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revision 1.1242 by heimbach, Wed Mar 24 21:56:45 2010 UTC revision 1.1424 by mlosch, Thu May 5 09:24:44 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      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
9      - improve error messages in ctrl_set_unpack_*
10    o OBC implementation in momentum:
11       use interior masks (maskInC,W & S) in momentum S/R:
12       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
13       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
14       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
15       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
16       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
17        (and also with Leith/Smagorinsky harmonic-viscosity).
18       Update output of experiment dome and exp4 (+nlfs).
19    o exp4 test-exp:
20      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
21        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
22        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
23        time-varying OB at Western-side for wVel (NonHyd); update output.
24      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
25        and biharmonic-viscosity ; also use prescribed time varying OB.
26    o pkg/obcs:
27      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
28    o model/src:
29      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
30      - initialise startTime & nIter0 with unlikely values: allows to set one
31        from the other without ambiguity.
32    o seaice_obcs test-exp.:
33      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
34    o pkg/obcs:
35      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
36        no longer needed with maskInC,W,S in pkg/generic_advdiff.
37    o pkg/seaice:
38      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
39        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
40      - fixed bug in the initialization of sea ice salinity variable HSALT
41        in seaice_init_varia.F  (removed dependence on ICE2WATR)
42    o fizhi-cs test exp.:
43       switch reference output convention for these 2 non-standard test-exp,
44        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
45          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
46       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
47    o model/inc:
48      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
49        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
50    o pkg/seaice:
51      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
52    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
53      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
54        and initial HSALT
55    
56    checkpoint62w (2011/04/26)
57    o pkg/mom_fluxform:
58      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
59      - use parameter "sideDragFactor" in no-slip BC side-drag part.
60      - update output of exp. global_ocean.90x40x15
61    o pkg/mom_vecinv:
62      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
63    o update seaice exp.:
64      use more consistent parameter values (remove "backward compatability only":
65       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
66      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
67       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
68    o update test-exp global_ocean.90x40x15:
69      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
70      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
71      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
72      o turn on zStar & viscA4 in standard set-up (dir input/)
73        and update output files: output.txt & output.dwnslp.txt
74    o new AD-test experiment: obcs_ctrl
75      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
76    o pkg/dic:
77      fix two bugs in handling water vapour pressure in carbonate chemistry
78      and air-sea fluxes. Found by Val Bennington and Galen McKinley
79      (add DIC Option = WATERVAP_BUG to recover old results)
80      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
81    o adding allowInteriorFreezing option to check for water below freezing point
82      at depth and bring the negative heat anomaly to the surface level
83    o pkgs _fields_load:
84      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
85      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
86        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
87        rbcs to get interpolation weights and time reccord number.
88      - fix multi-threading in aim_fields_load.F
89      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
90    o external_fields_load:
91      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
92       interpolation weights) to use in a periodic time-series ; do not divide by
93       time-step to convert to integer:
94       - this fixes case where externForcingPeriod is not multiple of time-step
95          (Thanks to Christopher L. Wolfe)
96       - this fixes case where externForcingPeriod is an odd multiple of time-step
97         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
98      store index of time-record which is currently loaded:
99       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
100       - needed for the adjoint but not yet used because of extensive recomputations;
101         (to be fixed soon)
102    
103    checkpoint62v (2011/04/02)
104    o verification/1D_ocean_ice_column added to test Ian Fenty's
105      pkg/seaice_growth.F modifications for improving sea ice code differentiability
106    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
107      (new velocity statistics after changing maskInW & maskInS definition)
108    o pkg/generic_advdiff with OBCS:
109      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
110      equivalent to assumption of no tracer gradient outside the OB region.
111      This will affect the results if using obcs+biharmonic diffusion.
112      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
113    o pkg/obcs:
114      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
115      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
116      in Interior region. No impact on solution but affects Velocity monitor stats.
117    o pkg/ptracers (adjoint)
118      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
119      tape file for each tracer
120    o model/inc/src and pkg/autodiff: add parameters that allow to turn
121      of parts of the adjoint code at run time. For now, there are only
122      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
123      parameters are set in data.pkg.
