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revision 1.1496 by jmc, Mon Aug 29 03:00:09 2011 UTC revision 1.1675 by heimbach, Mon Jun 25 19:25:41 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 verification/tutorial_tracer_adjsens/
8      - compile with ALLOW_CG2D_NSA
9      - run with nonlinFreeSurf=3
10      - update reference output_adm.txt
11    o tools/genmake2:
12      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
13        refine usePROFILES switching off (only when NetCDF is not available).
14    o verification (atmospheric set-up):
15      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
16    o pkg/profiles : refine profiles and files handling.
17    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
18    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
19      - changes to use model/src/the_main_loop.F rather than the ecco version
20        in ecco type adjoint runs.
21    o model/src:
22      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
23      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
24      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
25    o model/src:
26      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
27        update output of test experiment bottom_ctrl_5x5.
28    o pkg/generic_advdiff:
29      - implement vertical bi-harmonic diffusion (for now, only for T & S and
30        only explicitly).
31    o verification/bottom_ctrl_5x5/
32      update reference output (results changed quite some time ago,
33      not sure when; but new reference results look ok in terms of grdchk)
34    o verification/1D_ocean_ice_column/
35      For verification purposes, the exact adjoint rather than an approx.
36      should be used (e.g., to comare against F.D. or TLM).
37      removed autodiff_inadmode*_ad.F routines in code_ad/
38      Update results/ accordingly.
39    o pkg/cal:
40      - change cal_getdate.F so that output date is function of input time only
41        (less ambiguous, not mixed up with input iteration number).
42      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
43    o pkg/diagnostics:
44      - implement calendarDumps also for stats-diags
45      - implement calendarDumps also for snap-shot output (negative freq)
46      - for now, ignores calendarDumps if non-zero phase-lag.
47    
48    checkpoint63n (2012/06/04)
49    o model/src:
50      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
51        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
52      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
53        similar to calc_r_star.F); update results of experiment internal_wave and
54        tutorial_global_oce_in_p (affected @ truncation level).
55    o pkg/shelfice:
56      - add parameterisation of advective-diffusive flux into the ice shelf
57        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
58      - simply eps3/3a computation
59    o eesupp:
60     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
61       between tiles, just fill-in edges assuming locally periodic subdomain) and
62       add corresponding exchange subroutines (EXCH0);
63     - new CG-solver version (_EX0) for disconnected-tiles special case.
64    o model/src (CG-solvers):
65     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
66       (similar final residual output and max-Iter number as with standard version);
67     - allows to store and use lowest-residual solution (standard & _SR versions);
68     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
69     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
70    o eesup/src:
71     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
72       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
73    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
74    
75    checkpoint63m (2012/04/27)
76    o pkg/shelfice:
77     - account for partical cells in surface level below ice-shelf for hydrostatic
78       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
79    o ad test experiments:
80     - update and rename to "ad_optfile.local" local AD-optfile specific to a
81       particular adjoint verification experiment (in verification/*/code_ad/)
82    o pkg/seaice & pkg/exf:
83     - Part two of ECCO-CLIVAR code merges.
84       Completes merge of seaice area relax. code.
85       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
86       to be set in EXF_OPTIONS.h since this pkg controls its I/O
87       (and avoids second CPP option in SEAICE_OPTIONS.h)
88     - change default value of costIceStart & costIceEnd to a valid date.
89     - add snowPrecip to HSNOW in seaice_growth
90    o pkg/ptracers:
91     - move ptracers summary and setup check into separated S/R ; add a check for
92       valid PTRACERS_Iter0 value (error+stop or just warning).
93    o pkg/cal (+ pkg/ecco):
94     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
95       as input; and for AD, unless both are not differentiable (e.g., k index)).
96    o model/src:
97     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
98       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
99       temporary set to usingZCoords value (to be changed to F when using shelfice).
100     - hydrostatic pressure: implement partial cell near the surface also for
101       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
102       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
103    o pkg/ctrl/ctrl_init.F:
104     - add a formal parameter to s/r ctrl_init_rec to print
105       xx_$(ctrl_valiable)_file for easier debugging
106     - move call of cal_* routines into the if-block where they are really
107       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
108       to specify a startdate
109    o pkg/seaice:
110     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
111       global_ocean.cs32x15/code versions).
