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revision 1.1240 by jmc, Wed Mar 24 02:12:51 2010 UTC revision 1.1425 by mlosch, Mon May 9 08:56:59 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/ctrl:
8      - remove extra 2D field "for good measure" when initializing in
9        ctrl_set_globfld_[xy/xz/yz].F
10      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
11      - improve error messages in ctrl_set_unpack_*
12    o OBC implementation in momentum:
13       use interior masks (maskInC,W & S) in momentum S/R:
14       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
15       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
16       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
17       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
18       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
19        (and also with Leith/Smagorinsky harmonic-viscosity).
20       Update output of experiment dome and exp4 (+nlfs).
21    o exp4 test-exp:
22      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
23        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
24        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
25        time-varying OB at Western-side for wVel (NonHyd); update output.
26      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
27        and biharmonic-viscosity ; also use prescribed time varying OB.
28    o pkg/obcs:
29      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
30    o model/src:
31      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
32      - initialise startTime & nIter0 with unlikely values: allows to set one
33        from the other without ambiguity.
34    o seaice_obcs test-exp.:
35      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
36    o pkg/obcs:
37      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
38        no longer needed with maskInC,W,S in pkg/generic_advdiff.
39    o pkg/seaice:
40      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
41        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
42      - fixed bug in the initialization of sea ice salinity variable HSALT
43        in seaice_init_varia.F  (removed dependence on ICE2WATR)
44    o fizhi-cs test exp.:
45       switch reference output convention for these 2 non-standard test-exp,
46        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
47          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
48       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
49    o model/inc:
50      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
51        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
52    o pkg/seaice:
53      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
54    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
55      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
56        and initial HSALT
57    
58    checkpoint62w (2011/04/26)
59    o pkg/mom_fluxform:
60      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
61      - use parameter "sideDragFactor" in no-slip BC side-drag part.
62      - update output of exp. global_ocean.90x40x15
63    o pkg/mom_vecinv:
64      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
65    o update seaice exp.:
66      use more consistent parameter values (remove "backward compatability only":
67       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
68      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
69       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
70    o update test-exp global_ocean.90x40x15:
71      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
72      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
73      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
74      o turn on zStar & viscA4 in standard set-up (dir input/)
75        and update output files: output.txt & output.dwnslp.txt
76    o new AD-test experiment: obcs_ctrl
77      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
78    o pkg/dic:
79      fix two bugs in handling water vapour pressure in carbonate chemistry
80      and air-sea fluxes. Found by Val Bennington and Galen McKinley
81      (add DIC Option = WATERVAP_BUG to recover old results)
82      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
83    o adding allowInteriorFreezing option to check for water below freezing point
84      at depth and bring the negative heat anomaly to the surface level
85    o pkgs _fields_load:
86      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
87      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
88        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
89        rbcs to get interpolation weights and time reccord number.
90      - fix multi-threading in aim_fields_load.F
91      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
92    o external_fields_load:
93      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
94       interpolation weights) to use in a periodic time-series ; do not divide by
95       time-step to convert to integer:
96       - this fixes case where externForcingPeriod is not multiple of time-step
97          (Thanks to Christopher L. Wolfe)
98       - this fixes case where externForcingPeriod is an odd multiple of time-step
99         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
100      store index of time-record which is currently loaded:
101       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
102       - needed for the adjoint but not yet used because of extensive recomputations;
103         (to be fixed soon)
104    
105    checkpoint62v (2011/04/02)
106    o verification/1D_ocean_ice_column added to test Ian Fenty's
107      pkg/seaice_growth.F modifications for improving sea ice code differentiability
108    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
109      (new velocity statistics after changing maskInW & maskInS definition)
110    o pkg/generic_advdiff with OBCS:
111      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
112      equivalent to assumption of no tracer gradient outside the OB region.
113      This will affect the results if using obcs+biharmonic diffusion.
114      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
115    o pkg/obcs:
116      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
117      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
118      in Interior region. No impact on solution but affects Velocity monitor stats.