124      This is the lazy coward's version of doing this, but still useful for
125      debugging. In order to do it right, everything needs to be moved to
126      pkg/autodiff.
127    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
128      the end; this fixes the adjoint balancing code for open boundaries.
129    o pkg/ctrl:
130      - change behavior of xx_${varname}period to be analogous to exf-conventions:
131        xx_${varname}period =   0.,  means time-independent control part
132        xx_${varname}period = -12., means one-year-periodic monthly control part
133      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
134        clean up ctrl_init a little, remove unused variables
135      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
136      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
137    
138    checkpoint62u (2011/03/15)
139    o model/src:
140      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
141        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
142      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
143        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
144    o pkg/ctrl/obcs/ecco:
145      - remove obsolete, unused, and partially broken code:
146        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
147        ALLOW_CTRL_OBCS_BALANCE
148      - put a stop statement into ecco/cost_obcsvol.F, but also add
149        cost_obcsvol to ecco_ad_diff.list
150    o pkg/ecco: fix counting cost function contributions for obcs (code
151      by Matt M.) and diffkr for diagnostics
152    o pkg/ecco, pkg/ctrl, pkg/grdchk:
153      add cost penalty terms for initial uvel, vvel, eta controls
154      and I/O for prior error files
155    o pkg/mdsio:
156       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
157       (new argument) to check for tiled file in mdsioLocalDir : this fix the
158       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
159    o pkg/ctrl:
160     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
161       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
162       unused and superfluous variables
163     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
164    o pkg/ecco
165     - enable adjoint of Stevens OB
166    o pkg/ctrl/ecco/grdchk:
167      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
168        Fortunately, we do not have any tests for the numerous cpp-flagged
169        option of "obcs as control parameters" so we will never know
170        if this is an improvement (but at least now things compile).
171      - remove an obsolete initialization from ecco_cost_init_barfiles.F
172      - fix some problems within never used ifdefs to make the code compile
173    o pkg/obcs:
174     - Refine Interior mask definition to work with more complex OB (e.g.
175       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
176       read in Interior mask from file. Check if Interior mask is consistent
177       with OB list of indices.
178    o pkg/seaice
179     - beginning code for a seaice tracer package,
180       but currently only used for seaice age: SEAICE_AGE
181       SEAICE_num = 4
182       iTracer = 1: area-weighted ice age
183               = 2: volume-weighted ice age
184               = 3, 4: template for one-year vs. multi-year ice
185       data.seaice has new namelist SEAICE_PARM03 for arrays related to
186       SEAICE_num
187    
188    checkpoint62t (2011/03/05)
189    o pkg/obcs:
190     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
191       then normal component. This ensures that the normal component is set
192       correctly even when it conficts with tangential setting from an other OB.
193       Affects results of test-experiment seaice_obcs: update the output.txt
194    o pkg/obcs:
195     - add code to monitor statistics of dynamical fields at OB.
196     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
197       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
198       - change default: balance the Net inflow through all OB (instead of balancing
199         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
200     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
201       to match Nortern OB inflow (OBCS_balanceFacN=0).
202    o pkg/seaice:
203     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
204    o pkg/seaice (seaice_growth v 1.113):
205     - reverting seaice_growth to v 1.111 in order to have code with exact bit
206       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
207       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
208       runtime flag SEAICEareaFormula is kept but is inactive
209    o model/src:
210     - add new param to scale curvilinear grid distance and area when using
211       a different sphere radius from the grid-files.
212     - test/check multi-threads EXCH applied to local variable (cg2d_x)
213    o adjoint:
214     - enable adjoint of Stevens OB
215     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
216       (a bit delicate because of potentially modified adj. common block structure;
217       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
218    
219    checkpoint62s (2011/02/15)
220    o pkg/seaice (seaice_growth v 1.112):
221     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
222       computing the ice cover tendency from effective thickness tendencies. Include
223       Ian Fenty's formula.
224     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
225       SEAICEareaFormula.
226     - simplify notations for the various d_HEFF/d_AREA terms.
227    o pkg/gmredi:
228     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
229       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
230       add a verification test-run (front_relax.bvp) to test GM_useBVP.