112     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
113       verification experiment global_ocean.cs32x15.seaice and update results.
114    o pkg/exf:
115     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
116       (according to useExfYearlyFields).
117    o pkg/cal:
118     - move calendar setting & summary (previously in cal_readparams.F) into new
119       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
120       length of the simulation is set (after SET_PARMS call); This is an attempt
121       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
122     - For safety: keep a record of pkg/cal parameter settings status
123               to allow to STOP if one pkg/cal S/R is called too early.
124     - add a stop in all basic pkg/cal subroutines if called before setting is done.
125     - modify cal_getdate.F: stop when nothing was returned;
126       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
127       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
128    
129    checkpoint63l (2012/04/04)
130    o pkg/bbl:
131      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
132        update global_with_exf output.yearly.txt file.
133    o pkg/cal:
134      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
135      - remove 2 unsused and very short (1 line only) functions ;
136      - remove unsused subroutines from AD-Diff list.
137    o model/src:
138      - start to implement clean wait to stop in initialization S/R (config_check.F,
139         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
140    o folowing PRINT_MESSAGE changes:
141      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
142    o pkg/bbl:
143      - modification so it can work with z*
144      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
145      - global_with_exf/input.yearly verification; changes output.yearly.txt
146    o eesupp/src:
147      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
148        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
149      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
150        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
151      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
152      - when using MPI, always set usingMPI=T ; set default accordingly and stop
153        if not consistent.
154      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
155        argument is zero (in case called within single-thread section).
156    o pkg/fizhi:
157        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
158        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
159    o pkg/exch2:
160      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
161        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
162      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
163        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
164        with bad ones coming from a not-yet-updated halo.
165        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
166    o pkg/frazil:
167        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
168        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
169    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
170    o verification/lab_sea
171      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
172      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
173      * nTimeSteps 3 -> 4
174      * changed reference output accordingly
175    o pkg/ctrl:
176      * fix ctrl_get_gen for xx_sst, xx_sss
177    o pkg/fizhi:
178      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
179        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
180      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
181        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
182        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
183    o pkg/gmredi:
184      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
185    o pkg/fizhi:
186      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
187        (old)aces open64 tuv test.
188    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
189    o pkg/mom_vecinv:
190      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
191        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
192        with non-lin free-surf).
193    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
194      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
195      some compilers (gfortran 4.6.0 on MacOS)
196    o momentum:
197      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
198        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
199        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
200    
201    checkpoint63k (2012/03/17)
202    o model/src:
203       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
204         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
205       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
206         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
207    o model/src: solve_*diagonal.F
208       - replace division with multiplication by inverse (similar to original version)
209         update output of AD exp. global_ocean.90x40x15.
210       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
211         to enable the use of the vectorized & differentiable solve_tridiagonal.F
212       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
213         vertical advection (to get solve_tridiagonal tested in AD mode).
214    o pkg/seaice: ECCO-CLIVAR merge:
215      1. seaice AREA relaxation
216         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
217         * runtime flag: SEAICE_tauAreaObsRelax
218      2. modified global mean cost imbalance code: CPP option
219          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
220    o another iteration on solve_*diagonal.F
221       Make choices independent of AUTODIFF
222       Default will be the adjoinable vectorized version.
223       Alternative choices are:
224       * non-adjoinable original version with low memory footprint:
225         #define SOLVE_DIAGONAL_LOWMEMORY
226       * still adjoinable but does not vectorize (k as inner-most loop):
227         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
228    o testreport
229     - add option to use a home made wrapper around "make"
230     - remove MITGCM_IEEE env. variable (no longer active)
231    o pkg/shelfice
232     - improve computation of friction velocity for velocity dependent
233       exchange coefficients: include velocities into SHELFICEBoundaryLayer
234       block to average velocities vertically
235     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
236    o Modify diagonal solvers, now three versions (upon request):
237      #ifndef SOLVE_DIAGONAL_AUTODIFF
238        1. default version (dating back a while ago)
239      #else /* def SOLVE_DIAGONAL_AUTODIFF */
240      # ifdef SOLVE_DIAGONAL_KINNER
241        2. adjoinable version with k-innermost loop (G. Forget)
242      # else
243        3. adjoinable vectorized version of 2.
