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revision 1.1240 by jmc, Wed Mar 24 02:12:51 2010 UTC revision 1.1416 by jmc, Thu Apr 28 13:59:22 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    
8    o fizhi-cs test exp.:
9       switch reference output convention for these 2 non-standard test-exp,
10        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
11          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
12       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
13    o model/inc:
14      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
15        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
16    o pkg/seaice:
17      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
18    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
19      - updated affected output*.txt files due to salt and saltPlumeFlux bug fix
20    
21    checkpoint62w (2011/04/26)
22    o pkg/mom_fluxform:
23      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
24      - use parameter "sideDragFactor" in no-slip BC side-drag part.
25      - update output of exp. global_ocean.90x40x15
26    o pkg/mom_vecinv:
27      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
28    o update seaice exp.:
29      use more consistent parameter values (remove "backward compatability only":
30       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
31      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
32       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
33    o update test-exp global_ocean.90x40x15:
34      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
35      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
36      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
37      o turn on zStar & viscA4 in standard set-up (dir input/)
38        and update output files: output.txt & output.dwnslp.txt
39    o new AD-test experiment: obcs_ctrl
40      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
41    o pkg/dic:
42      fix two bugs in handling water vapour pressure in carbonate chemistry
43      and air-sea fluxes. Found by Val Bennington and Galen McKinley
44      (add DIC Option = WATERVAP_BUG to recover old results)
45      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
46    o adding allowInteriorFreezing option to check for water below freezing point
47      at depth and bring the negative heat anomaly to the surface level
48    o pkgs _fields_load:
49      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
50      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
51        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
52        rbcs to get interpolation weights and time reccord number.
53      - fix multi-threading in aim_fields_load.F
54      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
55    o external_fields_load:
56      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
57       interpolation weights) to use in a periodic time-series ; do not divide by
58       time-step to convert to integer:
59       - this fixes case where externForcingPeriod is not multiple of time-step
60          (Thanks to Christopher L. Wolfe)
61       - this fixes case where externForcingPeriod is an odd multiple of time-step
62         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
63      store index of time-record which is currently loaded:
64       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
65       - needed for the adjoint but not yet used because of extensive recomputations;
66         (to be fixed soon)
67    
68    checkpoint62v (2011/04/02)
69    o verification/1D_ocean_ice_column added to test Ian Fenty's
70      pkg/seaice_growth.F modifications for improving sea ice code differentiability
71    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
72      (new velocity statistics after changing maskInW & maskInS definition)
73    o pkg/generic_advdiff with OBCS:
74      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
75      equivalent to assumption of no tracer gradient outside the OB region.
76      This will affect the results if using obcs+biharmonic diffusion.
77      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
78    o pkg/obcs:
79      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
80      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
81      in Interior region. No impact on solution but affects Velocity monitor stats.
82    o pkg/ptracers (adjoint)
83      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
84      tape file for each tracer
85    o model/inc/src and pkg/autodiff: add parameters that allow to turn
86      of parts of the adjoint code at run time. For now, there are only
87      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
88      parameters are set in data.pkg.
89      This is the lazy coward's version of doing this, but still useful for
90      debugging. In order to do it right, everything needs to be moved to
91      pkg/autodiff.
92    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
93      the end; this fixes the adjoint balancing code for open boundaries.
