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revision 1.1519 by jmc, Tue Oct 25 12:35:08 2011 UTC revision 1.1676 by jmc, Tue Jun 26 02:14:33 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      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
9        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
10    o verification/tutorial_tracer_adjsens/
11      - compile with ALLOW_CG2D_NSA
12      - run with nonlinFreeSurf=3
13      - update reference output_adm.txt
14    o tools/genmake2:
15      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
16        refine usePROFILES switching off (only when NetCDF is not available).
17    o verification (atmospheric set-up):
18      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
19    o pkg/profiles : refine profiles and files handling.
20    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
21    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
22      - changes to use model/src/the_main_loop.F rather than the ecco version
23        in ecco type adjoint runs.
24    o model/src:
25      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
26      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
27      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
28    o model/src:
29      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
30        update output of test experiment bottom_ctrl_5x5.
31    o pkg/generic_advdiff:
32      - implement vertical bi-harmonic diffusion (for now, only for T & S and
33        only explicitly).
34    o verification/bottom_ctrl_5x5/
35      update reference output (results changed quite some time ago,
36      not sure when; but new reference results look ok in terms of grdchk)
37    o verification/1D_ocean_ice_column/
38      For verification purposes, the exact adjoint rather than an approx.
39      should be used (e.g., to comare against F.D. or TLM).
40      removed autodiff_inadmode*_ad.F routines in code_ad/
41      Update results/ accordingly.
42    o pkg/cal:
43      - change cal_getdate.F so that output date is function of input time only
44        (less ambiguous, not mixed up with input iteration number).
45      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
46    o pkg/diagnostics:
47      - implement calendarDumps also for stats-diags
48      - implement calendarDumps also for snap-shot output (negative freq)
49      - for now, ignores calendarDumps if non-zero phase-lag.
50    
51    checkpoint63n (2012/06/04)
52    o model/src:
53      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
54        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
55      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
56        similar to calc_r_star.F); update results of experiment internal_wave and
57        tutorial_global_oce_in_p (affected @ truncation level).
58    o pkg/shelfice:
59      - add parameterisation of advective-diffusive flux into the ice shelf
60        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
61      - simply eps3/3a computation
62    o eesupp:
63     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
64       between tiles, just fill-in edges assuming locally periodic subdomain) and
65       add corresponding exchange subroutines (EXCH0);
66     - new CG-solver version (_EX0) for disconnected-tiles special case.
67    o model/src (CG-solvers):
68     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
69       (similar final residual output and max-Iter number as with standard version);
70     - allows to store and use lowest-residual solution (standard & _SR versions);
71     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
72     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
73    o eesup/src:
74     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
75       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
76    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
77    
78    checkpoint63m (2012/04/27)
79    o pkg/shelfice:
80     - account for partical cells in surface level below ice-shelf for hydrostatic
81       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
82    o ad test experiments:
83     - update and rename to "ad_optfile.local" local AD-optfile specific to a
84       particular adjoint verification experiment (in verification/*/code_ad/)
85    o pkg/seaice & pkg/exf:
86     - Part two of ECCO-CLIVAR code merges.
87       Completes merge of seaice area relax. code.
88       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
89       to be set in EXF_OPTIONS.h since this pkg controls its I/O
90       (and avoids second CPP option in SEAICE_OPTIONS.h)
91     - change default value of costIceStart & costIceEnd to a valid date.
92     - add snowPrecip to HSNOW in seaice_growth
93    o pkg/ptracers:
94     - move ptracers summary and setup check into separated S/R ; add a check for
95       valid PTRACERS_Iter0 value (error+stop or just warning).
96    o pkg/cal (+ pkg/ecco):
97     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
98       as input; and for AD, unless both are not differentiable (e.g., k index)).
99    o model/src:
100     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
101       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
102       temporary set to usingZCoords value (to be changed to F when using shelfice).
103     - hydrostatic pressure: implement partial cell near the surface also for
104       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
105       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
106    o pkg/ctrl/ctrl_init.F:
107     - add a formal parameter to s/r ctrl_init_rec to print
108       xx_$(ctrl_valiable)_file for easier debugging
109     - move call of cal_* routines into the if-block where they are really
110       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
111       to specify a startdate
112    o pkg/seaice:
113     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
114       global_ocean.cs32x15/code versions).