244      # endif
245      #endif /* SOLVE_DIAGONAL_AUTODIFF */
246      All flags are currently set within routines, but could/should be moved to CPP-options.
247      Array bounds for 1. are as before, for 2.,3. cover the entire domain
248      (could be changed for 1. too).
249    o verification/lab_sea (fwd):
250      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
251        use 7 categories (except hb87), new solve4temp params (except salt_plume),
252        constant salinity (=4) or variable salinity (salt_plume) done through
253        SItracer.
254    o pkg/seaice:
255      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
256      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
257         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
258        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
259        SEAICE_freeze got retired) but already better than previously with
260        SEAICE_freeze=123456.7 deg.C;
261      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
262        (safer multi-threaded setting); always set SEAICEuseEVP;
263      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
264        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
265        stop if multiple specifications for the same coeff; make sure default
266        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
267    o pkg/obcs:
268      - allow to switch to upwind 1rst order advection scheme for the advective
269        flux computation at the open-boundary; disabled for adjoint built.
270    o pkg/ptracers:
271      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
272      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
273      - add parameter to decide when to start a tracer; use internal flag to
274        know which tracer to step-forward; switch this internal flag at the top
275        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
276        for adjoint built.
277    o pkg/seaice:
278      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
279      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
280      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
281    o pkg/ecco:
282      - fix writing of output file DiagnosCost_ClimSalt/Theta
283        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
284    o pkg/seaice:
285      - add missing initialisation of COR_ICE array in dynsolver.F
286      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
287        compiled either way, and is tested in all exps (multidim was only tested
288        in lab_sea ad before).
289      - cosmetic change to prepare for future addition of ITD. no change to results.
290        no defaults change.
291      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
292      - by lack of adequate verification experiments, I further used custom versions
293        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
294        should be correct.
295      - avoid recomputations in ad.
296    o array initialisation in adjoint mode:
297      1) pkg/mom_common/mom_calc_ke.F:
298        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
299        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
300        part this initialisation is gone, resulting in Floating Point Exception
301        (caught by open64 compiler with debug option).
302      2) model/src/convective_weights.F
303        set output convectCount over the full array range (instead of doing
304        an update): this fix a similar issue when called within recomputation (adjoint)
305        which could by-pass the initialisation (normally done in the caller S/R).
306    o pkg/seaice:
307      - final version of turbulent flux params, as agreed at MIT ice meet:
308           SEAICE_mcPheePiston (default is ~ 0.000875)
309           SEAICE_mcPheeTaper (default is 0.)
310           SEAICE_frazilFrac (defualt is 1.)
311           SEAICE_mcPheeStepFunc (default is false)
312      - changes results at trunction error level
313      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
314    o added pkg/frazil:
315      - see frazil_description.tex for details
316      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
317    o pkg/shelfice/shelfice_thermodynamics.F
318      - fix exponents for velocity dependent exchange coefficients: change
319        from 2/3(=0) to 0.66666666666666667
320      - move computation of velocity dependent exchange coefficients into
321        separate loop, so that it applies to both thermodynamics
322      - move some divisions by constants out of loops
323    
324    checkpoint63j (2012/02/16)
325    o pkg/seaice:
326      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
327      - SItracer:  added run time params, and allow coupling to ocn salinity.
328    o pkg/seaice: remove (almost) all divisions by constants within loops
329      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
330      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
331      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
332      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
333    o pkg/seaice :
334      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
335        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
336      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
337      - add permanent SItflux diag that corresponds to TFLUX but includes
338        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
339      - allow activation/testing of a fix for suspected missing term in
340        ocn-ice heat budget (to be confirmed). To test this, you want to
341        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
342        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
343      - no change in results, fwd or ad.
344    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
345      - switch to variable freezing point.
346           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
347      - bug fix : the sublimation term that was missing is now activated.
348           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
349      - bug fix : flooding sign term for SIsal0.NE.0.
350           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
351    o pkg/seaice:
352      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
353        is now the default, and the old default constant freezing point is recovered
354        with SEAICE_tempFrz0    = -1.96,
355             SEAICE_dTempFrz_dS = 0.,
356      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
357      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
358      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
359        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
360      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
361        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
362      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
363        seaice_growth r149 for legacy branch (no results change).
