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revision 1.1251 by jmc, Tue Apr 13 17:12:55 2010 UTC revision 1.1418 by jmc, Thu Apr 28 23:26:39 2011 UTC
# Line 5  $Name$ Line 5  $Name$
5      ==============================      ==============================
6    
7  o pkg/obcs:  o pkg/obcs:
8      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
9        no longer needed with maskInC,W,S in pkg/generic_advdiff.
10    o pkg/seaice:
11      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
12        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
13      - fixed bug in the initialization of sea ice salinity variable HSALT
14        in seaice_init_varia.F  (removed dependence on ICE2WATR)
15    o fizhi-cs test exp.:
16       switch reference output convention for these 2 non-standard test-exp,
17        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
18          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
19       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
20    o model/inc:
21      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
22        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
23    o pkg/seaice:
24      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
25    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
26      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
27        and initial HSALT
28    
29    checkpoint62w (2011/04/26)
30    o pkg/mom_fluxform:
31      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
32      - use parameter "sideDragFactor" in no-slip BC side-drag part.
33      - update output of exp. global_ocean.90x40x15
34    o pkg/mom_vecinv:
35      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
36    o update seaice exp.:
37      use more consistent parameter values (remove "backward compatability only":
38       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
39      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
40       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
41    o update test-exp global_ocean.90x40x15:
42      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
43      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
44      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
45      o turn on zStar & viscA4 in standard set-up (dir input/)
46        and update output files: output.txt & output.dwnslp.txt
47    o new AD-test experiment: obcs_ctrl
48      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
49    o pkg/dic:
50      fix two bugs in handling water vapour pressure in carbonate chemistry
51      and air-sea fluxes. Found by Val Bennington and Galen McKinley
52      (add DIC Option = WATERVAP_BUG to recover old results)
53      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
54    o adding allowInteriorFreezing option to check for water below freezing point
55      at depth and bring the negative heat anomaly to the surface level
56    o pkgs _fields_load:
57      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
58      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
59        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
60        rbcs to get interpolation weights and time reccord number.
61      - fix multi-threading in aim_fields_load.F
62      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
63    o external_fields_load:
64      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
65       interpolation weights) to use in a periodic time-series ; do not divide by
66       time-step to convert to integer:
67       - this fixes case where externForcingPeriod is not multiple of time-step
68          (Thanks to Christopher L. Wolfe)
69       - this fixes case where externForcingPeriod is an odd multiple of time-step
70         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
71      store index of time-record which is currently loaded:
72       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
73       - needed for the adjoint but not yet used because of extensive recomputations;
74         (to be fixed soon)
75    
76    checkpoint62v (2011/04/02)
77    o verification/1D_ocean_ice_column added to test Ian Fenty's
78      pkg/seaice_growth.F modifications for improving sea ice code differentiability
79    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
80      (new velocity statistics after changing maskInW & maskInS definition)
81    o pkg/generic_advdiff with OBCS:
82      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
83      equivalent to assumption of no tracer gradient outside the OB region.
84      This will affect the results if using obcs+biharmonic diffusion.
85      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
86    o pkg/obcs:
87      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
88      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
89      in Interior region. No impact on solution but affects Velocity monitor stats.
90    o pkg/ptracers (adjoint)
91      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
92      tape file for each tracer
93    o model/inc/src and pkg/autodiff: add parameters that allow to turn
94      of parts of the adjoint code at run time. For now, there are only
95      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
96      parameters are set in data.pkg.
97      This is the lazy coward's version of doing this, but still useful for
98      debugging. In order to do it right, everything needs to be moved to
99      pkg/autodiff.
100    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
101      the end; this fixes the adjoint balancing code for open boundaries.
