to trace down where pkg/cal error msg comes from)
806    o pkg/mom_vecinv/mom_vi_hdissip.F
807      - rearrange loops so that vectorization is improved and in particular
808        the adjoint routine vectorizes. The code is a little longer now, but I
809        think easier to read.
810        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
811    o pkg/seaice:
812      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
813    o pkg/exch2:
814      - alternative code (without tile x tile matrix) for cumulated (global) sum;
815        used as default; keep using matrix version in adjustment.cs-32x32x1.
816    o tools/build_options:
817      - after merging some MPI and/or multi-threads specific optfiles so that
818        the modified default optfile support both built (using genmake2 -mpi
819        for the MPI built, using genmake2 -omp for OpenMP built),
820        move now obsolete optfiles to tools/build_options/unsupported/
821       (add copy of email sent to support list in doc/optfiles_changes.txt)
822    
823    checkpoint63c (2011/09/28)
824    o pkg/ebm:
825      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
826        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
827    o pkg/seaice (SItracer pickup)
828    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
829      To be done:
830      - thorough testing of missing fields in S/R seaice_read_pickup
831      - thorough matching between generic tracers and specific fields used
832        (e.g. volume-weighted age, area-weighted age, salinity, ...)
833    o pkg/grdchk:
834      - all procs calculate and print finite-difference gradient (for testreport)
835      - change description output used by testreport;
836      - AD testing: also compare and report Finite-difference gradient;
837        => update all output_adm*.txt
838    o test exp. global_ocean_ebm:
839      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
840        and turn on exactConserve; update (fwd) output.
841    o pkg/seaice (LSR):
842      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
843      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
844        * identical results with non-CS topology (but save up to half of EXCH calls)
845        * no much changes in cs-32 verification tests since no ice at face edges
846         (differences due to convergence criteria, since nb of iterations changed)
847        * expect some differences on lat-lon-cap grid.
848        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
849    o pkg/exch2:
850      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
851        many tiles); until alternative coding is added, just add a stop.
852    o pkg/kpp:
853      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
854        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
855    o optfiles:
856      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
857        into corresponding standard one, which now support different build:
858        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
859      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
860    o pkg/obcs (seaice):
861      - add missing EXCH for uIce,vIce after applying OBCS;
862      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
863        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
864        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
865      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
866      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
867        and eedata.mth for MPI and mutlti-threaded testing.
868    o pkg/flt:
869      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
870      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
871      - fix pickup and trajectories + profiles output with multi-threads;
872      - add parameter to select group of fields to write along trajectory and
873        profile (default unchanged);
874      - only call PORT_RAND* function when flt_noise <> 0;
875      - add multi-threaded test for verification exp. flt_example.
876    o eesupp/src:
877      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
878      - USE_OMP_THREADING: check that number of threads (from eedata) matches
879        actual number (from env.var. setting).
880    o pkg/ebm:
881      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
882      - add multi-threaded test for verification exp. global_ocean_ebm
883    
884    checkpoint63b (2011/08/29)
885    o pkg/ebm:
886      - fix sign of runoff;
887      - update directly forcing fields (Qnet,EmPmR) to use standard
888        external_forcing_surf.F (remove ebm_forcing_surf.F);
889      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
890      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
891        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
892      - update global_ocean_ebm parameters file data and update output (fwd+ad).
893    o verification/matrix_example:
894      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
895        MPI and mutlti-threaded testing.
896    o pkg/matrix:
897      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
898      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
899      - fix for multi-threaded (remove DATA statement);
900      - use standard DIFFERENT_MULTIPLE function;
901      - add MATRIX_OPTIONS.h
902    o verification/matrix_example:
903       To allow to split the domain in several tiles, change the domain size
904        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
905        Western side) of land points.
906    o (*_)write_pickup:
907      - fix few bugs in mypackage_read/write_pickup.F
908      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
909        array of length 1 (was caught by compiler syntax-check).
910    o pkg/diagnostics (velocity potential solver):
911      - fix initialisation of main diagonal matrix (for overlap values)
912    o tools/build_options:
913      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
914        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
915      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
916        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
917        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
918        and use "-devel" testreport option for standard testing on baudelaire.