364      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
365        from I. Fenty).
366      - results did not change except for global_ocean.cs32x15, mostly due to the
367        switch to variable freezing point (see above item for detail).
368    o pkg/thsice:
369      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
370        seawater freezing in thsice_calc_thickn (not used).
371    o pkg/seaice: turbulent flux term specification via run time params.
372      - replace CPP switches with run time switches to facilitate testing
373      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
374                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
375      - added runtime parameter : SEAICEturbFluxFormula
376      - move Mcphee constants to SEAICE_PARAMS.h
377      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
378                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
379                 remove seaice_summary call (moved to seaice_init_fixed)
380      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
381        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
382      - seaice_summary.F : add missing report of read turbulent flux term set up
383                           and SITRACER.
384      - seaice_check.F : check range; inform and stop if retired CPPs are used
385                         (incl. SEAICE_AGE).
386      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
387             CPP switch, same computation as before for the different options.
388      - change results at the truncation level.
389    o pkg/seaice:
390      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
391        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
392        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
393      - update verification/*/input*/data.seaice:
394        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
395        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
396        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
397        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
398    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
399      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
400        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
401        difference in results only due to machine truncation.
402      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
403        MaykutPolySatVap; keep MIN_LWDOWN.
404      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
405      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
406        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
407    o pkg/salt_plume:
408      - isolate saltPlumeFlux array exch into a specific S/R called from
409        do_oceanic_phys.F
410      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
411    o verification:
412      - move untested set-up to MITgcm_contrib/verification_other.
413    o pkg/seaice:
414      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
415    o pkg/seaice:
416      - seaice_solve4temp.F (keeping results unchanged):
417        * add 2 future run-time params to select which saturation vapor pressure
418          formula is used and how post-iteration fluxes are set.
419          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
420        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
421          the linearized expression to stay consistent with tsurf finding.
422      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
423        can be < 0.
424    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
425      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
426        conductive heat flux F_c , and add it explicitly when updating tsurf as
427        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
428        so that now F_ia has a consistent meaning through the entire routine.
429        This causes differences at truncation level: update output of fwd exp.
430        global_ocean.cs32x15.seaice.
431    o pkg/seaice:
432      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
433        of arrays, sign/direction of fluxes; no effect on results.
434      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
435        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
436        note: this should have been done before changing celsius2K default.
437      - to keep results unchanged, add back old value of celsius2K in verification
438        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
439      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
440        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
441        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
442        freezing temp is consistent with value in seaice_growth.F ; this causes
443        differences at machine truncation level: update lab_sea AD output (3/4).
444    o pkg/seaice:
445      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
446        and climsst/sss even when using seaice (to prevent calculation that might
447        use SST on land); does not affect any verification exp.
448      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
449        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
450    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
451      over land (non-legacy code)
452    o vectorize salt_plume package:
453      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
454      - this code computes plumebk everywhere (also over land), thus requires
455        code to avoid divisions by zero and catch the case of kLev=Nr.
456      - efficiency of salt_plume_frac is still sub-optimal
457    o tools (genmake2):
458      - fix makefile NAME specification (option: -makefile NAME) by adding
459        "-f $MAKEFILE" in few places where it was missing including makedepend
460        command (contribution from Paul).
461    
462    checkpoint63i (2012/01/24)
463    o model/src:
464      - add factorized versions of some EOS code to find_rho.F,
465        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
466    o model/src:
467      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
468      - change default celsius2K from 273.16 to 273.15
469      - to keep results unchanged, add back old value of celsius2K in verification
470        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
471         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
472    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
473      to make TAF generate vectorizable code
474    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
475       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
476       have flags that do this more efficiently.
477    o pkg/diagnostics/diagstats_calc.F
478      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
479    o pkg/obcs (with exch2):
480      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
481        and remove code (in obcs_readparms.F) which was based on EXCH of indices
482        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
483    o pkg/exf and seaice exp:
484      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
485        so that switching off area & heff advection flags does not affect results.
486      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
487      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
488        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
489        results of verification experiments: 1D_ocean_ice_column(fwd),
490        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
491        and offline_exf_seaice (all 4).