102    o pkg/ctrl:
103      - change behavior of xx_${varname}period to be analogous to exf-conventions:
104        xx_${varname}period =   0.,  means time-independent control part
105        xx_${varname}period = -12., means one-year-periodic monthly control part
106      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
107        clean up ctrl_init a little, remove unused variables
108      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
109      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
110    
111    checkpoint62u (2011/03/15)
112    o model/src:
113      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
114        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
115      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
116        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
117    o pkg/ctrl/obcs/ecco:
118      - remove obsolete, unused, and partially broken code:
119        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
120        ALLOW_CTRL_OBCS_BALANCE
121      - put a stop statement into ecco/cost_obcsvol.F, but also add
122        cost_obcsvol to ecco_ad_diff.list
123    o pkg/ecco: fix counting cost function contributions for obcs (code
124      by Matt M.) and diffkr for diagnostics
125    o pkg/ecco, pkg/ctrl, pkg/grdchk:
126      add cost penalty terms for initial uvel, vvel, eta controls
127      and I/O for prior error files
128    o pkg/mdsio:
129       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
130       (new argument) to check for tiled file in mdsioLocalDir : this fix the
131       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
132    o pkg/ctrl:
133     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
134       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
135       unused and superfluous variables
136     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
137    o pkg/ecco
138     - enable adjoint of Stevens OB
139    o pkg/ctrl/ecco/grdchk:
140      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
141        Fortunately, we do not have any tests for the numerous cpp-flagged
142        option of "obcs as control parameters" so we will never know
143        if this is an improvement (but at least now things compile).
144      - remove an obsolete initialization from ecco_cost_init_barfiles.F
145      - fix some problems within never used ifdefs to make the code compile
146    o pkg/obcs:
147     - Refine Interior mask definition to work with more complex OB (e.g.
148       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
149       read in Interior mask from file. Check if Interior mask is consistent
150       with OB list of indices.
151    o pkg/seaice
152     - beginning code for a seaice tracer package,
153       but currently only used for seaice age: SEAICE_AGE
154       SEAICE_num = 4
155       iTracer = 1: area-weighted ice age
156               = 2: volume-weighted ice age
157               = 3, 4: template for one-year vs. multi-year ice
158       data.seaice has new namelist SEAICE_PARM03 for arrays related to
159       SEAICE_num
160    
161    checkpoint62t (2011/03/05)
162    o pkg/obcs:
163     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
164       then normal component. This ensures that the normal component is set
165       correctly even when it conficts with tangential setting from an other OB.
166       Affects results of test-experiment seaice_obcs: update the output.txt
167    o pkg/obcs:
168     - add code to monitor statistics of dynamical fields at OB.
169     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
170       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
171       - change default: balance the Net inflow through all OB (instead of balancing
172         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
173     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
174       to match Nortern OB inflow (OBCS_balanceFacN=0).
175    o pkg/seaice:
176     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
177    o pkg/seaice (seaice_growth v 1.113):
178     - reverting seaice_growth to v 1.111 in order to have code with exact bit
179       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
180       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
181       runtime flag SEAICEareaFormula is kept but is inactive
182    o model/src:
183     - add new param to scale curvilinear grid distance and area when using
184       a different sphere radius from the grid-files.
185     - test/check multi-threads EXCH applied to local variable (cg2d_x)
186    o adjoint:
187     - enable adjoint of Stevens OB
188     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
189       (a bit delicate because of potentially modified adj. common block structure;
190       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
191    
192    checkpoint62s (2011/02/15)
193    o pkg/seaice (seaice_growth v 1.112):
194     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
195       computing the ice cover tendency from effective thickness tendencies. Include
196       Ian Fenty's formula.
197     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
198       SEAICEareaFormula.
199     - simplify notations for the various d_HEFF/d_AREA terms.
200    o pkg/gmredi:
201     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
202       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
203       add a verification test-run (front_relax.bvp) to test GM_useBVP.
204    o pkg/seaice (seaice_growth v 1.111):
205     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
206     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
207       also melt ice.
208    o pkg/seaice:
209     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
210     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
211    o pkg/cheapaml:
212     - from Nico Wienders: New version of this package.
213    o pkg/flt:
214     - add CPP options to prevent floats to re-enter the opposite side of
215       a periodic domain (default: keep periodicity)
216    o pkg/gmredi:
217     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
218       (needed for multi-dim advection).
219     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
220    o model/src:
221     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
222    o tutorial_tracer_adjsens
223     - extend to NLFS and replace maskC by hFacC
224       (change reference output accordingly)
225    
226    checkpoint62r (2011/01/24)
227    o testreport:
228     - add option -deloutp (-do) to remove output file after successful run
229     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
230       extract exact list of procs from this file ; adjust COMMAND by
231       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
232    o pkg/ecco: replace old ineffective way of penalizing deviations from
233      first guess (of obcs) with code by Matt Mazloff
234    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
235      exf/cal
236      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
237        and handle case of obcs?period == 0
238        Not affected by these changes: There is still an inconsistency in
239        the computation of start/endrec for the obcs variables for ALLOW_CAL
240        defined (see comment by Menemenlis, 7-Mar-2003)
241      - make S/R ctrl_get_gen_rec return something meaningful even if
242        ALLOW_CAL is not defined
243      - ctrl_getobcs?: simplify code so that it does not need to use
244                       S/R exf_swapfields
245    o testreport:
246       allow to test MPI with different number of processors for each experiment:
247       create file "SIZE.h.mpi" in each build dir.