119    o pkg/ptracers (adjoint)
120      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
121      tape file for each tracer
122    o model/inc/src and pkg/autodiff: add parameters that allow to turn
123      of parts of the adjoint code at run time. For now, there are only
124      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
125      parameters are set in data.pkg.
126      This is the lazy coward's version of doing this, but still useful for
127      debugging. In order to do it right, everything needs to be moved to
128      pkg/autodiff.
129    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
130      the end; this fixes the adjoint balancing code for open boundaries.
131    o pkg/ctrl:
132      - change behavior of xx_${varname}period to be analogous to exf-conventions:
133        xx_${varname}period =   0.,  means time-independent control part
134        xx_${varname}period = -12., means one-year-periodic monthly control part
135      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
136        clean up ctrl_init a little, remove unused variables
137      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
138      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
139    
140    checkpoint62u (2011/03/15)
141    o model/src:
142      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
143        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
144      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
145        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
146    o pkg/ctrl/obcs/ecco:
147      - remove obsolete, unused, and partially broken code:
148        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
149        ALLOW_CTRL_OBCS_BALANCE
150      - put a stop statement into ecco/cost_obcsvol.F, but also add
151        cost_obcsvol to ecco_ad_diff.list
152    o pkg/ecco: fix counting cost function contributions for obcs (code
153      by Matt M.) and diffkr for diagnostics
154    o pkg/ecco, pkg/ctrl, pkg/grdchk:
155      add cost penalty terms for initial uvel, vvel, eta controls
156      and I/O for prior error files
157    o pkg/mdsio:
158       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
159       (new argument) to check for tiled file in mdsioLocalDir : this fix the
160       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
161    o pkg/ctrl:
162     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
163       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
164       unused and superfluous variables
165     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
166    o pkg/ecco
167     - enable adjoint of Stevens OB
168    o pkg/ctrl/ecco/grdchk:
169      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
170        Fortunately, we do not have any tests for the numerous cpp-flagged
171        option of "obcs as control parameters" so we will never know
172        if this is an improvement (but at least now things compile).
173      - remove an obsolete initialization from ecco_cost_init_barfiles.F
174      - fix some problems within never used ifdefs to make the code compile
175    o pkg/obcs:
176     - Refine Interior mask definition to work with more complex OB (e.g.
177       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
178       read in Interior mask from file. Check if Interior mask is consistent
179       with OB list of indices.
180    o pkg/seaice
181     - beginning code for a seaice tracer package,
182       but currently only used for seaice age: SEAICE_AGE
183       SEAICE_num = 4
184       iTracer = 1: area-weighted ice age
185               = 2: volume-weighted ice age
186               = 3, 4: template for one-year vs. multi-year ice
187       data.seaice has new namelist SEAICE_PARM03 for arrays related to
188       SEAICE_num
189    
190    checkpoint62t (2011/03/05)
191    o pkg/obcs:
192     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
193       then normal component. This ensures that the normal component is set
194       correctly even when it conficts with tangential setting from an other OB.
195       Affects results of test-experiment seaice_obcs: update the output.txt
196    o pkg/obcs:
197     - add code to monitor statistics of dynamical fields at OB.
198     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
199       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
200       - change default: balance the Net inflow through all OB (instead of balancing
201         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
202     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
203       to match Nortern OB inflow (OBCS_balanceFacN=0).
204    o pkg/seaice:
205     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
206    o pkg/seaice (seaice_growth v 1.113):
207     - reverting seaice_growth to v 1.111 in order to have code with exact bit
208       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
209       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
210       runtime flag SEAICEareaFormula is kept but is inactive
211    o model/src:
212     - add new param to scale curvilinear grid distance and area when using
213       a different sphere radius from the grid-files.
214     - test/check multi-threads EXCH applied to local variable (cg2d_x)
215    o adjoint:
216     - enable adjoint of Stevens OB
217     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
218       (a bit delicate because of potentially modified adj. common block structure;
219       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
220    
221    checkpoint62s (2011/02/15)
222    o pkg/seaice (seaice_growth v 1.112):
223     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
224       computing the ice cover tendency from effective thickness tendencies. Include
225       Ian Fenty's formula.
226     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
227       SEAICEareaFormula.
228     - simplify notations for the various d_HEFF/d_AREA terms.