94    o pkg/ctrl:
95      - change behavior of xx_${varname}period to be analogous to exf-conventions:
96        xx_${varname}period =   0.,  means time-independent control part
97        xx_${varname}period = -12., means one-year-periodic monthly control part
98      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
99        clean up ctrl_init a little, remove unused variables
100      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
101      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
102    
103    checkpoint62u (2011/03/15)
104    o model/src:
105      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
106        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
107      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
108        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
109    o pkg/ctrl/obcs/ecco:
110      - remove obsolete, unused, and partially broken code:
111        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
112        ALLOW_CTRL_OBCS_BALANCE
113      - put a stop statement into ecco/cost_obcsvol.F, but also add
114        cost_obcsvol to ecco_ad_diff.list
115    o pkg/ecco: fix counting cost function contributions for obcs (code
116      by Matt M.) and diffkr for diagnostics
117    o pkg/ecco, pkg/ctrl, pkg/grdchk:
118      add cost penalty terms for initial uvel, vvel, eta controls
119      and I/O for prior error files
120    o pkg/mdsio:
121       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
122       (new argument) to check for tiled file in mdsioLocalDir : this fix the
123       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
124    o pkg/ctrl:
125     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
126       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
127       unused and superfluous variables
128     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
129    o pkg/ecco
130     - enable adjoint of Stevens OB
131    o pkg/ctrl/ecco/grdchk:
132      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
133        Fortunately, we do not have any tests for the numerous cpp-flagged
134        option of "obcs as control parameters" so we will never know
135        if this is an improvement (but at least now things compile).
136      - remove an obsolete initialization from ecco_cost_init_barfiles.F
137      - fix some problems within never used ifdefs to make the code compile
138    o pkg/obcs:
139     - Refine Interior mask definition to work with more complex OB (e.g.
140       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
141       read in Interior mask from file. Check if Interior mask is consistent
142       with OB list of indices.
143    o pkg/seaice
144     - beginning code for a seaice tracer package,
145       but currently only used for seaice age: SEAICE_AGE
146       SEAICE_num = 4
147       iTracer = 1: area-weighted ice age
148               = 2: volume-weighted ice age
149               = 3, 4: template for one-year vs. multi-year ice
150       data.seaice has new namelist SEAICE_PARM03 for arrays related to
151       SEAICE_num
152    
153    checkpoint62t (2011/03/05)
154    o pkg/obcs:
155     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
156       then normal component. This ensures that the normal component is set
157       correctly even when it conficts with tangential setting from an other OB.
158       Affects results of test-experiment seaice_obcs: update the output.txt
159    o pkg/obcs:
160     - add code to monitor statistics of dynamical fields at OB.
161     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
162       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
163       - change default: balance the Net inflow through all OB (instead of balancing
164         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
165     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
166       to match Nortern OB inflow (OBCS_balanceFacN=0).
167    o pkg/seaice:
168     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
169    o pkg/seaice (seaice_growth v 1.113):
170     - reverting seaice_growth to v 1.111 in order to have code with exact bit
171       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
172       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
173       runtime flag SEAICEareaFormula is kept but is inactive
174    o model/src:
175     - add new param to scale curvilinear grid distance and area when using
176       a different sphere radius from the grid-files.
177     - test/check multi-threads EXCH applied to local variable (cg2d_x)
178    o adjoint:
179     - enable adjoint of Stevens OB
180     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
181       (a bit delicate because of potentially modified adj. common block structure;
182       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
183    
184    checkpoint62s (2011/02/15)
185    o pkg/seaice (seaice_growth v 1.112):
186     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
187       computing the ice cover tendency from effective thickness tendencies. Include
188       Ian Fenty's formula.
189     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
190       SEAICEareaFormula.
191     - simplify notations for the various d_HEFF/d_AREA terms.
192    o pkg/gmredi:
193     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
194       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
195       add a verification test-run (front_relax.bvp) to test GM_useBVP.
196    o pkg/seaice (seaice_growth v 1.111):
197     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
198     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
199       also melt ice.
200    o pkg/seaice:
201     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
202     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
203    o pkg/cheapaml:
204     - from Nico Wienders: New version of this package.
205    o pkg/flt:
206     - add CPP options to prevent floats to re-enter the opposite side of
207       a periodic domain (default: keep periodicity)
208    o pkg/gmredi:
209     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
210       (needed for multi-dim advection).