115     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
116       verification experiment global_ocean.cs32x15.seaice and update results.
117    o pkg/exf:
118     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
119       (according to useExfYearlyFields).
120    o pkg/cal:
121     - move calendar setting & summary (previously in cal_readparams.F) into new
122       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
123       length of the simulation is set (after SET_PARMS call); This is an attempt
124       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
125     - For safety: keep a record of pkg/cal parameter settings status
126               to allow to STOP if one pkg/cal S/R is called too early.
127     - add a stop in all basic pkg/cal subroutines if called before setting is done.
128     - modify cal_getdate.F: stop when nothing was returned;
129       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
130       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
131    
132    checkpoint63l (2012/04/04)
133    o pkg/bbl:
134      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
135        update global_with_exf output.yearly.txt file.
136    o pkg/cal:
137      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
138      - remove 2 unsused and very short (1 line only) functions ;
139      - remove unsused subroutines from AD-Diff list.
140    o model/src:
141      - start to implement clean wait to stop in initialization S/R (config_check.F,
142         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
143    o folowing PRINT_MESSAGE changes:
144      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
145    o pkg/bbl:
146      - modification so it can work with z*
147      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
148      - global_with_exf/input.yearly verification; changes output.yearly.txt
149    o eesupp/src:
150      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
151        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
152      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
153        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
154      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
155      - when using MPI, always set usingMPI=T ; set default accordingly and stop
156        if not consistent.
157      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
158        argument is zero (in case called within single-thread section).
159    o pkg/fizhi:
160        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
161        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
162    o pkg/exch2:
163      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
164        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
165      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
166        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
167        with bad ones coming from a not-yet-updated halo.
168        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
169    o pkg/frazil:
170        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
171        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
172    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
173    o verification/lab_sea
174      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
175      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
176      * nTimeSteps 3 -> 4
177      * changed reference output accordingly
178    o pkg/ctrl:
179      * fix ctrl_get_gen for xx_sst, xx_sss
180    o pkg/fizhi:
181      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
182        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
183      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
184        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
185        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
186    o pkg/gmredi:
187      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
188    o pkg/fizhi:
189      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
190        (old)aces open64 tuv test.
191    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
192    o pkg/mom_vecinv:
193      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
194        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
195        with non-lin free-surf).
196    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
197      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
198      some compilers (gfortran 4.6.0 on MacOS)
199    o momentum:
200      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
201        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
202        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
203    
204    checkpoint63k (2012/03/17)
205    o model/src:
206       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
207         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
208       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
209         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
210    o model/src: solve_*diagonal.F
211       - replace division with multiplication by inverse (similar to original version)
212         update output of AD exp. global_ocean.90x40x15.
213       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
214         to enable the use of the vectorized & differentiable solve_tridiagonal.F
215       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
216         vertical advection (to get solve_tridiagonal tested in AD mode).
217    o pkg/seaice: ECCO-CLIVAR merge:
218      1. seaice AREA relaxation
219         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
220         * runtime flag: SEAICE_tauAreaObsRelax
221      2. modified global mean cost imbalance code: CPP option
222          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
223    o another iteration on solve_*diagonal.F
224       Make choices independent of AUTODIFF
225       Default will be the adjoinable vectorized version.
226       Alternative choices are:
227       * non-adjoinable original version with low memory footprint:
228         #define SOLVE_DIAGONAL_LOWMEMORY
229       * still adjoinable but does not vectorize (k as inner-most loop):
230         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
231    o testreport
232     - add option to use a home made wrapper around "make"
233     - remove MITGCM_IEEE env. variable (no longer active)
234    o pkg/shelfice
235     - improve computation of friction velocity for velocity dependent
236       exchange coefficients: include velocities into SHELFICEBoundaryLayer
237       block to average velocities vertically
238     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
239    o Modify diagonal solvers, now three versions (upon request):
240      #ifndef SOLVE_DIAGONAL_AUTODIFF
241        1. default version (dating back a while ago)
242      #else /* def SOLVE_DIAGONAL_AUTODIFF */
243      # ifdef SOLVE_DIAGONAL_KINNER
244        2. adjoinable version with k-innermost loop (G. Forget)
245      # else
246        3. adjoinable vectorized version of 2.