229    o pkg/gmredi:
230     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
231       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
232       add a verification test-run (front_relax.bvp) to test GM_useBVP.
233    o pkg/seaice (seaice_growth v 1.111):
234     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
235     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
236       also melt ice.
237    o pkg/seaice:
238     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
239     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
240    o pkg/cheapaml:
241     - from Nico Wienders: New version of this package.
242    o pkg/flt:
243     - add CPP options to prevent floats to re-enter the opposite side of
244       a periodic domain (default: keep periodicity)
245    o pkg/gmredi:
246     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
247       (needed for multi-dim advection).
248     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
249    o model/src:
250     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
251    o tutorial_tracer_adjsens
252     - extend to NLFS and replace maskC by hFacC
253       (change reference output accordingly)
254    
255    checkpoint62r (2011/01/24)
256    o testreport:
257     - add option -deloutp (-do) to remove output file after successful run
258     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
259       extract exact list of procs from this file ; adjust COMMAND by
260       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
261    o pkg/ecco: replace old ineffective way of penalizing deviations from
262      first guess (of obcs) with code by Matt Mazloff
263    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
264      exf/cal
265      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
266        and handle case of obcs?period == 0
267        Not affected by these changes: There is still an inconsistency in
268        the computation of start/endrec for the obcs variables for ALLOW_CAL
269        defined (see comment by Menemenlis, 7-Mar-2003)
270      - make S/R ctrl_get_gen_rec return something meaningful even if
271        ALLOW_CAL is not defined
272      - ctrl_getobcs?: simplify code so that it does not need to use
273                       S/R exf_swapfields
274    o testreport:
275       allow to test MPI with different number of processors for each experiment:
276       create file "SIZE.h.mpi" in each build dir.
277       Note: update of "-command" argument not yet implemented.
278    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
279      alleviate the need for additional 3D tapes when using
280      the non-inear free surface in the adjoint. This is done
281      by adding an 'update' of hfacc etc. to their current
282      value at the beginning of forward_step.F.
283    o pkg/seaice
284      seaice_lsr: move stress-divergence computations out of outer pseudo-
285      timestepping loop
286    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
287      up, so that the calls of the ctrl_* subroutines are really at the end
288      of the routine.
289    o pkg/gmredi:
290      allow to specify a 2-D horizontal map and a 1-D vertical profil
291      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
292    o pkg/seaice:
293      move lsr iterations from seaice_dynsolver to seaice_lsr.
294    o pkg/seaice:
295      reduce memory footprint of seaice mutldim advection tapes,
296      by using a 2D tape independent of the generic_advdiff ones,
297      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
298    
299    checkpoint62q (2010/12/29)
300    o model/src:
301      - check horizontal grid-spacing for unset or zero/negative values.
302      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
303    o pkg/flt:
304      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
305      - precision of input and output files set according to readBinaryPrec
306        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
307      - initial float position from tiled file was not converted to index space
308        (looks like a bug): fixed to make it similar to initial pos. global file.
309    o global_ocean.cs32x15:
310       change SIZE.h of AD set-up to get same tiling as with MPI.
311       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
312    o model/src:
313       add flag to control printing of domain fields (bathymetry, hFac ...) in
314       ini_mask_etc (call to plot_fieds_xy*).
315    o pkg/thsice:
316       if useEXF, some forcing fields are not valid in overlap: fixed by computing
317       over the interior only + apply EXCH at the end (like with SEAICE advection).
318    o pkg/mdsio:
319      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
320        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
321      - change barrier call for safe multi-threads access to 3-D shared buffer.
322      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
323      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
324        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
325    o pkg/flt:
326      - add fourth-order Runge-Kutta integration
327      - add basic exch2 support (only 1 facet supported so far!)
328    o pkg/mdsio+rw:
329      new S/R to read local (or tile independent) vector (read counterpart of
330       mds_writevec_loc, and front-end write_glvec_rl/rs).
331    o global_ocean.cs32x15: additional input_ad.seaice experiment
332        that uses pkg/seaice rather than pkg/thsice.