211     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
212    o model/src:
213     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
214    o tutorial_tracer_adjsens
215     - extend to NLFS and replace maskC by hFacC
216       (change reference output accordingly)
217    
218    checkpoint62r (2011/01/24)
219    o testreport:
220     - add option -deloutp (-do) to remove output file after successful run
221     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
222       extract exact list of procs from this file ; adjust COMMAND by
223       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
224    o pkg/ecco: replace old ineffective way of penalizing deviations from
225      first guess (of obcs) with code by Matt Mazloff
226    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
227      exf/cal
228      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
229        and handle case of obcs?period == 0
230        Not affected by these changes: There is still an inconsistency in
231        the computation of start/endrec for the obcs variables for ALLOW_CAL
232        defined (see comment by Menemenlis, 7-Mar-2003)
233      - make S/R ctrl_get_gen_rec return something meaningful even if
234        ALLOW_CAL is not defined
235      - ctrl_getobcs?: simplify code so that it does not need to use
236                       S/R exf_swapfields
237    o testreport:
238       allow to test MPI with different number of processors for each experiment:
239       create file "SIZE.h.mpi" in each build dir.
240       Note: update of "-command" argument not yet implemented.
241    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
242      alleviate the need for additional 3D tapes when using
243      the non-inear free surface in the adjoint. This is done
244      by adding an 'update' of hfacc etc. to their current
245      value at the beginning of forward_step.F.
246    o pkg/seaice
247      seaice_lsr: move stress-divergence computations out of outer pseudo-
248      timestepping loop
249    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
250      up, so that the calls of the ctrl_* subroutines are really at the end
251      of the routine.
252    o pkg/gmredi:
253      allow to specify a 2-D horizontal map and a 1-D vertical profil
254      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
255    o pkg/seaice:
256      move lsr iterations from seaice_dynsolver to seaice_lsr.
257    o pkg/seaice:
258      reduce memory footprint of seaice mutldim advection tapes,
259      by using a 2D tape independent of the generic_advdiff ones,
260      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
261    
262    checkpoint62q (2010/12/29)
263    o model/src:
264      - check horizontal grid-spacing for unset or zero/negative values.
265      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
266    o pkg/flt:
267      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
268      - precision of input and output files set according to readBinaryPrec
269        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
270      - initial float position from tiled file was not converted to index space
271        (looks like a bug): fixed to make it similar to initial pos. global file.
272    o global_ocean.cs32x15:
273       change SIZE.h of AD set-up to get same tiling as with MPI.
274       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
275    o model/src:
276       add flag to control printing of domain fields (bathymetry, hFac ...) in
277       ini_mask_etc (call to plot_fieds_xy*).
278    o pkg/thsice:
279       if useEXF, some forcing fields are not valid in overlap: fixed by computing
280       over the interior only + apply EXCH at the end (like with SEAICE advection).
281    o pkg/mdsio:
282      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
283        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
284      - change barrier call for safe multi-threads access to 3-D shared buffer.
285      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
286      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
287        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
288    o pkg/flt:
289      - add fourth-order Runge-Kutta integration
290      - add basic exch2 support (only 1 facet supported so far!)
291    o pkg/mdsio+rw:
292      new S/R to read local (or tile independent) vector (read counterpart of
293       mds_writevec_loc, and front-end write_glvec_rl/rs).
294    o global_ocean.cs32x15: additional input_ad.seaice experiment
295        that uses pkg/seaice rather than pkg/thsice.
296        (using multidim advection for seaice)
297    o towards more F95 syntax for array specification in namelist:
298      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
299        of all verification experiments.
300           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
301          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
302      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
303    o global_ocean.cs32x15: additional input.seaice experiment
304        that uses pkg/seaice rather than pkg/thsice.
305    
306    checkpoint62p (2010/12/17)
307    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
308        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
309    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
310        allow for use of multim. advection in seaice adjoint.
311    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
312      - first attempt to close budgets by taking into account the freshwater
313        flux implied by the sublimation of snow and ice. So far only the
314        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
315        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
316    o eesupp/src:
317      new S/R with new option (NML_EXTENDED_F77) to change array specification
318      from F95 standard to commonly accepted extended F77 form.