247      # endif
248      #endif /* SOLVE_DIAGONAL_AUTODIFF */
249      All flags are currently set within routines, but could/should be moved to CPP-options.
250      Array bounds for 1. are as before, for 2.,3. cover the entire domain
251      (could be changed for 1. too).
252    o verification/lab_sea (fwd):
253      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
254        use 7 categories (except hb87), new solve4temp params (except salt_plume),
255        constant salinity (=4) or variable salinity (salt_plume) done through
256        SItracer.
257    o pkg/seaice:
258      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
259      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
260         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
261        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
262        SEAICE_freeze got retired) but already better than previously with
263        SEAICE_freeze=123456.7 deg.C;
264      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
265        (safer multi-threaded setting); always set SEAICEuseEVP;
266      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
267        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
268        stop if multiple specifications for the same coeff; make sure default
269        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
270    o pkg/obcs:
271      - allow to switch to upwind 1rst order advection scheme for the advective
272        flux computation at the open-boundary; disabled for adjoint built.
273    o pkg/ptracers:
274      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
275      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
276      - add parameter to decide when to start a tracer; use internal flag to
277        know which tracer to step-forward; switch this internal flag at the top
278        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
279        for adjoint built.
280    o pkg/seaice:
281      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
282      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
283      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
284    o pkg/ecco:
285      - fix writing of output file DiagnosCost_ClimSalt/Theta
286        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
287    o pkg/seaice:
288      - add missing initialisation of COR_ICE array in dynsolver.F
289      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
290        compiled either way, and is tested in all exps (multidim was only tested
291        in lab_sea ad before).
292      - cosmetic change to prepare for future addition of ITD. no change to results.
293        no defaults change.
294      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
295      - by lack of adequate verification experiments, I further used custom versions
296        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
297        should be correct.
298      - avoid recomputations in ad.
299    o array initialisation in adjoint mode:
300      1) pkg/mom_common/mom_calc_ke.F:
301        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
302        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
303        part this initialisation is gone, resulting in Floating Point Exception
304        (caught by open64 compiler with debug option).
305      2) model/src/convective_weights.F
306        set output convectCount over the full array range (instead of doing
307        an update): this fix a similar issue when called within recomputation (adjoint)
308        which could by-pass the initialisation (normally done in the caller S/R).
309    o pkg/seaice:
310      - final version of turbulent flux params, as agreed at MIT ice meet:
311           SEAICE_mcPheePiston (default is ~ 0.000875)
312           SEAICE_mcPheeTaper (default is 0.)
313           SEAICE_frazilFrac (defualt is 1.)
314           SEAICE_mcPheeStepFunc (default is false)
315      - changes results at trunction error level
316      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
317    o added pkg/frazil:
318      - see frazil_description.tex for details
319      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
320    o pkg/shelfice/shelfice_thermodynamics.F
321      - fix exponents for velocity dependent exchange coefficients: change
322        from 2/3(=0) to 0.66666666666666667
323      - move computation of velocity dependent exchange coefficients into
324        separate loop, so that it applies to both thermodynamics
325      - move some divisions by constants out of loops
326    
327    checkpoint63j (2012/02/16)
328    o pkg/seaice:
329      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
330      - SItracer:  added run time params, and allow coupling to ocn salinity.
331    o pkg/seaice: remove (almost) all divisions by constants within loops
332      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
333      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
334      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
335      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
336    o pkg/seaice :
337      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
338        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
339      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
340      - add permanent SItflux diag that corresponds to TFLUX but includes
341        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
342      - allow activation/testing of a fix for suspected missing term in
343        ocn-ice heat budget (to be confirmed). To test this, you want to
344        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
345        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
346      - no change in results, fwd or ad.
347    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
348      - switch to variable freezing point.
349           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
350      - bug fix : the sublimation term that was missing is now activated.
351           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
352      - bug fix : flooding sign term for SIsal0.NE.0.