333        (using multidim advection for seaice)
334    o towards more F95 syntax for array specification in namelist:
335      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
336        of all verification experiments.
337           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
338          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
339      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
340    o global_ocean.cs32x15: additional input.seaice experiment
341        that uses pkg/seaice rather than pkg/thsice.
342    
343    checkpoint62p (2010/12/17)
344    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
345        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
346    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
347        allow for use of multim. advection in seaice adjoint.
348    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
349      - first attempt to close budgets by taking into account the freshwater
350        flux implied by the sublimation of snow and ice. So far only the
351        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
352        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
353    o eesupp/src:
354      new S/R with new option (NML_EXTENDED_F77) to change array specification
355      from F95 standard to commonly accepted extended F77 form.
356      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
357      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
358      for less tolerant f77 compiler (e.g., pgf77, g77).
359    o globalFiles:
360      commented out in parameter file "data" since it's not safe with MPI
361      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
362      in this case); no longer commented out in restart test (tst_2+2).
363    o add adTapeDir to specify a special directory where adjoint tapes are
364      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
365      and cannot be used together with mdsioLocalDir.
366    o nesting pkgs:
367      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
368      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
369      - add parameter files + utils dir + output from short run on beagle.
370    o pkg/seaice:
371        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
372    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
373      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
374    
375    checkpoint62o (2010/11/25)
376    o pkg/exf:
377      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
378    o pkg/seaice:
379      - seaice_ocean_stress: split a loop for better vectorization of the
380        adjoint code
381      - seaice_growth.F: fix bug in conservation of freshwater connected to
382        capping of heff, put contribution into d_HEFFbyNEG
383      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
384        by something more sensible (parameters that are what their name implies)
385      - change some defaults, so that by default exf-parameters are used for
386        things like rhoAir, cpAir,latent/sensible heat parameters, in order
387        to reproduce the old results, many data.seaice now contain funny values
388        for cpAir and latent heat of sublimation
389    o packages_readparms.F: move exf_readparms up in line so that
390        exf-parameters are visible for other packages (e.g. seaice)
391    o debugMode & debugLevel=2:
392      - differentiate between debugMode & debugLevel=2:
393        debugMode: controls printing of debug messages (sequence of S/R calls).
394        debugLevel: controls printing of algorithm intermediate results and stats.
395      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
396        => allows to print debug-stats without all sequence of call messages.
397      - switch control of debug print from debugLevel to debugMode in many S/R.
398    o pkg/obcs (obcs-sponge):
399        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
400        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
401    o pkg/generic_advdiff:
402      - record overlap minimum size for each advection scheme;
403      - refine criteria on overlap minimum size;
404      - check and stop (in gad_check) if overlap size is too small.
405    o pkg/obcs:
406      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
407        once, in ptracers_implicit.F)
408      - with seaice: remove test on empty file name in obcs_apply_seaice (always
409        apply OB values when tile has OB)
410    o model/src, coriolis setting:
411      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
412        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
413        files (selectCoriMap=3) with any grid.
414      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
415    o pkg/seaice/seaice_growth.F:
416        a few cosmetic changes that reduce the number of lines of code
417    o pkg/obcs: add boundary conditions following Stevens (1990)
418      - the code follows old MOM/NAOSIM code
419      - so far it is only implemented for the eastern and western boundaries
420        and NOT for pTracers
421    o pkg/rbcs:
422      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
423        beginning of the first rbcs forcing period.
424      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
425        offline package, i.e., one file per time, labeled by iteration number;
426        deltaTrbcs sets the timestep with which the data was generated;
427        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
428      - rbcsForcingCycle=0 makes forcing non-cyclic.
429      - make arithmetic safe for negative times and odd forcing periods.
430    
431    checkpoint62n (2010/11/09)
432    o pkg/seaice:
433        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
434    o pkg/obcs:
435       New S/R to copy tracer value from the OB location to narrow band region
436        (width = same as overlap) beyond the OB: preserve OB value (needed for
437        high-order scheme) which were overwritten by EXCH call if in overlap
438        region. Applied to theta, salt, ptracer and advected seaice variables.