319      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
320      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
321      for less tolerant f77 compiler (e.g., pgf77, g77).
322    o globalFiles:
323      commented out in parameter file "data" since it's not safe with MPI
324      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
325      in this case); no longer commented out in restart test (tst_2+2).
326    o add adTapeDir to specify a special directory where adjoint tapes are
327      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
328      and cannot be used together with mdsioLocalDir.
329    o nesting pkgs:
330      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
331      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
332      - add parameter files + utils dir + output from short run on beagle.
333    o pkg/seaice:
334        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
335    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
336      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
337    
338    checkpoint62o (2010/11/25)
339    o pkg/exf:
340      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
341    o pkg/seaice:
342      - seaice_ocean_stress: split a loop for better vectorization of the
343        adjoint code
344      - seaice_growth.F: fix bug in conservation of freshwater connected to
345        capping of heff, put contribution into d_HEFFbyNEG
346      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
347        by something more sensible (parameters that are what their name implies)
348      - change some defaults, so that by default exf-parameters are used for
349        things like rhoAir, cpAir,latent/sensible heat parameters, in order
350        to reproduce the old results, many data.seaice now contain funny values
351        for cpAir and latent heat of sublimation
352    o packages_readparms.F: move exf_readparms up in line so that
353        exf-parameters are visible for other packages (e.g. seaice)
354    o debugMode & debugLevel=2:
355      - differentiate between debugMode & debugLevel=2:
356        debugMode: controls printing of debug messages (sequence of S/R calls).
357        debugLevel: controls printing of algorithm intermediate results and stats.
358      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
359        => allows to print debug-stats without all sequence of call messages.
360      - switch control of debug print from debugLevel to debugMode in many S/R.
361    o pkg/obcs (obcs-sponge):
362        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
363        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
364    o pkg/generic_advdiff:
365      - record overlap minimum size for each advection scheme;
366      - refine criteria on overlap minimum size;
367      - check and stop (in gad_check) if overlap size is too small.
368    o pkg/obcs:
369      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
370        once, in ptracers_implicit.F)
371      - with seaice: remove test on empty file name in obcs_apply_seaice (always
372        apply OB values when tile has OB)
373    o model/src, coriolis setting:
374      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
375        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
376        files (selectCoriMap=3) with any grid.
377      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
378    o pkg/seaice/seaice_growth.F:
379        a few cosmetic changes that reduce the number of lines of code
380    o pkg/obcs: add boundary conditions following Stevens (1990)
381      - the code follows old MOM/NAOSIM code
382      - so far it is only implemented for the eastern and western boundaries
383        and NOT for pTracers
384    o pkg/rbcs:
385      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
386        beginning of the first rbcs forcing period.
387      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
388        offline package, i.e., one file per time, labeled by iteration number;
389        deltaTrbcs sets the timestep with which the data was generated;
390        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
391      - rbcsForcingCycle=0 makes forcing non-cyclic.
392      - make arithmetic safe for negative times and odd forcing periods.
393    
394    checkpoint62n (2010/11/09)
395    o pkg/seaice:
396        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
397    o pkg/obcs:
398       New S/R to copy tracer value from the OB location to narrow band region
399        (width = same as overlap) beyond the OB: preserve OB value (needed for
400        high-order scheme) which were overwritten by EXCH call if in overlap
401        region. Applied to theta, salt, ptracer and advected seaice variables.
402       With seaice: use maskInC in similar way as in gad_advection.F,
403        in seaice_advection.F and advect.F.
404       Update output of experiment seaice_obcs and change exp4 to test OBCS with
405        4th order Adv.Scheme. for pasive salt and ptracer.
406    o tools/genmake2:
407      - when looking for an optfile (not specified), only search for Fortran compiler
408        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
409      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
410        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
411      - set default for CPP to "cpp -traditional -P" (was the case without specifying
412        an optfile, but otherwise default was just "cpp".