231    o pkg/seaice (seaice_growth v 1.111):
232     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
233     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
234       also melt ice.
235    o pkg/seaice:
236     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
237     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
238    o pkg/cheapaml:
239     - from Nico Wienders: New version of this package.
240    o pkg/flt:
241     - add CPP options to prevent floats to re-enter the opposite side of
242       a periodic domain (default: keep periodicity)
243    o pkg/gmredi:
244     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
245       (needed for multi-dim advection).
246     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
247    o model/src:
248     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
249    o tutorial_tracer_adjsens
250     - extend to NLFS and replace maskC by hFacC
251       (change reference output accordingly)
252    
253    checkpoint62r (2011/01/24)
254    o testreport:
255     - add option -deloutp (-do) to remove output file after successful run
256     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
257       extract exact list of procs from this file ; adjust COMMAND by
258       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
259    o pkg/ecco: replace old ineffective way of penalizing deviations from
260      first guess (of obcs) with code by Matt Mazloff
261    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
262      exf/cal
263      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
264        and handle case of obcs?period == 0
265        Not affected by these changes: There is still an inconsistency in
266        the computation of start/endrec for the obcs variables for ALLOW_CAL
267        defined (see comment by Menemenlis, 7-Mar-2003)
268      - make S/R ctrl_get_gen_rec return something meaningful even if
269        ALLOW_CAL is not defined
270      - ctrl_getobcs?: simplify code so that it does not need to use
271                       S/R exf_swapfields
272    o testreport:
273       allow to test MPI with different number of processors for each experiment:
274       create file "SIZE.h.mpi" in each build dir.
275       Note: update of "-command" argument not yet implemented.
276    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
277      alleviate the need for additional 3D tapes when using
278      the non-inear free surface in the adjoint. This is done
279      by adding an 'update' of hfacc etc. to their current
280      value at the beginning of forward_step.F.
281    o pkg/seaice
282      seaice_lsr: move stress-divergence computations out of outer pseudo-
283      timestepping loop
284    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
285      up, so that the calls of the ctrl_* subroutines are really at the end
286      of the routine.
287    o pkg/gmredi:
288      allow to specify a 2-D horizontal map and a 1-D vertical profil
289      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
290    o pkg/seaice:
291      move lsr iterations from seaice_dynsolver to seaice_lsr.
292    o pkg/seaice:
293      reduce memory footprint of seaice mutldim advection tapes,
294      by using a 2D tape independent of the generic_advdiff ones,
295      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
296    
297    checkpoint62q (2010/12/29)
298    o model/src:
299      - check horizontal grid-spacing for unset or zero/negative values.
300      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
301    o pkg/flt:
302      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
303      - precision of input and output files set according to readBinaryPrec
304        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
305      - initial float position from tiled file was not converted to index space
306        (looks like a bug): fixed to make it similar to initial pos. global file.
307    o global_ocean.cs32x15:
308       change SIZE.h of AD set-up to get same tiling as with MPI.
309       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
310    o model/src:
311       add flag to control printing of domain fields (bathymetry, hFac ...) in
312       ini_mask_etc (call to plot_fieds_xy*).
313    o pkg/thsice:
314       if useEXF, some forcing fields are not valid in overlap: fixed by computing
315       over the interior only + apply EXCH at the end (like with SEAICE advection).
316    o pkg/mdsio:
317      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
318        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
319      - change barrier call for safe multi-threads access to 3-D shared buffer.
320      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
321      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
322        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
323    o pkg/flt:
324      - add fourth-order Runge-Kutta integration
325      - add basic exch2 support (only 1 facet supported so far!)
326    o pkg/mdsio+rw:
327      new S/R to read local (or tile independent) vector (read counterpart of
328       mds_writevec_loc, and front-end write_glvec_rl/rs).
329    o global_ocean.cs32x15: additional input_ad.seaice experiment
330        that uses pkg/seaice rather than pkg/thsice.
331        (using multidim advection for seaice)
332    o towards more F95 syntax for array specification in namelist:
333      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
334        of all verification experiments.
