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revision 1.1216 by jahn, Tue Jan 12 23:58:04 2010 UTC revision 1.1417 by ifenty, Thu Apr 28 18:44:09 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
9        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
10      - fixed bug in the initialization of sea ice salinity variable HSALT
11        in seaice_init_varia.F  (removed dependence on ICE2WATR)
12    o fizhi-cs test exp.:
13       switch reference output convention for these 2 non-standard test-exp,
14        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
15          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
16       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
17    o model/inc:
18      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
19        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
20    o pkg/seaice:
21      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
22    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
23      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
24        and initial HSALT
25    
26    checkpoint62w (2011/04/26)
27    o pkg/mom_fluxform:
28      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
29      - use parameter "sideDragFactor" in no-slip BC side-drag part.
30      - update output of exp. global_ocean.90x40x15
31    o pkg/mom_vecinv:
32      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
33    o update seaice exp.:
34      use more consistent parameter values (remove "backward compatability only":
35       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
36      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
37       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
38    o update test-exp global_ocean.90x40x15:
39      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
40      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
41      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
42      o turn on zStar & viscA4 in standard set-up (dir input/)
43        and update output files: output.txt & output.dwnslp.txt
44    o new AD-test experiment: obcs_ctrl
45      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
46    o pkg/dic:
47      fix two bugs in handling water vapour pressure in carbonate chemistry
48      and air-sea fluxes. Found by Val Bennington and Galen McKinley
49      (add DIC Option = WATERVAP_BUG to recover old results)
50      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
51    o adding allowInteriorFreezing option to check for water below freezing point
52      at depth and bring the negative heat anomaly to the surface level
53    o pkgs _fields_load:
54      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
55      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
56        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
57        rbcs to get interpolation weights and time reccord number.
58      - fix multi-threading in aim_fields_load.F
59      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
60    o external_fields_load:
61      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
62       interpolation weights) to use in a periodic time-series ; do not divide by
63       time-step to convert to integer:
64       - this fixes case where externForcingPeriod is not multiple of time-step
65          (Thanks to Christopher L. Wolfe)
66       - this fixes case where externForcingPeriod is an odd multiple of time-step
67         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
68      store index of time-record which is currently loaded:
69       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
70       - needed for the adjoint but not yet used because of extensive recomputations;
71         (to be fixed soon)
72    
73    checkpoint62v (2011/04/02)
74    o verification/1D_ocean_ice_column added to test Ian Fenty's
75      pkg/seaice_growth.F modifications for improving sea ice code differentiability
76    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
77      (new velocity statistics after changing maskInW & maskInS definition)
78    o pkg/generic_advdiff with OBCS:
79      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
80      equivalent to assumption of no tracer gradient outside the OB region.
81      This will affect the results if using obcs+biharmonic diffusion.
82      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
83    o pkg/obcs:
84      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
85      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
86      in Interior region. No impact on solution but affects Velocity monitor stats.
87    o pkg/ptracers (adjoint)
88      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
89      tape file for each tracer
90    o model/inc/src and pkg/autodiff: add parameters that allow to turn
91      of parts of the adjoint code at run time. For now, there are only
92      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
93      parameters are set in data.pkg.
94      This is the lazy coward's version of doing this, but still useful for
95      debugging. In order to do it right, everything needs to be moved to
96      pkg/autodiff.
97    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
98      the end; this fixes the adjoint balancing code for open boundaries.
99    o pkg/ctrl:
100      - change behavior of xx_${varname}period to be analogous to exf-conventions:
101        xx_${varname}period =   0.,  means time-independent control part
102        xx_${varname}period = -12., means one-year-periodic monthly control part
103      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
104        clean up ctrl_init a little, remove unused variables
105      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
106      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
107    
108    checkpoint62u (2011/03/15)
109    o model/src:
110      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
111        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
112      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
113        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
114    o pkg/ctrl/obcs/ecco:
115      - remove obsolete, unused, and partially broken code:
116        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
117        ALLOW_CTRL_OBCS_BALANCE
118      - put a stop statement into ecco/cost_obcsvol.F, but also add
119        cost_obcsvol to ecco_ad_diff.list
120    o pkg/ecco: fix counting cost function contributions for obcs (code
121      by Matt M.) and diffkr for diagnostics
122    o pkg/ecco, pkg/ctrl, pkg/grdchk:
123      add cost penalty terms for initial uvel, vvel, eta controls
124      and I/O for prior error files
125    o pkg/mdsio:
126       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
127       (new argument) to check for tiled file in mdsioLocalDir : this fix the
128       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
129    o pkg/ctrl:
130     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
131       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
132       unused and superfluous variables
133     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
134    o pkg/ecco
135     - enable adjoint of Stevens OB
136    o pkg/ctrl/ecco/grdchk:
137      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
138        Fortunately, we do not have any tests for the numerous cpp-flagged
139        option of "obcs as control parameters" so we will never know
140        if this is an improvement (but at least now things compile).