353           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
354    o pkg/seaice:
355      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
356        is now the default, and the old default constant freezing point is recovered
357        with SEAICE_tempFrz0    = -1.96,
358             SEAICE_dTempFrz_dS = 0.,
359      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
360      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
361      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
362        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
363      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
364        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
365      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
366        seaice_growth r149 for legacy branch (no results change).
367      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
368        from I. Fenty).
369      - results did not change except for global_ocean.cs32x15, mostly due to the
370        switch to variable freezing point (see above item for detail).
371    o pkg/thsice:
372      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
373        seawater freezing in thsice_calc_thickn (not used).
374    o pkg/seaice: turbulent flux term specification via run time params.
375      - replace CPP switches with run time switches to facilitate testing
376      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
377                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
378      - added runtime parameter : SEAICEturbFluxFormula
379      - move Mcphee constants to SEAICE_PARAMS.h
380      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
381                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
382                 remove seaice_summary call (moved to seaice_init_fixed)
383      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
384        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
385      - seaice_summary.F : add missing report of read turbulent flux term set up
386                           and SITRACER.
387      - seaice_check.F : check range; inform and stop if retired CPPs are used
388                         (incl. SEAICE_AGE).
389      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
390             CPP switch, same computation as before for the different options.
391      - change results at the truncation level.
392    o pkg/seaice:
393      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
394        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
395        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
396      - update verification/*/input*/data.seaice:
397        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
398        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
399        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
400        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
401    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
402      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
403        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
404        difference in results only due to machine truncation.
405      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
406        MaykutPolySatVap; keep MIN_LWDOWN.
407      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
408      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
409        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
410    o pkg/salt_plume:
411      - isolate saltPlumeFlux array exch into a specific S/R called from
412        do_oceanic_phys.F
413      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
414    o verification:
415      - move untested set-up to MITgcm_contrib/verification_other.
416    o pkg/seaice:
417      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
418    o pkg/seaice:
419      - seaice_solve4temp.F (keeping results unchanged):
420        * add 2 future run-time params to select which saturation vapor pressure
421          formula is used and how post-iteration fluxes are set.
422          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
423        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
424          the linearized expression to stay consistent with tsurf finding.
425      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
426        can be < 0.
427    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
428      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
429        conductive heat flux F_c , and add it explicitly when updating tsurf as
430        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
431        so that now F_ia has a consistent meaning through the entire routine.
432        This causes differences at truncation level: update output of fwd exp.
433        global_ocean.cs32x15.seaice.
434    o pkg/seaice:
435      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
436        of arrays, sign/direction of fluxes; no effect on results.
437      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
438        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
439        note: this should have been done before changing celsius2K default.
440      - to keep results unchanged, add back old value of celsius2K in verification
441        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
442      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
443        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
444        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
445        freezing temp is consistent with value in seaice_growth.F ; this causes
446        differences at machine truncation level: update lab_sea AD output (3/4).
447    o pkg/seaice:
448      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
449        and climsst/sss even when using seaice (to prevent calculation that might
450        use SST on land); does not affect any verification exp.
451      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
452        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
453    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
454      over land (non-legacy code)
455    o vectorize salt_plume package:
456      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
457      - this code computes plumebk everywhere (also over land), thus requires
458        code to avoid divisions by zero and catch the case of kLev=Nr.
459      - efficiency of salt_plume_frac is still sub-optimal
460    o tools (genmake2):
461      - fix makefile NAME specification (option: -makefile NAME) by adding
462        "-f $MAKEFILE" in few places where it was missing including makedepend
463        command (contribution from Paul).
464    
465    checkpoint63i (2012/01/24)
466    o model/src:
467      - add factorized versions of some EOS code to find_rho.F,
468        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
469    o model/src:
470      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
471      - change default celsius2K from 273.16 to 273.15
472      - to keep results unchanged, add back old value of celsius2K in verification
473        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
474         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
475    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
476      to make TAF generate vectorizable code
477    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
478       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
479       have flags that do this more efficiently.
480    o pkg/diagnostics/diagstats_calc.F
481      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
482    o pkg/obcs (with exch2):
483      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
484        and remove code (in obcs_readparms.F) which was based on EXCH of indices
485        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
486    o pkg/exf and seaice exp:
487      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
488        so that switching off area & heff advection flags does not affect results.