439       With seaice: use maskInC in similar way as in gad_advection.F,
440        in seaice_advection.F and advect.F.
441       Update output of experiment seaice_obcs and change exp4 to test OBCS with
442        4th order Adv.Scheme. for pasive salt and ptracer.
443    o tools/genmake2:
444      - when looking for an optfile (not specified), only search for Fortran compiler
445        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
446      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
447        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
448      - set default for CPP to "cpp -traditional -P" (was the case without specifying
449        an optfile, but otherwise default was just "cpp".
450      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
451      - when "CC" is not set in the optfile, look for possible C compiler
452        (instead of just setting CC=cc)
453      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
454        => add a ".F" to ".o" rule for source files with no "#include" (such as
455           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
456      - move gfortran before g77 in list of possible Fortran compiler (consistent
457        with reference compiler switch from g77 to gfortran)
458    o pkg/seaice:
459      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
460        seaice_check that stops the model, when the CPP flag is used.
461      o seaice_growth.F: make capping of ice volume conserving by returning the
462        capped ice as freshwater to EmPmR. This does not change the verification
463        experiments but will change runs where the capping is acutally active
464    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
465      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
466         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
467         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
468    o tools/genmake2:
469      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
470      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
471      - clean previous genmake log files before anything else.
472      - change Makefile to remove testreport log files (*.tr_log) and genmake log
473        files only with "CLEAN" target (instead of "Clean");
474    o pkg/generic_advdiff:
475      Change OBCS in multiDim advection (gad_advection.F):
476       Use maskInC to prevent intermediate update of tracer-field in OB regions,
477       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
478       which were applying future time-step OB values.
479      This way, all explicit calculations use current-time-step OB values
480       (simpler and more consistent).
481      Affects results when set-up uses time-varying OBC and multi-dim advection;
482       update output of experiment seaice_obcs.
483    o pkg/seaice:
484      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
485       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
486         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
487      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
488       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
489       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
490    o pkg aim (2010/10/26):
491      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
492        formulation with obliquity, eccentricity, ... as run-time parameters,
493      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
494        upward shortwave radition at the surface (all-sky and clear-sky).
495    o pkg/obcs:
496      - writing sections with globalFiles=T does not work: switch to tiled-files
497        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
498      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
499      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
500    
501    checkpoint62m (2010/10/21)
502    o pkg/seaice: vectorize seaice_solve4temp.F
503      - move iterations loops outside of i/j-loops
504      - requires 2D arrays for TB and effConduct
505      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
506        modified in this routine
507      - a little bit of clean up, adjusting indentation, etc.
508      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
509        performance and '**TWO' by '**2' (because TWO is a float),
510        replaced ONE, ZERO
511    o eesupp/src:
512       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
513    o pkg/seaice/seaice_growth.F
514      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
515      merging process. The merged routine has two branches, and one activates the 'evolution'
516      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
517      In summary, here is what the '10/10 revision' did consist of
518        part 1: seaice_growth.F revisions 1.71 to 1.75
519          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
520            The emphasis here was on improving readability (e.g. by trying to use meaningful
521            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
522        part 1.5:
523          - revising the lab_sea experiment to make it a more useful (i.e. stable
524            and representative of an actual model run). This was done by generating a
525            (winter) pickup to start from, switching back the main experiment dynamic
526            solver from evp to lsr, having one of the experiments use the free drift solution.
527        part 2: seaice_growth.F revisions 1.76 to 1.85
528          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
529          - Sorting out the various fields units and sign (set early on and reset at the end)
530            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
531            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
532          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
533            and simplifying logical expressions to further improve readibility.
534        part 3: seaice_growth.F revisions 1.86 to 1.89
535          - Re-organize the blocks of code more logically.
536          - Merging the '_if.F' pieces that add something new.
537    o pkg/thsice:
538      - vectorize thsice_solve4temp and thsice_get_exf.