141      - remove an obsolete initialization from ecco_cost_init_barfiles.F
142      - fix some problems within never used ifdefs to make the code compile
143    o pkg/obcs:
144     - Refine Interior mask definition to work with more complex OB (e.g.
145       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
146       read in Interior mask from file. Check if Interior mask is consistent
147       with OB list of indices.
148    o pkg/seaice
149     - beginning code for a seaice tracer package,
150       but currently only used for seaice age: SEAICE_AGE
151       SEAICE_num = 4
152       iTracer = 1: area-weighted ice age
153               = 2: volume-weighted ice age
154               = 3, 4: template for one-year vs. multi-year ice
155       data.seaice has new namelist SEAICE_PARM03 for arrays related to
156       SEAICE_num
157    
158    checkpoint62t (2011/03/05)
159    o pkg/obcs:
160     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
161       then normal component. This ensures that the normal component is set
162       correctly even when it conficts with tangential setting from an other OB.
163       Affects results of test-experiment seaice_obcs: update the output.txt
164    o pkg/obcs:
165     - add code to monitor statistics of dynamical fields at OB.
166     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
167       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
168       - change default: balance the Net inflow through all OB (instead of balancing
169         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
170     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
171       to match Nortern OB inflow (OBCS_balanceFacN=0).
172    o pkg/seaice:
173     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
174    o pkg/seaice (seaice_growth v 1.113):
175     - reverting seaice_growth to v 1.111 in order to have code with exact bit
176       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
177       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
178       runtime flag SEAICEareaFormula is kept but is inactive
179    o model/src:
180     - add new param to scale curvilinear grid distance and area when using
181       a different sphere radius from the grid-files.
182     - test/check multi-threads EXCH applied to local variable (cg2d_x)
183    o adjoint:
184     - enable adjoint of Stevens OB
185     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
186       (a bit delicate because of potentially modified adj. common block structure;
187       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
188    
189    checkpoint62s (2011/02/15)
190    o pkg/seaice (seaice_growth v 1.112):
191     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
192       computing the ice cover tendency from effective thickness tendencies. Include
193       Ian Fenty's formula.
194     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
195       SEAICEareaFormula.
196     - simplify notations for the various d_HEFF/d_AREA terms.
197    o pkg/gmredi:
198     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
199       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
200       add a verification test-run (front_relax.bvp) to test GM_useBVP.
201    o pkg/seaice (seaice_growth v 1.111):
202     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
203     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
204       also melt ice.
205    o pkg/seaice:
206     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
207     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
208    o pkg/cheapaml:
209     - from Nico Wienders: New version of this package.
210    o pkg/flt:
211     - add CPP options to prevent floats to re-enter the opposite side of
212       a periodic domain (default: keep periodicity)
213    o pkg/gmredi:
214     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
215       (needed for multi-dim advection).
216     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
217    o model/src:
218     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
219    o tutorial_tracer_adjsens
220     - extend to NLFS and replace maskC by hFacC
221       (change reference output accordingly)
222    
223    checkpoint62r (2011/01/24)
224    o testreport:
225     - add option -deloutp (-do) to remove output file after successful run
226     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
227       extract exact list of procs from this file ; adjust COMMAND by
228       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
229    o pkg/ecco: replace old ineffective way of penalizing deviations from
230      first guess (of obcs) with code by Matt Mazloff
231    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
232      exf/cal
233      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
234        and handle case of obcs?period == 0
235        Not affected by these changes: There is still an inconsistency in
236        the computation of start/endrec for the obcs variables for ALLOW_CAL
237        defined (see comment by Menemenlis, 7-Mar-2003)
238      - make S/R ctrl_get_gen_rec return something meaningful even if
239        ALLOW_CAL is not defined
240      - ctrl_getobcs?: simplify code so that it does not need to use
241                       S/R exf_swapfields
242    o testreport:
243       allow to test MPI with different number of processors for each experiment:
244       create file "SIZE.h.mpi" in each build dir.