248       Note: update of "-command" argument not yet implemented.
249    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
250      alleviate the need for additional 3D tapes when using
251      the non-inear free surface in the adjoint. This is done
252      by adding an 'update' of hfacc etc. to their current
253      value at the beginning of forward_step.F.
254    o pkg/seaice
255      seaice_lsr: move stress-divergence computations out of outer pseudo-
256      timestepping loop
257    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
258      up, so that the calls of the ctrl_* subroutines are really at the end
259      of the routine.
260    o pkg/gmredi:
261      allow to specify a 2-D horizontal map and a 1-D vertical profil
262      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
263    o pkg/seaice:
264      move lsr iterations from seaice_dynsolver to seaice_lsr.
265    o pkg/seaice:
266      reduce memory footprint of seaice mutldim advection tapes,
267      by using a 2D tape independent of the generic_advdiff ones,
268      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
269    
270    checkpoint62q (2010/12/29)
271    o model/src:
272      - check horizontal grid-spacing for unset or zero/negative values.
273      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
274    o pkg/flt:
275      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
276      - precision of input and output files set according to readBinaryPrec
277        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
278      - initial float position from tiled file was not converted to index space
279        (looks like a bug): fixed to make it similar to initial pos. global file.
280    o global_ocean.cs32x15:
281       change SIZE.h of AD set-up to get same tiling as with MPI.
282       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
283    o model/src:
284       add flag to control printing of domain fields (bathymetry, hFac ...) in
285       ini_mask_etc (call to plot_fieds_xy*).
286    o pkg/thsice:
287       if useEXF, some forcing fields are not valid in overlap: fixed by computing
288       over the interior only + apply EXCH at the end (like with SEAICE advection).
289    o pkg/mdsio:
290      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
291        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
292      - change barrier call for safe multi-threads access to 3-D shared buffer.
293      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
294      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
295        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
296    o pkg/flt:
297      - add fourth-order Runge-Kutta integration
298      - add basic exch2 support (only 1 facet supported so far!)
299    o pkg/mdsio+rw:
300      new S/R to read local (or tile independent) vector (read counterpart of
301       mds_writevec_loc, and front-end write_glvec_rl/rs).
302    o global_ocean.cs32x15: additional input_ad.seaice experiment
303        that uses pkg/seaice rather than pkg/thsice.
304        (using multidim advection for seaice)
305    o towards more F95 syntax for array specification in namelist:
306      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
307        of all verification experiments.
308           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
309          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
310      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
311    o global_ocean.cs32x15: additional input.seaice experiment
312        that uses pkg/seaice rather than pkg/thsice.
313    
314    checkpoint62p (2010/12/17)
315    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
316        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
317    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
318        allow for use of multim. advection in seaice adjoint.
319    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
320      - first attempt to close budgets by taking into account the freshwater
321        flux implied by the sublimation of snow and ice. So far only the
322        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
323        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
324    o eesupp/src:
325      new S/R with new option (NML_EXTENDED_F77) to change array specification
326      from F95 standard to commonly accepted extended F77 form.
327      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
328      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
329      for less tolerant f77 compiler (e.g., pgf77, g77).
330    o globalFiles:
331      commented out in parameter file "data" since it's not safe with MPI
332      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
333      in this case); no longer commented out in restart test (tst_2+2).
334    o add adTapeDir to specify a special directory where adjoint tapes are
335      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
336      and cannot be used together with mdsioLocalDir.
337    o nesting pkgs:
338      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
339      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
340      - add parameter files + utils dir + output from short run on beagle.