489      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
490      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
491        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
492        results of verification experiments: 1D_ocean_ice_column(fwd),
493        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
494        and offline_exf_seaice (all 4).
495    o pkg/seaice:
496      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
497        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
498      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
499        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
500        not multi-dim advection;
501      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
502        SHORTWAVE_HEATING #undef.
503    o optim: make Makefile more robust (?)
504    o pkg/obcs:
505      * fix treatment of obcs_read_pickup for TAF
506    o pkg/shelfice:
507      * add missing initialisation of num_shifwflx
508      * new adjoint verification exp. for isomip
509      * change Prandtl and Schmidt numbers from generic formulations
510        (in terms of model diffus. and visc.) to separate runtime
511        parameters, with Holland and Jenkins (1999) default values.
512    o pkg/exf (interpolation):
513      - extended input field (2 rows) near the N & S poles:
514        * fill in with the symetric value (when even Nb of data in longitude)
515        * add average value at the poles only for scalar quantities ; for vector
516          component interpolation, skip the averaging and keep duplicated values,
517          unless the 2 components have same location (uvInterp=T) in which case
518          interpolate the 2 components together using S/R EXF_INTERP_UV.
519      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
520        together: this allows to account properly for local orientation when
521        averaging at N & S pole.
522      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
523        exf-interpolation near N & S poles. Undef by default.
524      - add debug check/print on 1rst iter if debugLevel >=2.
525    o pkg/exf:
526      - change masking flags definition (no longer "parameter"), put them in
527        common block and set them in S/R EXF_INIT_FIXED.
528      - change recognized masking flag from s,u,v to c,w,s since the mask
529        to use (maskC,W,S) depends on position on model grid and has little to
530        do with scalar/vector difference; fix masking if using P-coordinates.
531      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
532        and update results of exp. global_with_exf (x2).
533      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
534    o pkg/obcs
535      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
536    o pkg/exf (interpolation):
537      - assume periodicity in X only if input field cover full longitude range.
538      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
539        and should vectorise).
540      - fix input lat of the 2 added row (in case we provide N.pole data).
541    
542    checkpoint63h (2011/12/30)
543    o pkg/seaice:
544      - change declaration of UVM from _RL to _RS in order to get B-grid
545        uIce,vIce monitor when _RS = real*4
546    o pkg/offline:
547      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
548      - compute vertical velocity if not read from file (switch on exactConserv
549        & staggerTimeStep);
550      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
551    o verification:
552      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
553        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
554        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
555      - update output of exp. global_ocean.cs32x15.viscA4 after changing
556        grid-file angles (used here for coriolis-3d);
557      - remove (or gzip) few files not needed to run fizhi-cs experiments.
558    o pkg/exf (vector interpolation):
559      - rotate vector component toward local grid-axis orientation using grid-angles
560        (stored in GRID.h) instead of locally computed rotation angle; keep old code
561        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
562    o pkg/seaice:
563      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
564        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
565    o pkg/PKG_OPTIONS.h files:
566      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
567        outside of the #ifdef ALLOW_THISPKG / #endif block.
568      - update verification/*/code/PKG_OPTIONS.h files.
569    o add a verification experiment (offline_exf_seaice/input.seaice) that test
570      the B-grid LSOR solver
571    o pkg/seaice: sort out emissivity and long wave radiation step 2:
572      - add emissivity for snow and ice as new run-time parameters
573        (unfortunately) that default to the corresponding exf values; this
574        changes results in most verification experiments so that for backward
575        compatibility these parameter have to be set explicitly to inconsistent
576        values (ugly);
577      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
578        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
579        until we agree how to handle this bug properly
580    o pkg/exf (interpolation):
581      - add a set of run-time param ({inputfield}_interpMethod), one for
582        each interpolated input field, to select the interpolation method
583        with a value of zero switching off the interpolation;
584      - print interpolation parameters to standard output;
585      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
586        (to use instead runoff_interpMethod=0 in data.exf).
587      - simplify default setting of interpolation parameters (for all fields,
588        set position to match model grid cell-center position, leading to trivial
589        interpolation in case of regular Lat-Lon grid) and fix for the case of
590        non-uniform delY.