245       Note: update of "-command" argument not yet implemented.
246    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
247      alleviate the need for additional 3D tapes when using
248      the non-inear free surface in the adjoint. This is done
249      by adding an 'update' of hfacc etc. to their current
250      value at the beginning of forward_step.F.
251    o pkg/seaice
252      seaice_lsr: move stress-divergence computations out of outer pseudo-
253      timestepping loop
254    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
255      up, so that the calls of the ctrl_* subroutines are really at the end
256      of the routine.
257    o pkg/gmredi:
258      allow to specify a 2-D horizontal map and a 1-D vertical profil
259      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
260    o pkg/seaice:
261      move lsr iterations from seaice_dynsolver to seaice_lsr.
262    o pkg/seaice:
263      reduce memory footprint of seaice mutldim advection tapes,
264      by using a 2D tape independent of the generic_advdiff ones,
265      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
266    
267    checkpoint62q (2010/12/29)
268    o model/src:
269      - check horizontal grid-spacing for unset or zero/negative values.
270      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
271    o pkg/flt:
272      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
273      - precision of input and output files set according to readBinaryPrec
274        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
275      - initial float position from tiled file was not converted to index space
276        (looks like a bug): fixed to make it similar to initial pos. global file.
277    o global_ocean.cs32x15:
278       change SIZE.h of AD set-up to get same tiling as with MPI.
279       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
280    o model/src:
281       add flag to control printing of domain fields (bathymetry, hFac ...) in
282       ini_mask_etc (call to plot_fieds_xy*).
283    o pkg/thsice:
284       if useEXF, some forcing fields are not valid in overlap: fixed by computing
285       over the interior only + apply EXCH at the end (like with SEAICE advection).
286    o pkg/mdsio:
287      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
288        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
289      - change barrier call for safe multi-threads access to 3-D shared buffer.
290      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
291      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
292        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
293    o pkg/flt:
294      - add fourth-order Runge-Kutta integration
295      - add basic exch2 support (only 1 facet supported so far!)
296    o pkg/mdsio+rw:
297      new S/R to read local (or tile independent) vector (read counterpart of
298       mds_writevec_loc, and front-end write_glvec_rl/rs).
299    o global_ocean.cs32x15: additional input_ad.seaice experiment
300        that uses pkg/seaice rather than pkg/thsice.
301        (using multidim advection for seaice)
302    o towards more F95 syntax for array specification in namelist:
303      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
304        of all verification experiments.
305           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
306          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
307      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
308    o global_ocean.cs32x15: additional input.seaice experiment
309        that uses pkg/seaice rather than pkg/thsice.
310    
311    checkpoint62p (2010/12/17)
312    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
313        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
314    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
315        allow for use of multim. advection in seaice adjoint.
316    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
317      - first attempt to close budgets by taking into account the freshwater
318        flux implied by the sublimation of snow and ice. So far only the
319        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
320        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
321    o eesupp/src:
322      new S/R with new option (NML_EXTENDED_F77) to change array specification
323      from F95 standard to commonly accepted extended F77 form.
324      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
325      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
326      for less tolerant f77 compiler (e.g., pgf77, g77).
327    o globalFiles:
328      commented out in parameter file "data" since it's not safe with MPI
329      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
330      in this case); no longer commented out in restart test (tst_2+2).
331    o add adTapeDir to specify a special directory where adjoint tapes are
332      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
333      and cannot be used together with mdsioLocalDir.
334    o nesting pkgs:
335      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
336      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
337      - add parameter files + utils dir + output from short run on beagle.