341    o pkg/seaice:
342        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
343    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
344      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
345    
346    checkpoint62o (2010/11/25)
347    o pkg/exf:
348      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
349    o pkg/seaice:
350      - seaice_ocean_stress: split a loop for better vectorization of the
351        adjoint code
352      - seaice_growth.F: fix bug in conservation of freshwater connected to
353        capping of heff, put contribution into d_HEFFbyNEG
354      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
355        by something more sensible (parameters that are what their name implies)
356      - change some defaults, so that by default exf-parameters are used for
357        things like rhoAir, cpAir,latent/sensible heat parameters, in order
358        to reproduce the old results, many data.seaice now contain funny values
359        for cpAir and latent heat of sublimation
360    o packages_readparms.F: move exf_readparms up in line so that
361        exf-parameters are visible for other packages (e.g. seaice)
362    o debugMode & debugLevel=2:
363      - differentiate between debugMode & debugLevel=2:
364        debugMode: controls printing of debug messages (sequence of S/R calls).
365        debugLevel: controls printing of algorithm intermediate results and stats.
366      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
367        => allows to print debug-stats without all sequence of call messages.
368      - switch control of debug print from debugLevel to debugMode in many S/R.
369    o pkg/obcs (obcs-sponge):
370        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
371        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
372    o pkg/generic_advdiff:
373      - record overlap minimum size for each advection scheme;
374      - refine criteria on overlap minimum size;
375      - check and stop (in gad_check) if overlap size is too small.
376    o pkg/obcs:
377      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
378        once, in ptracers_implicit.F)
379      - with seaice: remove test on empty file name in obcs_apply_seaice (always
380        apply OB values when tile has OB)
381    o model/src, coriolis setting:
382      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
383        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
384        files (selectCoriMap=3) with any grid.
385      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
386    o pkg/seaice/seaice_growth.F:
387        a few cosmetic changes that reduce the number of lines of code
388    o pkg/obcs: add boundary conditions following Stevens (1990)
389      - the code follows old MOM/NAOSIM code
390      - so far it is only implemented for the eastern and western boundaries
391        and NOT for pTracers
392    o pkg/rbcs:
393      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
394        beginning of the first rbcs forcing period.
395      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
396        offline package, i.e., one file per time, labeled by iteration number;
397        deltaTrbcs sets the timestep with which the data was generated;
398        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
399      - rbcsForcingCycle=0 makes forcing non-cyclic.
400      - make arithmetic safe for negative times and odd forcing periods.
401    
402    checkpoint62n (2010/11/09)
403    o pkg/seaice:
404        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
405    o pkg/obcs:
406       New S/R to copy tracer value from the OB location to narrow band region
407        (width = same as overlap) beyond the OB: preserve OB value (needed for
408        high-order scheme) which were overwritten by EXCH call if in overlap
409        region. Applied to theta, salt, ptracer and advected seaice variables.
410       With seaice: use maskInC in similar way as in gad_advection.F,
411        in seaice_advection.F and advect.F.
412       Update output of experiment seaice_obcs and change exp4 to test OBCS with
413        4th order Adv.Scheme. for pasive salt and ptracer.
414    o tools/genmake2:
415      - when looking for an optfile (not specified), only search for Fortran compiler
416        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
417      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
418        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
419      - set default for CPP to "cpp -traditional -P" (was the case without specifying
420        an optfile, but otherwise default was just "cpp".
421      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
422      - when "CC" is not set in the optfile, look for possible C compiler
423        (instead of just setting CC=cc)
424      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
425        => add a ".F" to ".o" rule for source files with no "#include" (such as
426           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
427      - move gfortran before g77 in list of possible Fortran compiler (consistent
428        with reference compiler switch from g77 to gfortran)
429    o pkg/seaice:
430      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
431        seaice_check that stops the model, when the CPP flag is used.
432      o seaice_growth.F: make capping of ice volume conserving by returning the
433        capped ice as freshwater to EmPmR. This does not change the verification
434        experiments but will change runs where the capping is acutally active
435    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
436      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
437         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
438         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
439    o tools/genmake2:
440      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
441      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
442      - clean previous genmake log files before anything else.
443      - change Makefile to remove testreport log files (*.tr_log) and genmake log
444        files only with "CLEAN" target (instead of "Clean");
445    o pkg/generic_advdiff:
446      Change OBCS in multiDim advection (gad_advection.F):
447       Use maskInC to prevent intermediate update of tracer-field in OB regions,
448       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
449       which were applying future time-step OB values.
450      This way, all explicit calculations use current-time-step OB values
451       (simpler and more consistent).
452      Affects results when set-up uses time-varying OBC and multi-dim advection;
453       update output of experiment seaice_obcs.