591    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
592       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
593       this factor is absolutely required, because the lw exitance (= out-going
594       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
595       where the reflectivity rho = 1-emissivity for conservation reasons. Once
596       this is established, we can remove the CPP-Flag (if we want to).
597    o pkg/seaice:
598      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
599        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
600      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
601        what the name implies (and not emissivity*BoltzmannConstant), this means
602        the old default value of 5.5e-8 now means
603        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
604        S/R exf_readparms
605      - FV-discretization of the B-grid LSOR solver, turn on with
606        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
607        of the calling routine dynsolver, so that B and C-grid code look a
608        little more alike.
609      - fix index bugs in ostres.F (B-grid code)
610    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
611    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
612      default for SEAICE_emissivity, if useEXF; requires setting a wrong
613      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
614      backward compatiblity
615    o model/src: use sigmaR in calc_ivdc
616    
617    checkpoint63g (2011/12/16)
618    o pkg/seaice/seaice_growth.F:
619      fix heat conservation of the coupled ocean-seaice system.
620      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
621      solid vs liquid water treatment is resolved via QNET.
622    o pkg/seaice/seaice_growth.F:
623      add missing term for sublimation in saltFlux, which was breaking conservation.
624    o pkg/seaice/seaice_model.F:
625      Remove this patholigical case treatment in evolution branch,
626      where it is un-necessary and breaks conservation.
627      Update global_ocean.cs32x15/results accordingly for
628      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
629    o model/src:
630      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
631      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
632    o pkg/obcs:
633      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
634      tendency for temperature and salinity that is then applied to update
635      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
636      horizontal advection and diffusion contributions on the boundary (in
637      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
638      removing the mask in S/R timestep_tracer. The advantage of this approach is
639      that the updated tracer values include contributions from the surface
640      forcing and vertical diffusion.
641      This modification changes exp4.stevens because of vertical diffusion.
642    o model/src:
643      change non-curvilinear grid setting to also work with exch2 + blank tiles:
644      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
645        face dimensions.
646      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
647        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
648        and INI_SPHERICAL_POLAR_GRID.
649      change test-experiment global_ocean.90x40x15:
650      - split the domain in many more tiles (9x4 tiles of 10x10 each);
651      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
652      - update results of both test (std & dwnslp).
653    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
654       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
655    o model/src:
656      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
657        and fix initialisation when using sigma-coords.
658    o model/src:
659     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
660       to their current value at the beginning of forward_step.F": add a new run-time
661       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
662     - set doResetHFactors=T in the following test exp:
663        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
664        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
665        and tutorial_global_oce_in_p (nonLinFS in p)
666    o pkg/ecco
667      - added IES cost term
668    o verification/advect_xz
669      - scale down the depth by 1/100 (from 200 km to just 2.km)
670      - add secondary test using divergent flow, r-star and implicit vertical advection.
671      - add note (check_conserve_TS.txt) and matlab script to check global
672        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
673    o pkg/rbcs:
674      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
675    o pkg/obcs (Stevens BCs):
676      - fix various problems in the phase speed computations of the Stevens
677        boundary conditions:
678        - sign error for western and southern boundaries,
679        - time tendencies were underestimated by factor of dTracerLev and some just
680          zero (for multidim advection schemes) -> now estimate time tendencies
681          from difference between previous (n) time level and the one before (n-1);
682          this requires storing a field per tracer per boundary, also in the pickup
683          files.
684        - replace deltaTmom in cflMer/Zon computation with dTracerLev
685        - set default phase velocity to cflMer/Zon
686      - update verification experiment exp4.stevens
687    o pkg/generic_advdiff (implicit_r):
688      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
689        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
690      - fix implicit vertical diffusion or advection with NonLin FreeSurf
691        (was using current recip_hFacC instead of future recip_hFacC): set future
692        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
693        solver S/R ;
694      - fill diagnostics of vertical advective fluxes (computed from tendency)
695        when using implicit vert. advection;
696      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
697         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
698         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
699         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
700    o pkg/diagnostics:
701      - add diags for T & S tendency which goes through Adams-Bashforth.
702    
703    checkpoint63f (2011/11/30)
704    o pkg/obcs/obcs_calc_stevens.F:
705      - join some loops to reduce number of if-statements
706      - fix a bug in code for northern and southern boundaries.