338    o pkg/seaice:
339        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
340    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
341      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
342    
343    checkpoint62o (2010/11/25)
344    o pkg/exf:
345      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
346    o pkg/seaice:
347      - seaice_ocean_stress: split a loop for better vectorization of the
348        adjoint code
349      - seaice_growth.F: fix bug in conservation of freshwater connected to
350        capping of heff, put contribution into d_HEFFbyNEG
351      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
352        by something more sensible (parameters that are what their name implies)
353      - change some defaults, so that by default exf-parameters are used for
354        things like rhoAir, cpAir,latent/sensible heat parameters, in order
355        to reproduce the old results, many data.seaice now contain funny values
356        for cpAir and latent heat of sublimation
357    o packages_readparms.F: move exf_readparms up in line so that
358        exf-parameters are visible for other packages (e.g. seaice)
359    o debugMode & debugLevel=2:
360      - differentiate between debugMode & debugLevel=2:
361        debugMode: controls printing of debug messages (sequence of S/R calls).
362        debugLevel: controls printing of algorithm intermediate results and stats.
363      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
364        => allows to print debug-stats without all sequence of call messages.
365      - switch control of debug print from debugLevel to debugMode in many S/R.
366    o pkg/obcs (obcs-sponge):
367        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
368        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
369    o pkg/generic_advdiff:
370      - record overlap minimum size for each advection scheme;
371      - refine criteria on overlap minimum size;
372      - check and stop (in gad_check) if overlap size is too small.
373    o pkg/obcs:
374      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
375        once, in ptracers_implicit.F)
376      - with seaice: remove test on empty file name in obcs_apply_seaice (always
377        apply OB values when tile has OB)
378    o model/src, coriolis setting:
379      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
380        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
381        files (selectCoriMap=3) with any grid.
382      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
383    o pkg/seaice/seaice_growth.F:
384        a few cosmetic changes that reduce the number of lines of code
385    o pkg/obcs: add boundary conditions following Stevens (1990)
386      - the code follows old MOM/NAOSIM code
387      - so far it is only implemented for the eastern and western boundaries
388        and NOT for pTracers
389    o pkg/rbcs:
390      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
391        beginning of the first rbcs forcing period.
392      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
393        offline package, i.e., one file per time, labeled by iteration number;
394        deltaTrbcs sets the timestep with which the data was generated;
395        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
396      - rbcsForcingCycle=0 makes forcing non-cyclic.
397      - make arithmetic safe for negative times and odd forcing periods.
398    
399    checkpoint62n (2010/11/09)
400    o pkg/seaice:
401        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
402    o pkg/obcs:
403       New S/R to copy tracer value from the OB location to narrow band region
404        (width = same as overlap) beyond the OB: preserve OB value (needed for
405        high-order scheme) which were overwritten by EXCH call if in overlap
406        region. Applied to theta, salt, ptracer and advected seaice variables.
407       With seaice: use maskInC in similar way as in gad_advection.F,
408        in seaice_advection.F and advect.F.
409       Update output of experiment seaice_obcs and change exp4 to test OBCS with
410        4th order Adv.Scheme. for pasive salt and ptracer.
411    o tools/genmake2:
412      - when looking for an optfile (not specified), only search for Fortran compiler
413        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
414      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
415        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
416      - set default for CPP to "cpp -traditional -P" (was the case without specifying
417        an optfile, but otherwise default was just "cpp".
418      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
419      - when "CC" is not set in the optfile, look for possible C compiler
420        (instead of just setting CC=cc)
421      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
422        => add a ".F" to ".o" rule for source files with no "#include" (such as
423           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
424      - move gfortran before g77 in list of possible Fortran compiler (consistent
425        with reference compiler switch from g77 to gfortran)
426    o pkg/seaice:
427      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
428        seaice_check that stops the model, when the CPP flag is used.
429      o seaice_growth.F: make capping of ice volume conserving by returning the
430        capped ice as freshwater to EmPmR. This does not change the verification
431        experiments but will change runs where the capping is acutally active
432    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
433      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
434         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
435         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
436    o tools/genmake2:
437      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
438      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
439      - clean previous genmake log files before anything else.
440      - change Makefile to remove testreport log files (*.tr_log) and genmake log
441        files only with "CLEAN" target (instead of "Clean");
442    o pkg/generic_advdiff:
443      Change OBCS in multiDim advection (gad_advection.F):
444       Use maskInC to prevent intermediate update of tracer-field in OB regions,
445       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
446       which were applying future time-step OB values.
447      This way, all explicit calculations use current-time-step OB values
448       (simpler and more consistent).
449      Affects results when set-up uses time-varying OBC and multi-dim advection;
450       update output of experiment seaice_obcs.