492    o pkg/seaice:
493      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
494        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
495      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
496        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
497        not multi-dim advection;
498      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
499        SHORTWAVE_HEATING #undef.
500    o optim: make Makefile more robust (?)
501    o pkg/obcs:
502      * fix treatment of obcs_read_pickup for TAF
503    o pkg/shelfice:
504      * add missing initialisation of num_shifwflx
505      * new adjoint verification exp. for isomip
506      * change Prandtl and Schmidt numbers from generic formulations
507        (in terms of model diffus. and visc.) to separate runtime
508        parameters, with Holland and Jenkins (1999) default values.
509    o pkg/exf (interpolation):
510      - extended input field (2 rows) near the N & S poles:
511        * fill in with the symetric value (when even Nb of data in longitude)
512        * add average value at the poles only for scalar quantities ; for vector
513          component interpolation, skip the averaging and keep duplicated values,
514          unless the 2 components have same location (uvInterp=T) in which case
515          interpolate the 2 components together using S/R EXF_INTERP_UV.
516      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
517        together: this allows to account properly for local orientation when
518        averaging at N & S pole.
519      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
520        exf-interpolation near N & S poles. Undef by default.
521      - add debug check/print on 1rst iter if debugLevel >=2.
522    o pkg/exf:
523      - change masking flags definition (no longer "parameter"), put them in
524        common block and set them in S/R EXF_INIT_FIXED.
525      - change recognized masking flag from s,u,v to c,w,s since the mask
526        to use (maskC,W,S) depends on position on model grid and has little to
527        do with scalar/vector difference; fix masking if using P-coordinates.
528      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
529        and update results of exp. global_with_exf (x2).
530      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
531    o pkg/obcs
532      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
533    o pkg/exf (interpolation):
534      - assume periodicity in X only if input field cover full longitude range.
535      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
536        and should vectorise).
537      - fix input lat of the 2 added row (in case we provide N.pole data).
538    
539    checkpoint63h (2011/12/30)
540    o pkg/seaice:
541      - change declaration of UVM from _RL to _RS in order to get B-grid
542        uIce,vIce monitor when _RS = real*4
543    o pkg/offline:
544      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
545      - compute vertical velocity if not read from file (switch on exactConserv
546        & staggerTimeStep);
547      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
548    o verification:
549      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
550        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
551        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
552      - update output of exp. global_ocean.cs32x15.viscA4 after changing
553        grid-file angles (used here for coriolis-3d);
554      - remove (or gzip) few files not needed to run fizhi-cs experiments.
555    o pkg/exf (vector interpolation):
556      - rotate vector component toward local grid-axis orientation using grid-angles
557        (stored in GRID.h) instead of locally computed rotation angle; keep old code
558        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
559    o pkg/seaice:
560      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
561        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
562    o pkg/PKG_OPTIONS.h files:
563      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
564        outside of the #ifdef ALLOW_THISPKG / #endif block.
565      - update verification/*/code/PKG_OPTIONS.h files.
566    o add a verification experiment (offline_exf_seaice/input.seaice) that test
567      the B-grid LSOR solver
568    o pkg/seaice: sort out emissivity and long wave radiation step 2:
569      - add emissivity for snow and ice as new run-time parameters
570        (unfortunately) that default to the corresponding exf values; this
571        changes results in most verification experiments so that for backward
572        compatibility these parameter have to be set explicitly to inconsistent
573        values (ugly);
574      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
575        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
576        until we agree how to handle this bug properly
577    o pkg/exf (interpolation):
578      - add a set of run-time param ({inputfield}_interpMethod), one for
579        each interpolated input field, to select the interpolation method
580        with a value of zero switching off the interpolation;
581      - print interpolation parameters to standard output;
582      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
583        (to use instead runoff_interpMethod=0 in data.exf).
584      - simplify default setting of interpolation parameters (for all fields,
585        set position to match model grid cell-center position, leading to trivial
586        interpolation in case of regular Lat-Lon grid) and fix for the case of
587        non-uniform delY.
588    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
589       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
590       this factor is absolutely required, because the lw exitance (= out-going
591       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
592       where the reflectivity rho = 1-emissivity for conservation reasons. Once
593       this is established, we can remove the CPP-Flag (if we want to).