413      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
414      - when "CC" is not set in the optfile, look for possible C compiler
415        (instead of just setting CC=cc)
416      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
417        => add a ".F" to ".o" rule for source files with no "#include" (such as
418           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
419      - move gfortran before g77 in list of possible Fortran compiler (consistent
420        with reference compiler switch from g77 to gfortran)
421    o pkg/seaice:
422      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
423        seaice_check that stops the model, when the CPP flag is used.
424      o seaice_growth.F: make capping of ice volume conserving by returning the
425        capped ice as freshwater to EmPmR. This does not change the verification
426        experiments but will change runs where the capping is acutally active
427    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
428      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
429         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
430         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
431    o tools/genmake2:
432      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
433      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
434      - clean previous genmake log files before anything else.
435      - change Makefile to remove testreport log files (*.tr_log) and genmake log
436        files only with "CLEAN" target (instead of "Clean");
437    o pkg/generic_advdiff:
438      Change OBCS in multiDim advection (gad_advection.F):
439       Use maskInC to prevent intermediate update of tracer-field in OB regions,
440       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
441       which were applying future time-step OB values.
442      This way, all explicit calculations use current-time-step OB values
443       (simpler and more consistent).
444      Affects results when set-up uses time-varying OBC and multi-dim advection;
445       update output of experiment seaice_obcs.
446    o pkg/seaice:
447      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
448       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
449         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
450      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
451       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
452       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
453    o pkg aim (2010/10/26):
454      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
455        formulation with obliquity, eccentricity, ... as run-time parameters,
456      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
457        upward shortwave radition at the surface (all-sky and clear-sky).
458    o pkg/obcs:
459      - writing sections with globalFiles=T does not work: switch to tiled-files
460        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
461      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
462      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
463    
464    checkpoint62m (2010/10/21)
465    o pkg/seaice: vectorize seaice_solve4temp.F
466      - move iterations loops outside of i/j-loops
467      - requires 2D arrays for TB and effConduct
468      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
469        modified in this routine
470      - a little bit of clean up, adjusting indentation, etc.
471      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
472        performance and '**TWO' by '**2' (because TWO is a float),
473        replaced ONE, ZERO
474    o eesupp/src:
475       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
476    o pkg/seaice/seaice_growth.F
477      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
478      merging process. The merged routine has two branches, and one activates the 'evolution'
479      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
480      In summary, here is what the '10/10 revision' did consist of
481        part 1: seaice_growth.F revisions 1.71 to 1.75
482          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
483            The emphasis here was on improving readability (e.g. by trying to use meaningful
484            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
485        part 1.5:
486          - revising the lab_sea experiment to make it a more useful (i.e. stable
487            and representative of an actual model run). This was done by generating a
488            (winter) pickup to start from, switching back the main experiment dynamic
489            solver from evp to lsr, having one of the experiments use the free drift solution.
490        part 2: seaice_growth.F revisions 1.76 to 1.85
491          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
492          - Sorting out the various fields units and sign (set early on and reset at the end)
493            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
494            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
495          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
496            and simplifying logical expressions to further improve readibility.
497        part 3: seaice_growth.F revisions 1.86 to 1.89
498          - Re-organize the blocks of code more logically.
499          - Merging the '_if.F' pieces that add something new.
500    o pkg/thsice:
501      - vectorize thsice_solve4temp and thsice_get_exf.
502        Problem: thsice_solve4temp has an unvectorizable statement that
503        might also be problematic for TAF
504      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
505        does not change the verifcation experiment, but will change all
506        experiments that have this flag undefined (not tested in verification);
507        a little reorganization to save a few 2D fields and recomputations
508      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
509      - 2nd step:  fix some store dirs
510        o seems to work somewhat, i.e. using ifort but not g77
511        o likely cause are incomplete init. or recomputation
512        o start verification/global_ocean.cs32x15/input_ad.thsice
513    o pkg/obcs: add support for exch2
514      - the position of the boundary and prescribed values are specified using
515        a global domain with exch2 facets stacked
516        - in x for N,S boundaries (like W2_mapIO=-1)
517        - in y for E,W boundaries (so E,W boundaries do not overlap)
518    o pkg/mdsio: add support for writing global sections with exch2
519        file layout is as for obcs described above:
520        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
521        - for y-z sections, facets are stacked in y
522    o pkg/thsice:
523       - change a few routines for better vectorization: thsice_albedo.F,
524         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
525         not affected, but in particular the latter routine has changed
526         dramatically (not necessarily easier to read now).