451    o pkg/seaice:
452      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
453       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
454         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
455      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
456       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
457       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
458    o pkg aim (2010/10/26):
459      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
460        formulation with obliquity, eccentricity, ... as run-time parameters,
461      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
462        upward shortwave radition at the surface (all-sky and clear-sky).
463    o pkg/obcs:
464      - writing sections with globalFiles=T does not work: switch to tiled-files
465        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
466      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
467      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
468    
469    checkpoint62m (2010/10/21)
470    o pkg/seaice: vectorize seaice_solve4temp.F
471      - move iterations loops outside of i/j-loops
472      - requires 2D arrays for TB and effConduct
473      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
474        modified in this routine
475      - a little bit of clean up, adjusting indentation, etc.
476      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
477        performance and '**TWO' by '**2' (because TWO is a float),
478        replaced ONE, ZERO
479    o eesupp/src:
480       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
481    o pkg/seaice/seaice_growth.F
482      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
483      merging process. The merged routine has two branches, and one activates the 'evolution'
484      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
485      In summary, here is what the '10/10 revision' did consist of
486        part 1: seaice_growth.F revisions 1.71 to 1.75
487          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
488            The emphasis here was on improving readability (e.g. by trying to use meaningful
489            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
490        part 1.5:
491          - revising the lab_sea experiment to make it a more useful (i.e. stable
492            and representative of an actual model run). This was done by generating a
493            (winter) pickup to start from, switching back the main experiment dynamic
494            solver from evp to lsr, having one of the experiments use the free drift solution.
495        part 2: seaice_growth.F revisions 1.76 to 1.85
496          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
497          - Sorting out the various fields units and sign (set early on and reset at the end)
498            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
499            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
500          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
501            and simplifying logical expressions to further improve readibility.
502        part 3: seaice_growth.F revisions 1.86 to 1.89
503          - Re-organize the blocks of code more logically.
504          - Merging the '_if.F' pieces that add something new.
505    o pkg/thsice:
506      - vectorize thsice_solve4temp and thsice_get_exf.
507        Problem: thsice_solve4temp has an unvectorizable statement that
508        might also be problematic for TAF
509      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
510        does not change the verifcation experiment, but will change all
511        experiments that have this flag undefined (not tested in verification);
512        a little reorganization to save a few 2D fields and recomputations
513      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
514      - 2nd step:  fix some store dirs
515        o seems to work somewhat, i.e. using ifort but not g77
516        o likely cause are incomplete init. or recomputation
517        o start verification/global_ocean.cs32x15/input_ad.thsice
518    o pkg/obcs: add support for exch2
519      - the position of the boundary and prescribed values are specified using
520        a global domain with exch2 facets stacked
521        - in x for N,S boundaries (like W2_mapIO=-1)
522        - in y for E,W boundaries (so E,W boundaries do not overlap)
523    o pkg/mdsio: add support for writing global sections with exch2
524        file layout is as for obcs described above:
525        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
526        - for y-z sections, facets are stacked in y
527    o pkg/thsice:
528       - change a few routines for better vectorization: thsice_albedo.F,
529         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
530         not affected, but in particular the latter routine has changed
531         dramatically (not necessarily easier to read now).
532       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
533       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
534    o verification/lab_sea:
535      - overhaul of the forward model experiments. The main motivation
536        for this revision is that lab_sea has proven quite fragile (when
537        changing the sea-ice code, and switching platforms) to a point
538        when failures were very hard to attribute to specific code problems.
539      - the suspected reason for this fragility is noise amplification by evp so,
540        to start with, we decided to replace evp with lsr in the main experiment.
541      - the input.lsr experiment thus became obsolete and was removed.
542      - it was replaced with the input.fd experiment that uses an
543        analytical "free drift" solution as the ice velocity field.
544      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
545        will hopefully allow us to discriminate problems due to dynamic solvers
546        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
547        us to test additional options, along with the salt plume package.
548      - Finally a pickup was generated (at the end of a one year run) to
549        make the tests more representative of an actual model run. Previously
550        the tests starting point was a 1m thickness of ice everywhere.
551    o pkg/seaice:
552      - introducing S\R seaice_freedrift.F that compute the
553        analytical solution to an approximate ice momentum
554        equation (i.e. the simple stress/coriolis balance).