594    o pkg/seaice:
595      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
596        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
597      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
598        what the name implies (and not emissivity*BoltzmannConstant), this means
599        the old default value of 5.5e-8 now means
600        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
601        S/R exf_readparms
602      - FV-discretization of the B-grid LSOR solver, turn on with
603        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
604        of the calling routine dynsolver, so that B and C-grid code look a
605        little more alike.
606      - fix index bugs in ostres.F (B-grid code)
607    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
608    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
609      default for SEAICE_emissivity, if useEXF; requires setting a wrong
610      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
611      backward compatiblity
612    o model/src: use sigmaR in calc_ivdc
613    
614    checkpoint63g (2011/12/16)
615    o pkg/seaice/seaice_growth.F:
616      fix heat conservation of the coupled ocean-seaice system.
617      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
618      solid vs liquid water treatment is resolved via QNET.
619    o pkg/seaice/seaice_growth.F:
620      add missing term for sublimation in saltFlux, which was breaking conservation.
621    o pkg/seaice/seaice_model.F:
622      Remove this patholigical case treatment in evolution branch,
623      where it is un-necessary and breaks conservation.
624      Update global_ocean.cs32x15/results accordingly for
625      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
626    o model/src:
627      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
628      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
629    o pkg/obcs:
630      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
631      tendency for temperature and salinity that is then applied to update
632      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
633      horizontal advection and diffusion contributions on the boundary (in
634      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
635      removing the mask in S/R timestep_tracer. The advantage of this approach is
636      that the updated tracer values include contributions from the surface
637      forcing and vertical diffusion.
638      This modification changes exp4.stevens because of vertical diffusion.
639    o model/src:
640      change non-curvilinear grid setting to also work with exch2 + blank tiles:
641      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
642        face dimensions.
643      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
644        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
645        and INI_SPHERICAL_POLAR_GRID.
646      change test-experiment global_ocean.90x40x15:
647      - split the domain in many more tiles (9x4 tiles of 10x10 each);
648      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
649      - update results of both test (std & dwnslp).
650    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
651       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
652    o model/src:
653      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
654        and fix initialisation when using sigma-coords.
655    o model/src:
656     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
657       to their current value at the beginning of forward_step.F": add a new run-time
658       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
659     - set doResetHFactors=T in the following test exp:
660        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
661        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
662        and tutorial_global_oce_in_p (nonLinFS in p)
663    o pkg/ecco
664      - added IES cost term
665    o verification/advect_xz
666      - scale down the depth by 1/100 (from 200 km to just 2.km)
667      - add secondary test using divergent flow, r-star and implicit vertical advection.
668      - add note (check_conserve_TS.txt) and matlab script to check global
669        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
670    o pkg/rbcs:
671      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
672    o pkg/obcs (Stevens BCs):
673      - fix various problems in the phase speed computations of the Stevens
674        boundary conditions:
675        - sign error for western and southern boundaries,
676        - time tendencies were underestimated by factor of dTracerLev and some just
677          zero (for multidim advection schemes) -> now estimate time tendencies
678          from difference between previous (n) time level and the one before (n-1);
679          this requires storing a field per tracer per boundary, also in the pickup
680          files.
681        - replace deltaTmom in cflMer/Zon computation with dTracerLev
682        - set default phase velocity to cflMer/Zon
683      - update verification experiment exp4.stevens
684    o pkg/generic_advdiff (implicit_r):
685      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
686        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
687      - fix implicit vertical diffusion or advection with NonLin FreeSurf
688        (was using current recip_hFacC instead of future recip_hFacC): set future
689        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
690        solver S/R ;
691      - fill diagnostics of vertical advective fluxes (computed from tendency)
692        when using implicit vert. advection;
693      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
694         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
695         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
696         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
697    o pkg/diagnostics:
698      - add diags for T & S tendency which goes through Adams-Bashforth.
699    
700    checkpoint63f (2011/11/30)
701    o pkg/obcs/obcs_calc_stevens.F:
702      - join some loops to reduce number of if-statements
703      - fix a bug in code for northern and southern boundaries.