527       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
528       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
529    o verification/lab_sea:
530      - overhaul of the forward model experiments. The main motivation
531        for this revision is that lab_sea has proven quite fragile (when
532        changing the sea-ice code, and switching platforms) to a point
533        when failures were very hard to attribute to specific code problems.
534      - the suspected reason for this fragility is noise amplification by evp so,
535        to start with, we decided to replace evp with lsr in the main experiment.
536      - the input.lsr experiment thus became obsolete and was removed.
537      - it was replaced with the input.fd experiment that uses an
538        analytical "free drift" solution as the ice velocity field.
539      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
540        will hopefully allow us to discriminate problems due to dynamic solvers
541        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
542        us to test additional options, along with the salt plume package.
543      - Finally a pickup was generated (at the end of a one year run) to
544        make the tests more representative of an actual model run. Previously
545        the tests starting point was a 1m thickness of ice everywhere.
546    o pkg/seaice:
547      - introducing S\R seaice_freedrift.F that compute the
548        analytical solution to an approximate ice momentum
549        equation (i.e. the simple stress/coriolis balance).
550      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
551        of the free drift velocity field, and enable its use.
552        To actually use the free drift solution as the model ice
553        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
554    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
555    
556    checkpoint62l (2010/10/04)
557    o pkg/seaice:
558      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
559      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
560       version (with USE_ORIGINAL_SBI undef);
561    o add hooks for new packages OASIS, the package will follow
562      (hooks exclude the seaice pkg for now)
563    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
564      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
565      rather than mdsio_readvector.F/mdsio_writevector.F, within
566      adread_adwrite.F to read/write adjoint-related tapes to disk.
567    o eesupp and pkg/mdsio: ALLOW_WHIO
568      Option to write/read 2D fields to files including tiles halos.
569      The main purpose is for adjoint related "tape I/O".
570      The secondary purpose is for debugging phases.
571      A word on those rather specifically intended purposes.
572      The code was meant to be stripped down to the bare minimum.
573      Typically, there is a unique and basic mapping to the global
574      buffer (tile by tile, then proc by proc, then level by level), and
575      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
576      meant to generate user friendly outputs of various shapes and forms.
577      Rather it is intended, for the knowledgeabale developers,
578      to be largely independent of the many mdsio options, to allow
579      outputs of tiles+halos in debugging phases and in adjoint runs,
580      and to allow some flexibility in tuning (adoint) I/O depending on each
581      file system behavior. With regard to tuning, most of the potential knobs
582      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
583      to specify directories, to specify the typical size of I/O calls, etc.)
584      are not yet included, and will be added if they prove useful.
585    o pkg/seaice:
586       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
587    o pkg/seaice:
588       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
589       code (seaice_budget_ice_if.F) which enable to recover old standard
590       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
591       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
592    o model/src (rStar):
593       use simple average (not area weighted) of rStarFac at U,V point when using
594       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
595       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
596    
597    checkpoint62k (2010/09/17)
598    o adjoint
599       * changed verification/global_ocean.cs32x15 ; adjoint now tests
600         Adams-Bashforth 3 + NLFS + RSTAR
601       * some more modifs required for ECCO-GODAE v4
602    o pkg/seaice
603       add SEAICE_AGE_VOL option to use volume instead of area for
604       integrating SEAICE_AGE
605    o model/src:
606       first check-in of sigma & hybrid-sigma coordinate code ; also includes
607       non-linear free-surface parts ; but pressure-gradient not yet coded.