454    o pkg/seaice:
455      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
456       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
457         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
458      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
459       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
460       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
461    o pkg aim (2010/10/26):
462      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
463        formulation with obliquity, eccentricity, ... as run-time parameters,
464      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
465        upward shortwave radition at the surface (all-sky and clear-sky).
466    o pkg/obcs:
467      - writing sections with globalFiles=T does not work: switch to tiled-files
468        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
469      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
470      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
471    
472    checkpoint62m (2010/10/21)
473    o pkg/seaice: vectorize seaice_solve4temp.F
474      - move iterations loops outside of i/j-loops
475      - requires 2D arrays for TB and effConduct
476      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
477        modified in this routine
478      - a little bit of clean up, adjusting indentation, etc.
479      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
480        performance and '**TWO' by '**2' (because TWO is a float),
481        replaced ONE, ZERO
482    o eesupp/src:
483       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
484    o pkg/seaice/seaice_growth.F
485      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
486      merging process. The merged routine has two branches, and one activates the 'evolution'
487      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
488      In summary, here is what the '10/10 revision' did consist of
489        part 1: seaice_growth.F revisions 1.71 to 1.75
490          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
491            The emphasis here was on improving readability (e.g. by trying to use meaningful
492            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
493        part 1.5:
494          - revising the lab_sea experiment to make it a more useful (i.e. stable
495            and representative of an actual model run). This was done by generating a
496            (winter) pickup to start from, switching back the main experiment dynamic
497            solver from evp to lsr, having one of the experiments use the free drift solution.
498        part 2: seaice_growth.F revisions 1.76 to 1.85
499          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
500          - Sorting out the various fields units and sign (set early on and reset at the end)
501            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
502            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
503          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
504            and simplifying logical expressions to further improve readibility.
505        part 3: seaice_growth.F revisions 1.86 to 1.89
506          - Re-organize the blocks of code more logically.
507          - Merging the '_if.F' pieces that add something new.
508    o pkg/thsice:
509      - vectorize thsice_solve4temp and thsice_get_exf.
510        Problem: thsice_solve4temp has an unvectorizable statement that
511        might also be problematic for TAF
512      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
513        does not change the verifcation experiment, but will change all
514        experiments that have this flag undefined (not tested in verification);
515        a little reorganization to save a few 2D fields and recomputations
516      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
517      - 2nd step:  fix some store dirs
518        o seems to work somewhat, i.e. using ifort but not g77
519        o likely cause are incomplete init. or recomputation
520        o start verification/global_ocean.cs32x15/input_ad.thsice
521    o pkg/obcs: add support for exch2
522      - the position of the boundary and prescribed values are specified using
523        a global domain with exch2 facets stacked
524        - in x for N,S boundaries (like W2_mapIO=-1)
525        - in y for E,W boundaries (so E,W boundaries do not overlap)
526    o pkg/mdsio: add support for writing global sections with exch2
527        file layout is as for obcs described above:
528        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
529        - for y-z sections, facets are stacked in y
530    o pkg/thsice:
531       - change a few routines for better vectorization: thsice_albedo.F,
532         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
533         not affected, but in particular the latter routine has changed
534         dramatically (not necessarily easier to read now).
535       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
536       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
537    o verification/lab_sea:
538      - overhaul of the forward model experiments. The main motivation
539        for this revision is that lab_sea has proven quite fragile (when
540        changing the sea-ice code, and switching platforms) to a point
541        when failures were very hard to attribute to specific code problems.
542      - the suspected reason for this fragility is noise amplification by evp so,
543        to start with, we decided to replace evp with lsr in the main experiment.
544      - the input.lsr experiment thus became obsolete and was removed.
545      - it was replaced with the input.fd experiment that uses an
546        analytical "free drift" solution as the ice velocity field.
547      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
548        will hopefully allow us to discriminate problems due to dynamic solvers
549        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
550        us to test additional options, along with the salt plume package.
551      - Finally a pickup was generated (at the end of a one year run) to
552        make the tests more representative of an actual model run. Previously
553        the tests starting point was a 1m thickness of ice everywhere.
554    o pkg/seaice:
555      - introducing S\R seaice_freedrift.F that compute the
556        analytical solution to an approximate ice momentum
557        equation (i.e. the simple stress/coriolis balance).
558      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
559        of the free drift velocity field, and enable its use.