335           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
336          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
337      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
338    o global_ocean.cs32x15: additional input.seaice experiment
339        that uses pkg/seaice rather than pkg/thsice.
340    
341    checkpoint62p (2010/12/17)
342    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
343        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
344    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
345        allow for use of multim. advection in seaice adjoint.
346    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
347      - first attempt to close budgets by taking into account the freshwater
348        flux implied by the sublimation of snow and ice. So far only the
349        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
350        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
351    o eesupp/src:
352      new S/R with new option (NML_EXTENDED_F77) to change array specification
353      from F95 standard to commonly accepted extended F77 form.
354      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
355      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
356      for less tolerant f77 compiler (e.g., pgf77, g77).
357    o globalFiles:
358      commented out in parameter file "data" since it's not safe with MPI
359      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
360      in this case); no longer commented out in restart test (tst_2+2).
361    o add adTapeDir to specify a special directory where adjoint tapes are
362      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
363      and cannot be used together with mdsioLocalDir.
364    o nesting pkgs:
365      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
366      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
367      - add parameter files + utils dir + output from short run on beagle.
368    o pkg/seaice:
369        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
370    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
371      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
372    
373    checkpoint62o (2010/11/25)
374    o pkg/exf:
375      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
376    o pkg/seaice:
377      - seaice_ocean_stress: split a loop for better vectorization of the
378        adjoint code
379      - seaice_growth.F: fix bug in conservation of freshwater connected to
380        capping of heff, put contribution into d_HEFFbyNEG
381      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
382        by something more sensible (parameters that are what their name implies)
383      - change some defaults, so that by default exf-parameters are used for
384        things like rhoAir, cpAir,latent/sensible heat parameters, in order
385        to reproduce the old results, many data.seaice now contain funny values
386        for cpAir and latent heat of sublimation
387    o packages_readparms.F: move exf_readparms up in line so that
388        exf-parameters are visible for other packages (e.g. seaice)
389    o debugMode & debugLevel=2:
390      - differentiate between debugMode & debugLevel=2:
391        debugMode: controls printing of debug messages (sequence of S/R calls).
392        debugLevel: controls printing of algorithm intermediate results and stats.
393      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
394        => allows to print debug-stats without all sequence of call messages.
395      - switch control of debug print from debugLevel to debugMode in many S/R.
396    o pkg/obcs (obcs-sponge):
397        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
398        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
399    o pkg/generic_advdiff:
400      - record overlap minimum size for each advection scheme;
401      - refine criteria on overlap minimum size;
402      - check and stop (in gad_check) if overlap size is too small.
403    o pkg/obcs:
404      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
405        once, in ptracers_implicit.F)
406      - with seaice: remove test on empty file name in obcs_apply_seaice (always
407        apply OB values when tile has OB)
408    o model/src, coriolis setting:
409      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
410        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
411        files (selectCoriMap=3) with any grid.
412      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
413    o pkg/seaice/seaice_growth.F:
414        a few cosmetic changes that reduce the number of lines of code
415    o pkg/obcs: add boundary conditions following Stevens (1990)
416      - the code follows old MOM/NAOSIM code
417      - so far it is only implemented for the eastern and western boundaries
418        and NOT for pTracers
419    o pkg/rbcs:
420      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
421        beginning of the first rbcs forcing period.
422      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
423        offline package, i.e., one file per time, labeled by iteration number;
424        deltaTrbcs sets the timestep with which the data was generated;
425        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
426      - rbcsForcingCycle=0 makes forcing non-cyclic.
427      - make arithmetic safe for negative times and odd forcing periods.
428    
429    checkpoint62n (2010/11/09)
430    o pkg/seaice:
431        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
432    o pkg/obcs:
433       New S/R to copy tracer value from the OB location to narrow band region
434        (width = same as overlap) beyond the OB: preserve OB value (needed for
435        high-order scheme) which were overwritten by EXCH call if in overlap
436        region. Applied to theta, salt, ptracer and advected seaice variables.
437       With seaice: use maskInC in similar way as in gad_advection.F,
438        in seaice_advection.F and advect.F.
439       Update output of experiment seaice_obcs and change exp4 to test OBCS with
440        4th order Adv.Scheme. for pasive salt and ptracer.