608    o pkg/ptracers:
609       option for ptracer to convert Salt Relax into additional EmP.
610        tested in exp. global_ocean.90x40x15.dwnslp (update output)
611    
612    checkpoint62j (2010/08/25)
613    o pkg/ggl90:
614       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
615    o pkg/dic: car_flux.F, phos_flux.F
616      - reduce number of exp-calls in order to improve performance
617      - clean up a little (replace fields by their macros, etc., fix
618        typo in CPP-flag)
619    o pkg/ggl90: minor changes
620      - GGL90diffKrS was removed --> always use GGL90diffKr
621      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
622      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
623        (commented out for now)
624      - change in max/min operations to ensure that smoothing is ok
625      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
626      - always use diffKrNrT as background profile (i.e. never use diffKr field)
627    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
628    o pkg/dic:
629      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
630        vectorization
631      - small bug fix in insol for the unlikely case of a cartesian grid
632      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
633        + now vectorize, which also removes adjoint recomputations;
634        + replace integer maksp1 by _RL maskp1
635        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
636    
637    checkpoint62i (2010/07/21)
638    o pkg/flt:
639      - with OBCS: stop floats which enter the OB region
640    o model/src:
641      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
642        for implicit vertical advection.
643    o pkg/seaice:
644     - account for melting in seaice age evolution.
645     - remove double counting of seaice ridging effect on seaice age.
646    
647    checkpoint62h (2010/06/18)
648    o pkg/exch2:
649     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
650    o tools/genmake2
651      - remove "-pdefault" option: redundant with the use of "packages.conf";
652      - remove file pkg/pkg_default : set the default as a pkg group
653        ("default_pkg_list") defined in pkg/pkg_groups;
654      - fix for case pkg/pkg_depend is missing (was hanging before);
655      - add option "-pgroups" to specify a different pkg_groups than the default.
656    o verification/adjustment.cs-32x32x1:
657       add a "minimal" set-up test (code_min & input_min) which only compiles
658       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
659    o tools/genmake2
660      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
661      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
662    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
663      files are nearly the same anyway.
664      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
665       - redefinition of tau(i,i) (by a factor of ustar)
666       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
667       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
668       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
669       - replace
670         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
671         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
672         by
673         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
674         (changes results)
675       -> exf_bulkformulae v1.22,
676          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
677          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
678                    output.txt 1.63
679           offline_exf_seaice: output.seaicetd.txt 1.7
680           seaice_obcs: output.txt 1.10)
681      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
682       -> exf_bulkformulae v1.23,
683          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
684          and global_ocean.cs32x15.icedyn (only 11 matching digits)
685      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
686    o adjoint of exch-1:
687     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
688       (note: was already like this when using EXCH-2) and remove flow dir
689       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
690     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
691     - update pkg/exch2 diff list.
692    
693    checkpoint62g (2010/05/19)
694    o eesupp/src (exch-1):
695     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
696       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
697       (renamed to exch1_*rx_cube.F).
698     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
699       to call new exch1 S/R ; update Makefile and .cvsignore.
700     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
701       exch2_xy_rx later)
702      Note: after updating your code, need to run "make clean" in eesupp/src
703    o test experiment bottom_ctrl_5x5:
704       new output_adm.txt with fewer grdchk & less monitor output.
705    o model/src:
706      remove the call to ini_cori in initialise_varia.F (just keep the usual one
707       in initialise_fixed.F). More consistent with coriolis & horizontal grid
708       beeing treated in the same way (ini_grid is not called a 2nd time).
709    o pkg/exf:
710      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
711      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
712      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
713      - cosmetic changes to exf_bulkformulae.F to make it look more like
714        exf_bulk_largeyeager04.F
715    o eesupp/src (exch-1):
716      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
717      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
718        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
719        (even without using MPI).
720      - Message mode: move RecvAck setting (indicator of buffer being ready)
721        from send_put to recv_get S/R (was useless before, but not sure if
722        it's much more useful now);
723      - Switch the order of sync: MPI-proc 1rst and then threads;
724      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
725      - fix AD code for communication mode ='get' (but not used).