555      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
556        of the free drift velocity field, and enable its use.
557        To actually use the free drift solution as the model ice
558        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
559    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
560    
561    checkpoint62l (2010/10/04)
562    o pkg/seaice:
563      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
564      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
565       version (with USE_ORIGINAL_SBI undef);
566    o add hooks for new packages OASIS, the package will follow
567      (hooks exclude the seaice pkg for now)
568    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
569      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
570      rather than mdsio_readvector.F/mdsio_writevector.F, within
571      adread_adwrite.F to read/write adjoint-related tapes to disk.
572    o eesupp and pkg/mdsio: ALLOW_WHIO
573      Option to write/read 2D fields to files including tiles halos.
574      The main purpose is for adjoint related "tape I/O".
575      The secondary purpose is for debugging phases.
576      A word on those rather specifically intended purposes.
577      The code was meant to be stripped down to the bare minimum.
578      Typically, there is a unique and basic mapping to the global
579      buffer (tile by tile, then proc by proc, then level by level), and
580      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
581      meant to generate user friendly outputs of various shapes and forms.
582      Rather it is intended, for the knowledgeabale developers,
583      to be largely independent of the many mdsio options, to allow
584      outputs of tiles+halos in debugging phases and in adjoint runs,
585      and to allow some flexibility in tuning (adoint) I/O depending on each
586      file system behavior. With regard to tuning, most of the potential knobs
587      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
588      to specify directories, to specify the typical size of I/O calls, etc.)
589      are not yet included, and will be added if they prove useful.
590    o pkg/seaice:
591       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
592    o pkg/seaice:
593       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
594       code (seaice_budget_ice_if.F) which enable to recover old standard
595       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
596       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
597    o model/src (rStar):
598       use simple average (not area weighted) of rStarFac at U,V point when using
599       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
600       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
601    
602    checkpoint62k (2010/09/17)
603    o adjoint
604       * changed verification/global_ocean.cs32x15 ; adjoint now tests
605         Adams-Bashforth 3 + NLFS + RSTAR
606       * some more modifs required for ECCO-GODAE v4
607    o pkg/seaice
608       add SEAICE_AGE_VOL option to use volume instead of area for
609       integrating SEAICE_AGE
610    o model/src:
611       first check-in of sigma & hybrid-sigma coordinate code ; also includes
612       non-linear free-surface parts ; but pressure-gradient not yet coded.
613    o pkg/ptracers:
614       option for ptracer to convert Salt Relax into additional EmP.
615        tested in exp. global_ocean.90x40x15.dwnslp (update output)
616    
617    checkpoint62j (2010/08/25)
618    o pkg/ggl90:
619       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
620    o pkg/dic: car_flux.F, phos_flux.F
621      - reduce number of exp-calls in order to improve performance
622      - clean up a little (replace fields by their macros, etc., fix
623        typo in CPP-flag)
624    o pkg/ggl90: minor changes
625      - GGL90diffKrS was removed --> always use GGL90diffKr
626      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
627      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
628        (commented out for now)
629      - change in max/min operations to ensure that smoothing is ok
630      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
631      - always use diffKrNrT as background profile (i.e. never use diffKr field)
632    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
633    o pkg/dic:
634      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
635        vectorization
636      - small bug fix in insol for the unlikely case of a cartesian grid
637      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
638        + now vectorize, which also removes adjoint recomputations;
639        + replace integer maksp1 by _RL maskp1
640        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
641    
642    checkpoint62i (2010/07/21)
643    o pkg/flt:
644      - with OBCS: stop floats which enter the OB region
645    o model/src:
646      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
647        for implicit vertical advection.
648    o pkg/seaice:
649     - account for melting in seaice age evolution.
650     - remove double counting of seaice ridging effect on seaice age.
651    
652    checkpoint62h (2010/06/18)
653    o pkg/exch2:
654     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
655    o tools/genmake2
656      - remove "-pdefault" option: redundant with the use of "packages.conf";
657      - remove file pkg/pkg_default : set the default as a pkg group
658        ("default_pkg_list") defined in pkg/pkg_groups;
659      - fix for case pkg/pkg_depend is missing (was hanging before);
660      - add option "-pgroups" to specify a different pkg_groups than the default.