441    o tools/genmake2:
442      - when looking for an optfile (not specified), only search for Fortran compiler
443        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
444      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
445        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
446      - set default for CPP to "cpp -traditional -P" (was the case without specifying
447        an optfile, but otherwise default was just "cpp".
448      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
449      - when "CC" is not set in the optfile, look for possible C compiler
450        (instead of just setting CC=cc)
451      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
452        => add a ".F" to ".o" rule for source files with no "#include" (such as
453           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
454      - move gfortran before g77 in list of possible Fortran compiler (consistent
455        with reference compiler switch from g77 to gfortran)
456    o pkg/seaice:
457      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
458        seaice_check that stops the model, when the CPP flag is used.
459      o seaice_growth.F: make capping of ice volume conserving by returning the
460        capped ice as freshwater to EmPmR. This does not change the verification
461        experiments but will change runs where the capping is acutally active
462    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
463      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
464         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
465         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
466    o tools/genmake2:
467      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
468      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
469      - clean previous genmake log files before anything else.
470      - change Makefile to remove testreport log files (*.tr_log) and genmake log
471        files only with "CLEAN" target (instead of "Clean");
472    o pkg/generic_advdiff:
473      Change OBCS in multiDim advection (gad_advection.F):
474       Use maskInC to prevent intermediate update of tracer-field in OB regions,
475       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
476       which were applying future time-step OB values.
477      This way, all explicit calculations use current-time-step OB values
478       (simpler and more consistent).
479      Affects results when set-up uses time-varying OBC and multi-dim advection;
480       update output of experiment seaice_obcs.
481    o pkg/seaice:
482      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
483       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
484         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
485      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
486       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
487       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
488    o pkg aim (2010/10/26):
489      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
490        formulation with obliquity, eccentricity, ... as run-time parameters,
491      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
492        upward shortwave radition at the surface (all-sky and clear-sky).
493    o pkg/obcs:
494      - writing sections with globalFiles=T does not work: switch to tiled-files
495        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
496      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
497      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
498    
499    checkpoint62m (2010/10/21)
500    o pkg/seaice: vectorize seaice_solve4temp.F
501      - move iterations loops outside of i/j-loops
502      - requires 2D arrays for TB and effConduct
503      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
504        modified in this routine
505      - a little bit of clean up, adjusting indentation, etc.
506      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
507        performance and '**TWO' by '**2' (because TWO is a float),
508        replaced ONE, ZERO
509    o eesupp/src:
510       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
511    o pkg/seaice/seaice_growth.F
512      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
513      merging process. The merged routine has two branches, and one activates the 'evolution'
514      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
515      In summary, here is what the '10/10 revision' did consist of
516        part 1: seaice_growth.F revisions 1.71 to 1.75
517          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
518            The emphasis here was on improving readability (e.g. by trying to use meaningful
519            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
520        part 1.5:
521          - revising the lab_sea experiment to make it a more useful (i.e. stable
522            and representative of an actual model run). This was done by generating a
523            (winter) pickup to start from, switching back the main experiment dynamic
524            solver from evp to lsr, having one of the experiments use the free drift solution.
525        part 2: seaice_growth.F revisions 1.76 to 1.85
526          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
527          - Sorting out the various fields units and sign (set early on and reset at the end)
528            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
529            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
530          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
531            and simplifying logical expressions to further improve readibility.
532        part 3: seaice_growth.F revisions 1.86 to 1.89
533          - Re-organize the blocks of code more logically.
534          - Merging the '_if.F' pieces that add something new.
535    o pkg/thsice:
536      - vectorize thsice_solve4temp and thsice_get_exf.