704    o pkg/seaice/seaice_init_varia.F
705      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
706        caused zero ice-velocities for the B-grid code
707    o pkg/seaice/seaice_init_fixed.F
708      - fix a bug in the initialisation of the second metric terms
709        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
710      - this affects all seaice configurations with useCurviLinearGrid = .true.
711        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
712        = .true. (default)
713      - the only verification experiment affected is global_ocean.cs32x15:
714        icedyn, seaice, and seaice_dynmix (AD)
715    o pkg/thsice/thsice_diagnostics_state.F
716      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
717        not contain garbage that can lead to surprises in diagstats_calc.F
718    o model/src:
719      - move bi,bj loops inside INTEGR_CONTINUITY ;
720      - call INTEGR_CONTINUITY directly from forward_step.F
721        (previously called from momentum_correction_step.F)
722      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
723        forward_step.F and pkg/ecco/the_main_loop.F
724    o model/src/do_oceanic_phys.F:
725      - reset addMass to zero only if useICEFRONT ;
726      - separated k-loop for rhoInSitu calculation ;
727      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
728        and at constant T,S (= WdRHOdP);
729      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
730        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
731        transport of locally-referenced potential density);
732        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
733    o gluemnc:
734      - replace ncrcat with ncks when adding variables to *.glob.nc
735      - change the way variables without record dimensions are handled so that
736        files that have variables with and without record variables can be glued:
737        add a record dimension with a new unique name to be able to differentiate
738        between variable with and without a-prior record dimensions. Remove
739        this record dimension before adding the variable to the *.glob.nc file.
740        This procedure automatically works also for grid.*.nc files that do not
741        have any record dimension.
742    o verification/cpl_aim+ocn:
743      - generate new reference output on baudelaire (gfortran, mpich2) (previously
744        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
745    o pkg/obcs/obcs_calc_stevens.F:
746      - add code for northern and southern boundaries.
747      - reorder some loops to save some operations and so that drFBar can be scalar
748    o model/src:
749      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
750        truncation) and add diagnostics for Adams-Bashforth tendency increment.
751      - update test-exp. AD output:
752        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
753      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
754        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
755        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
756        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
757        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
758        tutorial_plume_on_slope.
759    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
760      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
761      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
762      does not even come with an F77 compiler anymore, this should not be
763      a limitation
764    
765    checkpoint63e (2011/11/06)
766    o pkg/seaice adjoint of LSR:
767      - substantially rework STORE dirs.
768      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
769        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
770        and only perform SOLV_MAX_FIXED adjoint iters.
771        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
772        always goes to same record, meaning that the last forward field will be
773        the one used in the adjoint - an approximation.
774      - now produces non-zero LSR-related gradients, and acceptable gradients for
775        An's zonal (x-z) test case (to be checked in)
776      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
777        (but these are screwed up by the thermodynamics in the first place);
778        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
779        output_adm.txt also reflects changes to seaice_lsr
780      - global_ocean.cs32x15:
781        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
782          (output_adm.seaice.txt was updated)
783        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
784          (output_adm.seaice_dynmix.txt)
785    o test-exp. exp4+stevens:
786      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
787    o pkg/seaice (lsr solver):
788      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
789        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
790      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
791      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
792        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
793      - compute (with new S/R) and print initial (+ free-driff sol. if available)
794        and final residual of linearised system.
795    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
796      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
797    o pkg/obcs: Stevens BCs (still only for east and west)
798      - fix Stevens BCs by using intermediate velocities of previous
799        time step as "baroclinic" contribution rather velocity of one grid cell
800        inside the boundaries; more consistent but makes the entire treatment
801        more complicated, requires new pickup files and two new S/Rs:
802        obcs_copy_uv_n and obcs_save_uv_n
803        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
804        (undefined by default)
805      - silently move computation of some grid factors into separate loops to
806        save some recomputations
807      - add a hack for non-linear free surface
808      - add a verification experiment to exp4 that tests this code
809    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
810    
811    checkpoint63d (2011/10/25)
812    o pkg/obcs + seaice-dynamics:
813      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
814        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
815        values (consistent with an implicit method).
816      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
817        return to older implementation (same results as before); note that none of
818        the "experimental" OBCS_SEAICE options are implemented in the new version.
819      - switch test exp. seaice_obcs to use new version (update output).