726    o model/src:
727      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
728      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
729    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
730    o pkg/ctrl: require a specific set of control variables and exf-flags for
731      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
732    o model/src:
733     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
734       1rst forward sweep, to avoid over-writing output files during recomputations
735       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
736     b) 2nd version:
737      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
738      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
739         writePickupAtEnd) + seaice & ptracers output;
740      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
741    o model/src:
742      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
743    o pkg/exch2:
744      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
745      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
746    o pkg/autodiff & exch2:
747      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
748      (for now, only if ALLOW_EXCH2 is defined).
749    o pkg/autodiff:
750      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
751        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
752       + clean-up comments (_RS is not always real*4)
753      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
754      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
755        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
756    o testreport (AD-tests):
757      no longer link files from dir "../input" (1rst link files from
758      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
759    
760    checkpoint62f (2010/04/29)
761    o model/src/the_main_loop.F:
762      adjust store directives for seaice evp and multicategory according to
763      pkg/ecco/the_main_loop.F
764    o adjoint:
765      global_sum_ad was incomplete (noted many times by many people ;)
766      nice description by Jean U. as follows:
767      * allreduce(var) in global_sum.F can be interpreted as
768        reduce(sum) followed by broadcast of sum.
769      * The adjoint of that is
770        sum(adjoint) followed by broadcast(summed adjoint value)
771        or in other words, allreduce(sum, adjoint vars)
772      We were missing the sum(adjoint)!
773      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
774      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
775      The fix should produce 16-digit accuracy between
776      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
777      multi-CPU single-tile (e.g. nSx=1, nPx-2)
778      We'll probably change this yet again shortly
779    o eesupp/src:
780      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
781    o pkg/icefront
782      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
783        specification of addmass array based on a 2D field, which is added
784        at bottommost wet level at each horizontal location.
785    o model/src:
786     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
787     layout; (not always compatible with delX,delY setting; commented out for now).
788    o pkg/exch2:
789     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
790     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
791    
792    checkpoint62e (2010/04/15)
793    o pkg/obcs:
794      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
795    o pkg/dic:
796      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
797        (note: not presently tested in any forward verification exp.)
798       update tutorial_global_oce_biogeo AD output file.
799    o pkg/exf:
800      - account for the variation of albedo as a function of zenith angle
801        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
802    o build_options:
803     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
804    o pkg/dic:
805      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
806      - use binary pickup file for restart;
807      - initialise atmos-CO2 box from dic_pCO2 parameter;
808      - fix multi-threaded.
809    o pkg/rbcs:
810     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
811       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
812     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
813       and update output.txt
814    o pkg/kpp:
815     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
816     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
817       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
818       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
819     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
820       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
821    o pkg/offline:
822      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
823      (bug was added in version 1.10 on 2007-08-23).
824    o pkg/offline:
825      - no need to specify periodicExternalForcing, etc ... to use offline pack
826      - offline input files no longer just single prec --> parameter offlineLoadPrec
827    o verification/lab_sea:
828      change AD test to multi-tile setup and update all 4 AD output.
829      NOTE: while cost function values remain very similar,
830      gradients are very different, although gradient checks are self-consistent
831      Should try to get to the bottom of this (cost function summation order?)
832    o pkg/dic:
833      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
834      a weakness of TAF that drops part of double precision in log10 derivative.
835      <= changes removed since problem has been fixed in current TAF version 1.9.71
836      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
837  o pkg/ecco:  o pkg/ecco:
838    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
839    update all 4 lab_sea AD output.    update all 4 lab_sea AD output.
# Line 41  o tools/build_options: Line 871  o tools/build_options:
871      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
872  o pkg/ecco  o pkg/ecco
873    - allow user defined cost function contributions    - allow user defined cost function contributions
874          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
875          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
876    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
877        the two options are complementary.        the two options are complementary.
878  o pkg/smooth  o pkg/smooth
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