919    o pkg/grdchk:
920      - Assume that all gradient-check position are within the same tile
921        corresponding to global indices (iGloTile,jGloTile) and that
922        positions (i,j indices or nbeg) are local to this tile;
923      - set tile local-indices and proc. number according to tile global-indices;
924      - remove grdchkwhichproc from namelist (retired param);
925      - send adjoint gradient to all procs so that all procs print it to STDOUT;
926      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
927    o adding package bbl (Bottom Boundary Layer)
928      description in MITgcm/pkg/bbl/bbl_description.tex
929      example/test experiment in MITgcm_contrib/bbl
930    o adjoint verifications
931      - changed 5 experiments to multi-tiles
932        * global_ocean.90x40x15
933        * obcs_ctrl
934        * offline_exf_seaice
935        * tutorial_dic_adjoffline
936        * tutorial_tracer_adjsens
937        changed reference output for those that crossed tile boundaries
938        (changed choices of gradient check positions)
939      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
940      - temporary bug fix in grdchk_loc.F for obcs
941    o genmake2 & testreport
942      - add target "obj" (just for OBJFILES files) to Makefile;
943      - add option to specify FEXTRAFLAGS on command line.
944    o pkg/mypackage:
945      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
946    
947    checkpoint63a (2011/08/02)
948    o pkg/diagnostics (velocity potential):
949      - fix velocity-potential calculation when using OBCS: balance net inflow
950        at each level (new S/R OBCS_DIAG_BALANCE).
951      - fix some of the problems with OBCS in stream-function calculation.
952    o pkg/exf/exf_readparms.F
953      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
954        EXF_NML_OBCS) more consistent, so that you need not have these lists
955        in data.exf when they are not used.
956    o optim/optim_readdata.F:
957      - add some output about obcs variables that might help debugging
958      - add a check about nvarlength
959    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
960    o pkg/diagnostics (velocity potential):
961      - fix mask for OBCS (still problems in stream-function with OBCS);
962      - add specific parameter (default = main code CG2D params) for solver;
963      - in case of poor convergence, use solution corresponding to lowest residual.
964    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
965      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
966      and should be avoided where possible.
967    o model/src (rStar):
968      - include r* effect on reference-state (PhiRef) in totPhiHyd
969        (so that it's really the potential anomaly at the cell center);
970        affect solution only if z* with full pressure in EOS.
971      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
972        update output (because of z* in totPhiHyd and viscA4 changes);
973      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
974        @ constant r) until interpolation at constant r is implemented.
975    o pkg/diagnostics
976      - fix RCENTER diagnostics in case cell center is not at interface middle
977    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
978      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
979      that THETA and SALT are "conservative temperature" and "absolute
980      salinity"
981    o pkg/ctrl
982      - fix computation of endrec in s/r ctrl_init_rec
983      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
984    o pkg/seaice/seaice_growth.F
985      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
986        remove then obsolete STORE directives
987      - fix STORE directives for tice and tices, so that only the
988        appropriate part of the fields are stored (and not the entire
989        field); update global_ocean.cs32x15.seaice AD output.
990      - cosmetic changes: adjust CPP flags and indentation for better
991        legibilty
992    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
993      Chris Wilson)
994    o pkg/gmredi:
995       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
996       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
997    
998    checkpoint63  (2011/07/11)
999    o pkg/exch2:
1000     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1001     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1002       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1003       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1004    o pkg/diagnostics:
1005     - deal with pairs of post-processed diags which are computed together; in
1006       particular, re-order list of diags within 1 file to save 2nd computation.
1007     - add S/R to compute velocity stream-function (called after velocity-potential
1008       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1009     - add parameter to select grid-point location where PsiVEL == 0.
1010    o eesupp/src:
1011       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1012       (specific S/R needed with exch2 topology - for now, just print an error msg)
1013  o pkg/shelfice  o pkg/shelfice
1014   - Implement friction velocity-dependent transfer coefficients following   - Implement friction velocity-dependent transfer coefficients following
1015     Holland and Jenkins, JPO, 1999     Holland and Jenkins, JPO, 1999
# Line 27  o pkg/seaice/seaice_growth.F: Line 1033  o pkg/seaice/seaice_growth.F:
1033      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1034      non-legacy seaice_solve4temp.      non-legacy seaice_solve4temp.
1035    - add diagnostic of the residual sublimation freshwater flux (the freshwater    - add diagnostic of the residual sublimation freshwater flux (the freshwater
1036      flux taken from the ocean if the total actual latent heat fluxes exceed      flux taken from the ocean if the total actual latent heat fluxes exceed
1037      the maximum)      the maximum)
1038    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1039     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
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