539        Problem: thsice_solve4temp has an unvectorizable statement that
540        might also be problematic for TAF
541      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
542        does not change the verifcation experiment, but will change all
543        experiments that have this flag undefined (not tested in verification);
544        a little reorganization to save a few 2D fields and recomputations
545      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
546      - 2nd step:  fix some store dirs
547        o seems to work somewhat, i.e. using ifort but not g77
548        o likely cause are incomplete init. or recomputation
549        o start verification/global_ocean.cs32x15/input_ad.thsice
550    o pkg/obcs: add support for exch2
551      - the position of the boundary and prescribed values are specified using
552        a global domain with exch2 facets stacked
553        - in x for N,S boundaries (like W2_mapIO=-1)
554        - in y for E,W boundaries (so E,W boundaries do not overlap)
555    o pkg/mdsio: add support for writing global sections with exch2
556        file layout is as for obcs described above:
557        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
558        - for y-z sections, facets are stacked in y
559    o pkg/thsice:
560       - change a few routines for better vectorization: thsice_albedo.F,
561         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
562         not affected, but in particular the latter routine has changed
563         dramatically (not necessarily easier to read now).
564       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
565       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
566    o verification/lab_sea:
567      - overhaul of the forward model experiments. The main motivation
568        for this revision is that lab_sea has proven quite fragile (when
569        changing the sea-ice code, and switching platforms) to a point
570        when failures were very hard to attribute to specific code problems.
571      - the suspected reason for this fragility is noise amplification by evp so,
572        to start with, we decided to replace evp with lsr in the main experiment.
573      - the input.lsr experiment thus became obsolete and was removed.
574      - it was replaced with the input.fd experiment that uses an
575        analytical "free drift" solution as the ice velocity field.
576      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
577        will hopefully allow us to discriminate problems due to dynamic solvers
578        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
579        us to test additional options, along with the salt plume package.
580      - Finally a pickup was generated (at the end of a one year run) to
581        make the tests more representative of an actual model run. Previously
582        the tests starting point was a 1m thickness of ice everywhere.
583    o pkg/seaice:
584      - introducing S\R seaice_freedrift.F that compute the
585        analytical solution to an approximate ice momentum
586        equation (i.e. the simple stress/coriolis balance).
587      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
588        of the free drift velocity field, and enable its use.
589        To actually use the free drift solution as the model ice
590        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
591    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
592    
593    checkpoint62l (2010/10/04)
594    o pkg/seaice:
595      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
596      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
597       version (with USE_ORIGINAL_SBI undef);
598    o add hooks for new packages OASIS, the package will follow
599      (hooks exclude the seaice pkg for now)
600    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
601      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
602      rather than mdsio_readvector.F/mdsio_writevector.F, within
603      adread_adwrite.F to read/write adjoint-related tapes to disk.
604    o eesupp and pkg/mdsio: ALLOW_WHIO
605      Option to write/read 2D fields to files including tiles halos.
606      The main purpose is for adjoint related "tape I/O".
607      The secondary purpose is for debugging phases.
608      A word on those rather specifically intended purposes.
609      The code was meant to be stripped down to the bare minimum.
610      Typically, there is a unique and basic mapping to the global
611      buffer (tile by tile, then proc by proc, then level by level), and
612      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
613      meant to generate user friendly outputs of various shapes and forms.
614      Rather it is intended, for the knowledgeabale developers,
615      to be largely independent of the many mdsio options, to allow
616      outputs of tiles+halos in debugging phases and in adjoint runs,
617      and to allow some flexibility in tuning (adoint) I/O depending on each
618      file system behavior. With regard to tuning, most of the potential knobs
619      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
620      to specify directories, to specify the typical size of I/O calls, etc.)
621      are not yet included, and will be added if they prove useful.
622    o pkg/seaice:
623       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
624    o pkg/seaice:
625       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
626       code (seaice_budget_ice_if.F) which enable to recover old standard
627       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
628       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
629    o model/src (rStar):
630       use simple average (not area weighted) of rStarFac at U,V point when using
631       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
632       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
633    
634    checkpoint62k (2010/09/17)
635    o adjoint
636       * changed verification/global_ocean.cs32x15 ; adjoint now tests
637         Adams-Bashforth 3 + NLFS + RSTAR
638       * some more modifs required for ECCO-GODAE v4
639    o pkg/seaice
640       add SEAICE_AGE_VOL option to use volume instead of area for
641       integrating SEAICE_AGE
642    o model/src:
643       first check-in of sigma & hybrid-sigma coordinate code ; also includes
644       non-linear free-surface parts ; but pressure-gradient not yet coded.