707    o pkg/seaice/seaice_init_varia.F
708      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
709        caused zero ice-velocities for the B-grid code
710    o pkg/seaice/seaice_init_fixed.F
711      - fix a bug in the initialisation of the second metric terms
712        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
713      - this affects all seaice configurations with useCurviLinearGrid = .true.
714        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
715        = .true. (default)
716      - the only verification experiment affected is global_ocean.cs32x15:
717        icedyn, seaice, and seaice_dynmix (AD)
718    o pkg/thsice/thsice_diagnostics_state.F
719      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
720        not contain garbage that can lead to surprises in diagstats_calc.F
721    o model/src:
722      - move bi,bj loops inside INTEGR_CONTINUITY ;
723      - call INTEGR_CONTINUITY directly from forward_step.F
724        (previously called from momentum_correction_step.F)
725      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
726        forward_step.F and pkg/ecco/the_main_loop.F
727    o model/src/do_oceanic_phys.F:
728      - reset addMass to zero only if useICEFRONT ;
729      - separated k-loop for rhoInSitu calculation ;
730      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
731        and at constant T,S (= WdRHOdP);
732      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
733        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
734        transport of locally-referenced potential density);
735        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
736    o gluemnc:
737      - replace ncrcat with ncks when adding variables to *.glob.nc
738      - change the way variables without record dimensions are handled so that
739        files that have variables with and without record variables can be glued:
740        add a record dimension with a new unique name to be able to differentiate
741        between variable with and without a-prior record dimensions. Remove
742        this record dimension before adding the variable to the *.glob.nc file.
743        This procedure automatically works also for grid.*.nc files that do not
744        have any record dimension.
745    o verification/cpl_aim+ocn:
746      - generate new reference output on baudelaire (gfortran, mpich2) (previously
747        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
748    o pkg/obcs/obcs_calc_stevens.F:
749      - add code for northern and southern boundaries.
750      - reorder some loops to save some operations and so that drFBar can be scalar
751    o model/src:
752      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
753        truncation) and add diagnostics for Adams-Bashforth tendency increment.
754      - update test-exp. AD output:
755        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
756      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
757        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
758        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
759        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
760        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
761        tutorial_plume_on_slope.
762    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
763      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
764      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
765      does not even come with an F77 compiler anymore, this should not be
766      a limitation
767    
768    checkpoint63e (2011/11/06)
769    o pkg/seaice adjoint of LSR:
770      - substantially rework STORE dirs.
771      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
772        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
773        and only perform SOLV_MAX_FIXED adjoint iters.
774        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
775        always goes to same record, meaning that the last forward field will be
776        the one used in the adjoint - an approximation.
777      - now produces non-zero LSR-related gradients, and acceptable gradients for
778        An's zonal (x-z) test case (to be checked in)
779      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
780        (but these are screwed up by the thermodynamics in the first place);
781        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
782        output_adm.txt also reflects changes to seaice_lsr
783      - global_ocean.cs32x15:
784        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
785          (output_adm.seaice.txt was updated)
786        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
787          (output_adm.seaice_dynmix.txt)
788    o test-exp. exp4+stevens:
789      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
790    o pkg/seaice (lsr solver):
791      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
792        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
793      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
794      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
795        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
796      - compute (with new S/R) and print initial (+ free-driff sol. if available)
797        and final residual of linearised system.
798    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
799      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
800    o pkg/obcs: Stevens BCs (still only for east and west)
801      - fix Stevens BCs by using intermediate velocities of previous
802        time step as "baroclinic" contribution rather velocity of one grid cell
803        inside the boundaries; more consistent but makes the entire treatment
804        more complicated, requires new pickup files and two new S/Rs:
805        obcs_copy_uv_n and obcs_save_uv_n
806        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
807        (undefined by default)
808      - silently move computation of some grid factors into separate loops to
809        save some recomputations
810      - add a hack for non-linear free surface
811      - add a verification experiment to exp4 that tests this code
812    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
813    
814  checkpoint63d (2011/10/25)  checkpoint63d (2011/10/25)
815  o pkg/obcs + seaice-dynamics:  o pkg/obcs + seaice-dynamics:
816    - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before    - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
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