820    o pkg/seaice:
821      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
822      - add parenthesis in Water-Ice drag calculations (evp & lsr);
823      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
824        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
825      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
826        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
827    o pkg/layers:
828      - Include potential density as new coordinate (Thanks to David Munday)
829    o pkg/dic:
830      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
831        carbonate computation/output to CALC_PCO2_APPROX
832    o pkg/generic_advdiff
833      - make TAF generate code that vectorizes:
834        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
835    o model/src:
836      - improve vectorization also for adjoint code of
837        solve_tridiagonal and solve_pentadiagonal. As this requires up to
838        5 new 3D-fields, this code is only turned on for the combination of
839        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
840        for singular matrix check (only for TARGET_NEC_SX).
841      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
842        ALLOW_AUTODIFF. This flag now needs to be set outside of
843        solve_tri/pentadiagonal.F
844    o pkg/exf:
845      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
846        optional namelist EXF_NML_OBCS).
847      - add many debug-print (to trace down where pkg/cal error msg comes from)
848    o pkg/mom_vecinv/mom_vi_hdissip.F
849      - rearrange loops so that vectorization is improved and in particular
850        the adjoint routine vectorizes. The code is a little longer now, but I
851        think easier to read.
852        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
853    o pkg/seaice:
854      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
855    o pkg/exch2:
856      - alternative code (without tile x tile matrix) for cumulated (global) sum;
857        used as default; keep using matrix version in adjustment.cs-32x32x1.
858    o tools/build_options:
859      - after merging some MPI and/or multi-threads specific optfiles so that
860        the modified default optfile support both built (using genmake2 -mpi
861        for the MPI built, using genmake2 -omp for OpenMP built),
862        move now obsolete optfiles to tools/build_options/unsupported/
863       (add copy of email sent to support list in doc/optfiles_changes.txt)
864    
865    checkpoint63c (2011/09/28)
866    o pkg/ebm:
867      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
868        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
869    o pkg/seaice (SItracer pickup)
870    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
871      To be done:
872      - thorough testing of missing fields in S/R seaice_read_pickup
873      - thorough matching between generic tracers and specific fields used
874        (e.g. volume-weighted age, area-weighted age, salinity, ...)
875    o pkg/grdchk:
876      - all procs calculate and print finite-difference gradient (for testreport)
877      - change description output used by testreport;
878      - AD testing: also compare and report Finite-difference gradient;
879        => update all output_adm*.txt
880    o test exp. global_ocean_ebm:
881      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
882        and turn on exactConserve; update (fwd) output.
883    o pkg/seaice (LSR):
884      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
885      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
886        * identical results with non-CS topology (but save up to half of EXCH calls)
887        * no much changes in cs-32 verification tests since no ice at face edges
888         (differences due to convergence criteria, since nb of iterations changed)
889        * expect some differences on lat-lon-cap grid.
890        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
891    o pkg/exch2:
892      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
893        many tiles); until alternative coding is added, just add a stop.
894    o pkg/kpp:
895      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
896        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
897    o optfiles:
898      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
899        into corresponding standard one, which now support different build:
900        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
901      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
902    o pkg/obcs (seaice):
903      - add missing EXCH for uIce,vIce after applying OBCS;
904      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
905        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
906        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
907      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
908      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
909        and eedata.mth for MPI and mutlti-threaded testing.
910    o pkg/flt:
911      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
912      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
913      - fix pickup and trajectories + profiles output with multi-threads;
914      - add parameter to select group of fields to write along trajectory and
915        profile (default unchanged);
916      - only call PORT_RAND* function when flt_noise <> 0;
917      - add multi-threaded test for verification exp. flt_example.
918    o eesupp/src:
919      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
920      - USE_OMP_THREADING: check that number of threads (from eedata) matches
921        actual number (from env.var. setting).
922    o pkg/ebm:
923      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
924      - add multi-threaded test for verification exp. global_ocean_ebm
925    
926    checkpoint63b (2011/08/29)
927  o pkg/ebm:  o pkg/ebm:
928    - fix sign of runoff;    - fix sign of runoff;
929    - update directly forcing fields (Qnet,EmPmR) to use standard    - update directly forcing fields (Qnet,EmPmR) to use standard
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