645    o pkg/ptracers:
646       option for ptracer to convert Salt Relax into additional EmP.
647        tested in exp. global_ocean.90x40x15.dwnslp (update output)
648    
649    checkpoint62j (2010/08/25)
650    o pkg/ggl90:
651       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
652    o pkg/dic: car_flux.F, phos_flux.F
653      - reduce number of exp-calls in order to improve performance
654      - clean up a little (replace fields by their macros, etc., fix
655        typo in CPP-flag)
656    o pkg/ggl90: minor changes
657      - GGL90diffKrS was removed --> always use GGL90diffKr
658      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
659      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
660        (commented out for now)
661      - change in max/min operations to ensure that smoothing is ok
662      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
663      - always use diffKrNrT as background profile (i.e. never use diffKr field)
664    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
665    o pkg/dic:
666      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
667        vectorization
668      - small bug fix in insol for the unlikely case of a cartesian grid
669      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
670        + now vectorize, which also removes adjoint recomputations;
671        + replace integer maksp1 by _RL maskp1
672        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
673    
674    checkpoint62i (2010/07/21)
675    o pkg/flt:
676      - with OBCS: stop floats which enter the OB region
677    o model/src:
678      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
679        for implicit vertical advection.
680    o pkg/seaice:
681     - account for melting in seaice age evolution.
682     - remove double counting of seaice ridging effect on seaice age.
683    
684    checkpoint62h (2010/06/18)
685    o pkg/exch2:
686     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
687    o tools/genmake2
688      - remove "-pdefault" option: redundant with the use of "packages.conf";
689      - remove file pkg/pkg_default : set the default as a pkg group
690        ("default_pkg_list") defined in pkg/pkg_groups;
691      - fix for case pkg/pkg_depend is missing (was hanging before);
692      - add option "-pgroups" to specify a different pkg_groups than the default.
693    o verification/adjustment.cs-32x32x1:
694       add a "minimal" set-up test (code_min & input_min) which only compiles
695       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
696    o tools/genmake2
697      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
698      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
699    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
700      files are nearly the same anyway.
701      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
702       - redefinition of tau(i,i) (by a factor of ustar)
703       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
704       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
705       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
706       - replace
707         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
708         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
709         by
710         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
711         (changes results)
712       -> exf_bulkformulae v1.22,
713          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
714          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
715                    output.txt 1.63
716           offline_exf_seaice: output.seaicetd.txt 1.7
717           seaice_obcs: output.txt 1.10)
718      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
719       -> exf_bulkformulae v1.23,
720          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
721          and global_ocean.cs32x15.icedyn (only 11 matching digits)
722      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
723    o adjoint of exch-1:
724     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
725       (note: was already like this when using EXCH-2) and remove flow dir
726       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
727     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
728     - update pkg/exch2 diff list.
729    
730    checkpoint62g (2010/05/19)
731    o eesupp/src (exch-1):
732     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
733       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
734       (renamed to exch1_*rx_cube.F).
735     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
736       to call new exch1 S/R ; update Makefile and .cvsignore.
737     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
738       exch2_xy_rx later)
739      Note: after updating your code, need to run "make clean" in eesupp/src
740    o test experiment bottom_ctrl_5x5:
741       new output_adm.txt with fewer grdchk & less monitor output.
742    o model/src:
743      remove the call to ini_cori in initialise_varia.F (just keep the usual one
744       in initialise_fixed.F). More consistent with coriolis & horizontal grid
745       beeing treated in the same way (ini_grid is not called a 2nd time).
746    o pkg/exf:
747      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
748      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
749      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
750      - cosmetic changes to exf_bulkformulae.F to make it look more like
751        exf_bulk_largeyeager04.F
752    o eesupp/src (exch-1):
753      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
754      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
755        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
756        (even without using MPI).