537        Problem: thsice_solve4temp has an unvectorizable statement that
538        might also be problematic for TAF
539      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
540        does not change the verifcation experiment, but will change all
541        experiments that have this flag undefined (not tested in verification);
542        a little reorganization to save a few 2D fields and recomputations
543      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
544      - 2nd step:  fix some store dirs
545        o seems to work somewhat, i.e. using ifort but not g77
546        o likely cause are incomplete init. or recomputation
547        o start verification/global_ocean.cs32x15/input_ad.thsice
548    o pkg/obcs: add support for exch2
549      - the position of the boundary and prescribed values are specified using
550        a global domain with exch2 facets stacked
551        - in x for N,S boundaries (like W2_mapIO=-1)
552        - in y for E,W boundaries (so E,W boundaries do not overlap)
553    o pkg/mdsio: add support for writing global sections with exch2
554        file layout is as for obcs described above:
555        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
556        - for y-z sections, facets are stacked in y
557    o pkg/thsice:
558       - change a few routines for better vectorization: thsice_albedo.F,
559         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
560         not affected, but in particular the latter routine has changed
561         dramatically (not necessarily easier to read now).
562       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
563       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
564    o verification/lab_sea:
565      - overhaul of the forward model experiments. The main motivation
566        for this revision is that lab_sea has proven quite fragile (when
567        changing the sea-ice code, and switching platforms) to a point
568        when failures were very hard to attribute to specific code problems.
569      - the suspected reason for this fragility is noise amplification by evp so,
570        to start with, we decided to replace evp with lsr in the main experiment.
571      - the input.lsr experiment thus became obsolete and was removed.
572      - it was replaced with the input.fd experiment that uses an
573        analytical "free drift" solution as the ice velocity field.
574      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
575        will hopefully allow us to discriminate problems due to dynamic solvers
576        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
577        us to test additional options, along with the salt plume package.
578      - Finally a pickup was generated (at the end of a one year run) to
579        make the tests more representative of an actual model run. Previously
580        the tests starting point was a 1m thickness of ice everywhere.
581    o pkg/seaice:
582      - introducing S\R seaice_freedrift.F that compute the
583        analytical solution to an approximate ice momentum
584        equation (i.e. the simple stress/coriolis balance).
585      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
586        of the free drift velocity field, and enable its use.
587        To actually use the free drift solution as the model ice
588        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
589    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
590    
591    checkpoint62l (2010/10/04)
592    o pkg/seaice:
593      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
594      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
595       version (with USE_ORIGINAL_SBI undef);
596    o add hooks for new packages OASIS, the package will follow
597      (hooks exclude the seaice pkg for now)
598    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
599      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
600      rather than mdsio_readvector.F/mdsio_writevector.F, within
601      adread_adwrite.F to read/write adjoint-related tapes to disk.
602    o eesupp and pkg/mdsio: ALLOW_WHIO
603      Option to write/read 2D fields to files including tiles halos.
604      The main purpose is for adjoint related "tape I/O".
605      The secondary purpose is for debugging phases.
606      A word on those rather specifically intended purposes.
607      The code was meant to be stripped down to the bare minimum.
608      Typically, there is a unique and basic mapping to the global
609      buffer (tile by tile, then proc by proc, then level by level), and
610      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
611      meant to generate user friendly outputs of various shapes and forms.
612      Rather it is intended, for the knowledgeabale developers,
613      to be largely independent of the many mdsio options, to allow
614      outputs of tiles+halos in debugging phases and in adjoint runs,
615      and to allow some flexibility in tuning (adoint) I/O depending on each
616      file system behavior. With regard to tuning, most of the potential knobs
617      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
618      to specify directories, to specify the typical size of I/O calls, etc.)
619      are not yet included, and will be added if they prove useful.
620    o pkg/seaice:
621       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
622    o pkg/seaice:
623       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
624       code (seaice_budget_ice_if.F) which enable to recover old standard
625       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
626       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
627    o model/src (rStar):
628       use simple average (not area weighted) of rStarFac at U,V point when using
629       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
630       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
631    
632    checkpoint62k (2010/09/17)
633    o adjoint
634       * changed verification/global_ocean.cs32x15 ; adjoint now tests
635         Adams-Bashforth 3 + NLFS + RSTAR
636       * some more modifs required for ECCO-GODAE v4
637    o pkg/seaice
638       add SEAICE_AGE_VOL option to use volume instead of area for
639       integrating SEAICE_AGE
640    o model/src:
641       first check-in of sigma & hybrid-sigma coordinate code ; also includes
642       non-linear free-surface parts ; but pressure-gradient not yet coded.