560        To actually use the free drift solution as the model ice
561        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
562    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
563    
564    checkpoint62l (2010/10/04)
565    o pkg/seaice:
566      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
567      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
568       version (with USE_ORIGINAL_SBI undef);
569    o add hooks for new packages OASIS, the package will follow
570      (hooks exclude the seaice pkg for now)
571    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
572      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
573      rather than mdsio_readvector.F/mdsio_writevector.F, within
574      adread_adwrite.F to read/write adjoint-related tapes to disk.
575    o eesupp and pkg/mdsio: ALLOW_WHIO
576      Option to write/read 2D fields to files including tiles halos.
577      The main purpose is for adjoint related "tape I/O".
578      The secondary purpose is for debugging phases.
579      A word on those rather specifically intended purposes.
580      The code was meant to be stripped down to the bare minimum.
581      Typically, there is a unique and basic mapping to the global
582      buffer (tile by tile, then proc by proc, then level by level), and
583      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
584      meant to generate user friendly outputs of various shapes and forms.
585      Rather it is intended, for the knowledgeabale developers,
586      to be largely independent of the many mdsio options, to allow
587      outputs of tiles+halos in debugging phases and in adjoint runs,
588      and to allow some flexibility in tuning (adoint) I/O depending on each
589      file system behavior. With regard to tuning, most of the potential knobs
590      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
591      to specify directories, to specify the typical size of I/O calls, etc.)
592      are not yet included, and will be added if they prove useful.
593    o pkg/seaice:
594       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
595    o pkg/seaice:
596       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
597       code (seaice_budget_ice_if.F) which enable to recover old standard
598       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
599       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
600    o model/src (rStar):
601       use simple average (not area weighted) of rStarFac at U,V point when using
602       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
603       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
604    
605    checkpoint62k (2010/09/17)
606    o adjoint
607       * changed verification/global_ocean.cs32x15 ; adjoint now tests
608         Adams-Bashforth 3 + NLFS + RSTAR
609       * some more modifs required for ECCO-GODAE v4
610    o pkg/seaice
611       add SEAICE_AGE_VOL option to use volume instead of area for
612       integrating SEAICE_AGE
613    o model/src:
614       first check-in of sigma & hybrid-sigma coordinate code ; also includes
615       non-linear free-surface parts ; but pressure-gradient not yet coded.
616    o pkg/ptracers:
617       option for ptracer to convert Salt Relax into additional EmP.
618        tested in exp. global_ocean.90x40x15.dwnslp (update output)
619    
620    checkpoint62j (2010/08/25)
621    o pkg/ggl90:
622       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
623    o pkg/dic: car_flux.F, phos_flux.F
624      - reduce number of exp-calls in order to improve performance
625      - clean up a little (replace fields by their macros, etc., fix
626        typo in CPP-flag)
627    o pkg/ggl90: minor changes
628      - GGL90diffKrS was removed --> always use GGL90diffKr
629      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
630      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
631        (commented out for now)
632      - change in max/min operations to ensure that smoothing is ok
633      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
634      - always use diffKrNrT as background profile (i.e. never use diffKr field)
635    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
636    o pkg/dic:
637      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
638        vectorization
639      - small bug fix in insol for the unlikely case of a cartesian grid
640      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
641        + now vectorize, which also removes adjoint recomputations;
642        + replace integer maksp1 by _RL maskp1
643        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
644    
645    checkpoint62i (2010/07/21)
646    o pkg/flt:
647      - with OBCS: stop floats which enter the OB region
648    o model/src:
649      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
650        for implicit vertical advection.
651    o pkg/seaice:
652     - account for melting in seaice age evolution.
653     - remove double counting of seaice ridging effect on seaice age.
654    
655    checkpoint62h (2010/06/18)
656    o pkg/exch2:
657     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
658    o tools/genmake2
659      - remove "-pdefault" option: redundant with the use of "packages.conf";
660      - remove file pkg/pkg_default : set the default as a pkg group
661        ("default_pkg_list") defined in pkg/pkg_groups;
662      - fix for case pkg/pkg_depend is missing (was hanging before);
663      - add option "-pgroups" to specify a different pkg_groups than the default.
664    o verification/adjustment.cs-32x32x1:
665       add a "minimal" set-up test (code_min & input_min) which only compiles
666       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
667    o tools/genmake2
668      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
669      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
670    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
671      files are nearly the same anyway.