661    o verification/adjustment.cs-32x32x1:
662       add a "minimal" set-up test (code_min & input_min) which only compiles
663       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
664    o tools/genmake2
665      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
666      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
667    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
668      files are nearly the same anyway.
669      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
670       - redefinition of tau(i,i) (by a factor of ustar)
671       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
672       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
673       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
674       - replace
675         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
676         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
677         by
678         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
679         (changes results)
680       -> exf_bulkformulae v1.22,
681          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
682          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
683                    output.txt 1.63
684           offline_exf_seaice: output.seaicetd.txt 1.7
685           seaice_obcs: output.txt 1.10)
686      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
687       -> exf_bulkformulae v1.23,
688          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
689          and global_ocean.cs32x15.icedyn (only 11 matching digits)
690      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
691    o adjoint of exch-1:
692     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
693       (note: was already like this when using EXCH-2) and remove flow dir
694       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
695     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
696     - update pkg/exch2 diff list.
697    
698    checkpoint62g (2010/05/19)
699    o eesupp/src (exch-1):
700     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
701       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
702       (renamed to exch1_*rx_cube.F).
703     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
704       to call new exch1 S/R ; update Makefile and .cvsignore.
705     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
706       exch2_xy_rx later)
707      Note: after updating your code, need to run "make clean" in eesupp/src
708    o test experiment bottom_ctrl_5x5:
709       new output_adm.txt with fewer grdchk & less monitor output.
710    o model/src:
711      remove the call to ini_cori in initialise_varia.F (just keep the usual one
712       in initialise_fixed.F). More consistent with coriolis & horizontal grid
713       beeing treated in the same way (ini_grid is not called a 2nd time).
714    o pkg/exf:
715      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
716      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
717      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
718      - cosmetic changes to exf_bulkformulae.F to make it look more like
719        exf_bulk_largeyeager04.F
720    o eesupp/src (exch-1):
721      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
722      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
723        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
724        (even without using MPI).
725      - Message mode: move RecvAck setting (indicator of buffer being ready)
726        from send_put to recv_get S/R (was useless before, but not sure if
727        it's much more useful now);
728      - Switch the order of sync: MPI-proc 1rst and then threads;
729      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
730      - fix AD code for communication mode ='get' (but not used).
731    o model/src:
732      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
733      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
734    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
735    o pkg/ctrl: require a specific set of control variables and exf-flags for
736      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
737    o model/src:
738     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
739       1rst forward sweep, to avoid over-writing output files during recomputations
740       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
741     b) 2nd version:
742      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
743      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
744         writePickupAtEnd) + seaice & ptracers output;
745      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
746    o model/src:
747      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
748    o pkg/exch2:
749      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
750      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
751    o pkg/autodiff & exch2:
752      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
753      (for now, only if ALLOW_EXCH2 is defined).
754    o pkg/autodiff:
755      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
756        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
757       + clean-up comments (_RS is not always real*4)
758      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
759      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
760        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
761    o testreport (AD-tests):
762      no longer link files from dir "../input" (1rst link files from
763      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
764    
765    checkpoint62f (2010/04/29)
766    o model/src/the_main_loop.F:
767      adjust store directives for seaice evp and multicategory according to
768      pkg/ecco/the_main_loop.F
769    o adjoint:
770      global_sum_ad was incomplete (noted many times by many people ;)
771      nice description by Jean U. as follows:
772      * allreduce(var) in global_sum.F can be interpreted as
773        reduce(sum) followed by broadcast of sum.
774      * The adjoint of that is
775        sum(adjoint) followed by broadcast(summed adjoint value)
776        or in other words, allreduce(sum, adjoint vars)
777      We were missing the sum(adjoint)!
778      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
779      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
780      The fix should produce 16-digit accuracy between
781      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
782      multi-CPU single-tile (e.g. nSx=1, nPx-2)
783      We'll probably change this yet again shortly
784    o eesupp/src:
785      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
786    o pkg/icefront
787      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
788        specification of addmass array based on a 2D field, which is added
789        at bottommost wet level at each horizontal location.
790    o model/src:
791     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
792     layout; (not always compatible with delX,delY setting; commented out for now).
793    o pkg/exch2:
794     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
795     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
796    
797    checkpoint62e (2010/04/15)
798    o pkg/obcs:
799      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
800    o pkg/dic:
801      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
802        (note: not presently tested in any forward verification exp.)