643    o pkg/ptracers:
644       option for ptracer to convert Salt Relax into additional EmP.
645        tested in exp. global_ocean.90x40x15.dwnslp (update output)
646    
647    checkpoint62j (2010/08/25)
648    o pkg/ggl90:
649       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
650    o pkg/dic: car_flux.F, phos_flux.F
651      - reduce number of exp-calls in order to improve performance
652      - clean up a little (replace fields by their macros, etc., fix
653        typo in CPP-flag)
654    o pkg/ggl90: minor changes
655      - GGL90diffKrS was removed --> always use GGL90diffKr
656      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
657      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
658        (commented out for now)
659      - change in max/min operations to ensure that smoothing is ok
660      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
661      - always use diffKrNrT as background profile (i.e. never use diffKr field)
662    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
663    o pkg/dic:
664      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
665        vectorization
666      - small bug fix in insol for the unlikely case of a cartesian grid
667      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
668        + now vectorize, which also removes adjoint recomputations;
669        + replace integer maksp1 by _RL maskp1
670        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
671    
672    checkpoint62i (2010/07/21)
673    o pkg/flt:
674      - with OBCS: stop floats which enter the OB region
675    o model/src:
676      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
677        for implicit vertical advection.
678    o pkg/seaice:
679     - account for melting in seaice age evolution.
680     - remove double counting of seaice ridging effect on seaice age.
681    
682    checkpoint62h (2010/06/18)
683    o pkg/exch2:
684     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
685    o tools/genmake2
686      - remove "-pdefault" option: redundant with the use of "packages.conf";
687      - remove file pkg/pkg_default : set the default as a pkg group
688        ("default_pkg_list") defined in pkg/pkg_groups;
689      - fix for case pkg/pkg_depend is missing (was hanging before);
690      - add option "-pgroups" to specify a different pkg_groups than the default.
691    o verification/adjustment.cs-32x32x1:
692       add a "minimal" set-up test (code_min & input_min) which only compiles
693       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
694    o tools/genmake2
695      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
696      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
697    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
698      files are nearly the same anyway.
699      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
700       - redefinition of tau(i,i) (by a factor of ustar)
701       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
702       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
703       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
704       - replace
705         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
706         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
707         by
708         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
709         (changes results)
710       -> exf_bulkformulae v1.22,
711          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
712          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
713                    output.txt 1.63
714           offline_exf_seaice: output.seaicetd.txt 1.7
715           seaice_obcs: output.txt 1.10)
716      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
717       -> exf_bulkformulae v1.23,
718          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
719          and global_ocean.cs32x15.icedyn (only 11 matching digits)
720      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
721    o adjoint of exch-1:
722     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
723       (note: was already like this when using EXCH-2) and remove flow dir
724       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
725     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
726     - update pkg/exch2 diff list.
727    
728    checkpoint62g (2010/05/19)
729    o eesupp/src (exch-1):
730     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
731       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
732       (renamed to exch1_*rx_cube.F).
733     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
734       to call new exch1 S/R ; update Makefile and .cvsignore.
735     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
736       exch2_xy_rx later)
737      Note: after updating your code, need to run "make clean" in eesupp/src
738    o test experiment bottom_ctrl_5x5:
739       new output_adm.txt with fewer grdchk & less monitor output.
740    o model/src:
741      remove the call to ini_cori in initialise_varia.F (just keep the usual one
742       in initialise_fixed.F). More consistent with coriolis & horizontal grid
743       beeing treated in the same way (ini_grid is not called a 2nd time).
744    o pkg/exf:
745      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
746      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
747      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
748      - cosmetic changes to exf_bulkformulae.F to make it look more like
749        exf_bulk_largeyeager04.F
750    o eesupp/src (exch-1):
751      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
752      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
753        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
754        (even without using MPI).
755      - Message mode: move RecvAck setting (indicator of buffer being ready)
756        from send_put to recv_get S/R (was useless before, but not sure if
757        it's much more useful now);
758      - Switch the order of sync: MPI-proc 1rst and then threads;
759      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
760      - fix AD code for communication mode ='get' (but not used).