757      - Message mode: move RecvAck setting (indicator of buffer being ready)
758        from send_put to recv_get S/R (was useless before, but not sure if
759        it's much more useful now);
760      - Switch the order of sync: MPI-proc 1rst and then threads;
761      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
762      - fix AD code for communication mode ='get' (but not used).
763    o model/src:
764      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
765      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
766    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
767    o pkg/ctrl: require a specific set of control variables and exf-flags for
768      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
769    o model/src:
770     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
771       1rst forward sweep, to avoid over-writing output files during recomputations
772       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
773     b) 2nd version:
774      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
775      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
776         writePickupAtEnd) + seaice & ptracers output;
777      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
778    o model/src:
779      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
780    o pkg/exch2:
781      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
782      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
783    o pkg/autodiff & exch2:
784      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
785      (for now, only if ALLOW_EXCH2 is defined).
786    o pkg/autodiff:
787      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
788        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
789       + clean-up comments (_RS is not always real*4)
790      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
791      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
792        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
793    o testreport (AD-tests):
794      no longer link files from dir "../input" (1rst link files from
795      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
796    
797    checkpoint62f (2010/04/29)
798    o model/src/the_main_loop.F:
799      adjust store directives for seaice evp and multicategory according to
800      pkg/ecco/the_main_loop.F
801    o adjoint:
802      global_sum_ad was incomplete (noted many times by many people ;)
803      nice description by Jean U. as follows:
804      * allreduce(var) in global_sum.F can be interpreted as
805        reduce(sum) followed by broadcast of sum.
806      * The adjoint of that is
807        sum(adjoint) followed by broadcast(summed adjoint value)
808        or in other words, allreduce(sum, adjoint vars)
809      We were missing the sum(adjoint)!
810      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
811      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
812      The fix should produce 16-digit accuracy between
813      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
814      multi-CPU single-tile (e.g. nSx=1, nPx-2)
815      We'll probably change this yet again shortly
816    o eesupp/src:
817      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
818    o pkg/icefront
819      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
820        specification of addmass array based on a 2D field, which is added
821        at bottommost wet level at each horizontal location.
822    o model/src:
823     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
824     layout; (not always compatible with delX,delY setting; commented out for now).
825    o pkg/exch2:
826     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
827     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
828    
829    checkpoint62e (2010/04/15)
830    o pkg/obcs:
831      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
832    o pkg/dic:
833      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
834        (note: not presently tested in any forward verification exp.)
835       update tutorial_global_oce_biogeo AD output file.
836    o pkg/exf:
837      - account for the variation of albedo as a function of zenith angle
838        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
839    o build_options:
840     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
841    o pkg/dic:
842      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
843      - use binary pickup file for restart;
844      - initialise atmos-CO2 box from dic_pCO2 parameter;
845      - fix multi-threaded.
846    o pkg/rbcs:
847     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
848       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
849     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
850       and update output.txt
851    o pkg/kpp:
852     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
853     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
854       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
855       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
856     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
857       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
858    o pkg/offline:
859      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
860      (bug was added in version 1.10 on 2007-08-23).
861    o pkg/offline:
862      - no need to specify periodicExternalForcing, etc ... to use offline pack
863      - offline input files no longer just single prec --> parameter offlineLoadPrec
864    o verification/lab_sea:
865      change AD test to multi-tile setup and update all 4 AD output.
866      NOTE: while cost function values remain very similar,
867      gradients are very different, although gradient checks are self-consistent
868      Should try to get to the bottom of this (cost function summation order?)
869    o pkg/dic:
870      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
871      a weakness of TAF that drops part of double precision in log10 derivative.
872      <= changes removed since problem has been fixed in current TAF version 1.9.71
873      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
874  o pkg/ecco:  o pkg/ecco:
875    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
876    update all 4 lab_sea AD output.    update all 4 lab_sea AD output.
# Line 41  o tools/build_options: Line 908  o tools/build_options:
908      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
909  o pkg/ecco  o pkg/ecco
910    - allow user defined cost function contributions    - allow user defined cost function contributions
911          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
912          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
913    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
914        the two options are complementary.        the two options are complementary.
915  o pkg/smooth  o pkg/smooth
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