803       update tutorial_global_oce_biogeo AD output file.
804    o pkg/exf:
805      - account for the variation of albedo as a function of zenith angle
806        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
807    o build_options:
808     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
809    o pkg/dic:
810      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
811      - use binary pickup file for restart;
812      - initialise atmos-CO2 box from dic_pCO2 parameter;
813      - fix multi-threaded.
814    o pkg/rbcs:
815     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
816       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
817     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
818       and update output.txt
819    o pkg/kpp:
820     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
821     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
822       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
823       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
824     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
825       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
826    o pkg/offline:
827      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
828      (bug was added in version 1.10 on 2007-08-23).
829    o pkg/offline:
830      - no need to specify periodicExternalForcing, etc ... to use offline pack
831      - offline input files no longer just single prec --> parameter offlineLoadPrec
832    o verification/lab_sea:
833      change AD test to multi-tile setup and update all 4 AD output.
834      NOTE: while cost function values remain very similar,
835      gradients are very different, although gradient checks are self-consistent
836      Should try to get to the bottom of this (cost function summation order?)
837    o pkg/dic:
838      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
839      a weakness of TAF that drops part of double precision in log10 derivative.
840      <= changes removed since problem has been fixed in current TAF version 1.9.71
841      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
842    o pkg/ecco:
843      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
844      update all 4 lab_sea AD output.
845    
846    checkpoint62d (2010/03/22)
847    o build_options:
848      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
849    o remove unbalanced quote (single or double) in commented line of source code
850      (may cause some warning with some preprocessor/makedepend versions).
851    o pkg/seaice:
852      fix seaice_model.F for adjoint (gael) and update AD results of experiments
853       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
854    o testreport:
855      add option '-runonly' (short: '-ro') to just do the run part (without make).
856    o eesupp: remove JAM communication code (obsolete).
857    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
858      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
859      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
860      (update also the output).
861    
862    checkpoint62c (2010/03/02)
863    o tools/build_options :
864       move (some) old optfiles from build_options/ to build_options/unsupported/
865    o model/src and pkg/exf
866       surface relaxation -- separating data and data.exf options
867       The point is to ensure that we specify the surface relaxation
868       either in data or in data.exf (but not half and half) and to
869       avoid an accidental relaxation to 0 (which happened if a time
870       scale was specified but the file name was left empty)
871    o model/src model/inc and pkg/mom_common
872       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
873       => addition to the viscosity field as computed by others schemes
874    o tools/build_options:
875      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
876        but keep the former optfile for few weeks for smooth transition
877    o pkg/ecco
878      - allow user defined cost function contributions
879         CPP: ALLOW_USERCOST_CONTRIBUTION
880         USAGE: compute contributions in cost_usercost_all.F
881      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
882          the two options are complementary.
883    o pkg/smooth
884      - migration from contrib to the main repository
885    
886    checkpoint62b (2010/01/26)
887    o pkg/monitor:
888      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
889        (in case someone forgot to update customized pieces of code)
890    o nonHydrostatic:
891      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
892      - add a simple 2-D experiment (short_surf_wave) to test it.
893    o pkg/icefront:
894       adding the shell of, and the hooks to, a new package that
895       will model melting and freezing of vertical glacier ice fronts
896    o momentum:
897      add diagnostics of momentum tendency from Hydrostatic pressure gradient
898       (without surf.pressure term: would need a 2nd filling since implicit term).
899    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
900      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
901      cannot deal with the former
902    o cleaning:
903      - remove all (except OpenAD) old TLM output from results_ad dirs.
904      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
905      - comment out maskH definition (replaced by maskInC)
906    o pkg/monitor:
907      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
908        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
909    
910    checkpoint62a (2010/01/15)
911    o model/src:
912      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
913    o pkg/diagnostics:
914      - add optional level number diagnostics (i.e., level number to be define
915        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
916      - strictly check for valid parser-code(10) ;
917      - check if adding diag to the list from the right place.
918  o pkg/longstep:  o pkg/longstep:
919    - change parameters and fix tracer conservation with rstar/nonlinear free surface    - change parameters and fix tracer conservation with rstar/nonlinear free surface
920  o diagnostics:  o diagnostics:
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