761    o model/src:
762      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
763      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
764    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
765    o pkg/ctrl: require a specific set of control variables and exf-flags for
766      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
767    o model/src:
768     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
769       1rst forward sweep, to avoid over-writing output files during recomputations
770       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
771     b) 2nd version:
772      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
773      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
774         writePickupAtEnd) + seaice & ptracers output;
775      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
776    o model/src:
777      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
778    o pkg/exch2:
779      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
780      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
781    o pkg/autodiff & exch2:
782      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
783      (for now, only if ALLOW_EXCH2 is defined).
784    o pkg/autodiff:
785      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
786        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
787       + clean-up comments (_RS is not always real*4)
788      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
789      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
790        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
791    o testreport (AD-tests):
792      no longer link files from dir "../input" (1rst link files from
793      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
794    
795    checkpoint62f (2010/04/29)
796    o model/src/the_main_loop.F:
797      adjust store directives for seaice evp and multicategory according to
798      pkg/ecco/the_main_loop.F
799    o adjoint:
800      global_sum_ad was incomplete (noted many times by many people ;)
801      nice description by Jean U. as follows:
802      * allreduce(var) in global_sum.F can be interpreted as
803        reduce(sum) followed by broadcast of sum.
804      * The adjoint of that is
805        sum(adjoint) followed by broadcast(summed adjoint value)
806        or in other words, allreduce(sum, adjoint vars)
807      We were missing the sum(adjoint)!
808      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
809      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
810      The fix should produce 16-digit accuracy between
811      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
812      multi-CPU single-tile (e.g. nSx=1, nPx-2)
813      We'll probably change this yet again shortly
814    o eesupp/src:
815      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
816    o pkg/icefront
817      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
818        specification of addmass array based on a 2D field, which is added
819        at bottommost wet level at each horizontal location.
820    o model/src:
821     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
822     layout; (not always compatible with delX,delY setting; commented out for now).
823    o pkg/exch2:
824     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
825     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
826    
827    checkpoint62e (2010/04/15)
828    o pkg/obcs:
829      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
830    o pkg/dic:
831      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
832        (note: not presently tested in any forward verification exp.)
833       update tutorial_global_oce_biogeo AD output file.
834    o pkg/exf:
835      - account for the variation of albedo as a function of zenith angle
836        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
837    o build_options:
838     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
839    o pkg/dic:
840      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
841      - use binary pickup file for restart;
842      - initialise atmos-CO2 box from dic_pCO2 parameter;
843      - fix multi-threaded.
844    o pkg/rbcs:
845     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
846       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
847     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
848       and update output.txt
849    o pkg/kpp:
850     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
851     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
852       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
853       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
854     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
855       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
856    o pkg/offline:
857      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
858      (bug was added in version 1.10 on 2007-08-23).
859    o pkg/offline:
860      - no need to specify periodicExternalForcing, etc ... to use offline pack
861      - offline input files no longer just single prec --> parameter offlineLoadPrec
862  o verification/lab_sea:  o verification/lab_sea:
863    change to multi-tile setup.    change AD test to multi-tile setup and update all 4 AD output.
864    NOTE: while cost function values remain very similar,    NOTE: while cost function values remain very similar,
865    gradients are very different, although gradient checks are self-consistent    gradients are very different, although gradient checks are self-consistent
866    Should try to get to the bottom of this (cost function summation order?)    Should try to get to the bottom of this (cost function summation order?)
867  o pkg/dic:  o pkg/dic:
868    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
869    a weakness of TAF that drops part of double precision in log10 derivative.    a weakness of TAF that drops part of double precision in log10 derivative.
870      <= changes removed since problem has been fixed in current TAF version 1.9.71
871    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
872  o pkg/ecco:  o pkg/ecco:
873    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
# Line 50  o tools/build_options: Line 906  o tools/build_options:
906      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
907  o pkg/ecco  o pkg/ecco
908    - allow user defined cost function contributions    - allow user defined cost function contributions
909          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
910          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
911    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
912        the two options are complementary.        the two options are complementary.
913  o pkg/smooth  o pkg/smooth
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