672      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
673       - redefinition of tau(i,i) (by a factor of ustar)
674       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
675       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
676       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
677       - replace
678         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
679         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
680         by
681         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
682         (changes results)
683       -> exf_bulkformulae v1.22,
684          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
685          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
686                    output.txt 1.63
687           offline_exf_seaice: output.seaicetd.txt 1.7
688           seaice_obcs: output.txt 1.10)
689      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
690       -> exf_bulkformulae v1.23,
691          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
692          and global_ocean.cs32x15.icedyn (only 11 matching digits)
693      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
694    o adjoint of exch-1:
695     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
696       (note: was already like this when using EXCH-2) and remove flow dir
697       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
698     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
699     - update pkg/exch2 diff list.
700    
701    checkpoint62g (2010/05/19)
702    o eesupp/src (exch-1):
703     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
704       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
705       (renamed to exch1_*rx_cube.F).
706     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
707       to call new exch1 S/R ; update Makefile and .cvsignore.
708     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
709       exch2_xy_rx later)
710      Note: after updating your code, need to run "make clean" in eesupp/src
711    o test experiment bottom_ctrl_5x5:
712       new output_adm.txt with fewer grdchk & less monitor output.
713    o model/src:
714      remove the call to ini_cori in initialise_varia.F (just keep the usual one
715       in initialise_fixed.F). More consistent with coriolis & horizontal grid
716       beeing treated in the same way (ini_grid is not called a 2nd time).
717    o pkg/exf:
718      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
719      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
720      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
721      - cosmetic changes to exf_bulkformulae.F to make it look more like
722        exf_bulk_largeyeager04.F
723    o eesupp/src (exch-1):
724      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
725      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
726        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
727        (even without using MPI).
728      - Message mode: move RecvAck setting (indicator of buffer being ready)
729        from send_put to recv_get S/R (was useless before, but not sure if
730        it's much more useful now);
731      - Switch the order of sync: MPI-proc 1rst and then threads;
732      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
733      - fix AD code for communication mode ='get' (but not used).
734    o model/src:
735      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
736      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
737    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
738    o pkg/ctrl: require a specific set of control variables and exf-flags for
739      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
740    o model/src:
741     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
742       1rst forward sweep, to avoid over-writing output files during recomputations
743       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
744     b) 2nd version:
745      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
746      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
747         writePickupAtEnd) + seaice & ptracers output;
748      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
749    o model/src:
750      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
751    o pkg/exch2:
752      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
753      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
754    o pkg/autodiff & exch2:
755      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
756      (for now, only if ALLOW_EXCH2 is defined).
757    o pkg/autodiff:
758      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
759        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
760       + clean-up comments (_RS is not always real*4)
761      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
762      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
763        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
764    o testreport (AD-tests):
765      no longer link files from dir "../input" (1rst link files from
766      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
767    
768    checkpoint62f (2010/04/29)
769    o model/src/the_main_loop.F:
770      adjust store directives for seaice evp and multicategory according to
771      pkg/ecco/the_main_loop.F
772    o adjoint:
773      global_sum_ad was incomplete (noted many times by many people ;)
774      nice description by Jean U. as follows:
775      * allreduce(var) in global_sum.F can be interpreted as
776        reduce(sum) followed by broadcast of sum.
777      * The adjoint of that is
778        sum(adjoint) followed by broadcast(summed adjoint value)
779        or in other words, allreduce(sum, adjoint vars)
780      We were missing the sum(adjoint)!
781      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
782      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
783      The fix should produce 16-digit accuracy between
784      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
785      multi-CPU single-tile (e.g. nSx=1, nPx-2)
786      We'll probably change this yet again shortly
787    o eesupp/src:
788      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
789    o pkg/icefront
790      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
791        specification of addmass array based on a 2D field, which is added
792        at bottommost wet level at each horizontal location.
793    o model/src:
794     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
795     layout; (not always compatible with delX,delY setting; commented out for now).
796    o pkg/exch2:
797     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
798     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
799    
800    checkpoint62e (2010/04/15)
801    o pkg/obcs:
802    - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).    - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
803  o pkg/dic:  o pkg/dic:
804    -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;    -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
# Line 85  o tools/build_options: Line 879  o tools/build_options:
879      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
880  o pkg/ecco  o pkg/ecco
881    - allow user defined cost function contributions    - allow user defined cost function contributions
882          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
883          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
884    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
885        the two options are complementary.        the two options are complementary.
886  o pkg/smooth  o pkg/smooth
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