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revision 1.1231 by gforget, Wed Feb 17 21:21:05 2010 UTC revision 1.1439 by jmc, Tue May 24 22:45:28 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/obcs:
8      - split header file "OBCS.h" into 4 separated files:
9        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
10       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
11         (contain no conditional statement that depends on OBCS options).
12    o ctrl, cost, grdchk & autodiff pkgs:
13      - make options file more standard (like other {PKG}_OPTIONS.h file but
14        with AD_CONFIG.h); clean-up some of the included header files.
15    o pkg/obcs:
16      - do not mask tracer when applying OB (tracer == 0 could generate problems)
17      - apply tracer OB values to tracer field only at OB location (instead of
18        over a band of OLx width)
19      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
20      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
21        obcs_apply_tloc.F & obcs_apply_sloc.F
22    o obcs in model/src:
23      - call OBCS_APPLY_W only if NonHydrostatic.
24      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
25      - reset dEtaHdt and wVel to zero outside OB interior region ;
26      - leave tracer unchanged outside OB interior region: This has no effect
27        on the solution but just to prevent unrealistic tracer value outside OB.
28      - zero out velocity outside OB interior region: This has no effect on
29        the solution but just to prevent unrealistic velocity outside OB.
30    o obcs and non-lin free-surf:
31       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
32       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
33       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
34       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
35       update results of test-exp. exp4(nlfs).
36    o exp4 (nlfs) test-exp:
37       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
38       with NonLin-FreeSurf); update output.nlfs.txt
39    o obcs and 2d/3d solver norm:
40       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
41       and outside OB interior region (will allow to place OB further inside the
42       domain). Depending on the domain, can affects cg2d-Norm (previous
43       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
44       and cg3d-Norm (previous Norm was computed before canceling OB terms),
45       e.g. in tutorial_plume_on_slope.
46      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
47    o pkg rbcs:
48      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
49      - add capability to apply relaxation to horizontal velocity uVel & vVel.
50    o pkg/grdchk: add gradient check for control variable xx_shifwflx
51    o pkg/shelfice/shelfice_init_fixed.F
52      fix CPP-flag combinations
53    o pkg/seaice: Merge iceage code of Pierre Rampal
54      * update/change/correct ice age calculations
55      * add age updates for pathological cases
56      Probably needs more testing...
57    
58    checkpoint62x (2011/05/13)
59    o pkg/mom_vecinv:
60       high-order vorticity scheme: use interior masks (maskInW & S)
61       to zero-out (outside OB) gradient of vorticity.
62    o verification exp.:
63       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
64       hs94.128x64x5 and seaice_obcs ; update results.
65    o pkg/obcs:
66      fix bug in OBeta for YZ sections in obcs_exf_load.F
67    o pkg/ctrl, pkg/shelfice, and optim:
68      - add new control variable xx_shifwflx (fresh water flux underneath ice
69        shelves). This is almost as tedious as obcs-ctrl, because the
70        variables needs its own mask.
71      - add a cost function term that penalizes the deviation of xx_shifwflx
72        from the first guess (zero) in analogy to other control variables
73    o pkg/shelfice:
74      - start basic adjoint
75    o pkg/ctrl:
76      - remove extra 2D field "for good measure" when initializing in
77        ctrl_set_globfld_[xy/xz/yz].F
78      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
79      - improve error messages in ctrl_set_unpack_*
80    o OBC implementation in momentum:
81       use interior masks (maskInC,W & S) in momentum S/R:
82       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
83       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
84       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
85       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
86       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
87        (and also with Leith/Smagorinsky harmonic-viscosity).
88       Update output of experiment dome and exp4 (+nlfs).
89    o exp4 test-exp:
90      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
91        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
92        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
93        time-varying OB at Western-side for wVel (NonHyd); update output.
94      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
95        and biharmonic-viscosity ; also use prescribed time varying OB.
96    o pkg/obcs:
97      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
98    o model/src:
99      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
100      - initialise startTime & nIter0 with unlikely values: allows to set one
101        from the other without ambiguity.
102    o seaice_obcs test-exp.:
103      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
104    o pkg/obcs:
105      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
106        no longer needed with maskInC,W,S in pkg/generic_advdiff.
107    o pkg/seaice:
108      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
109        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
110      - fixed bug in the initialization of sea ice salinity variable HSALT
111        in seaice_init_varia.F  (removed dependence on ICE2WATR)
112    o fizhi-cs test exp.:
113       switch reference output convention for these 2 non-standard test-exp,
114        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
115          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
116       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
117    o model/inc:
118      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
119        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
120    o pkg/seaice:
121      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
122    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
123      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
124        and initial HSALT
125    
126    checkpoint62w (2011/04/26)
127    o pkg/mom_fluxform:
128      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
129      - use parameter "sideDragFactor" in no-slip BC side-drag part.
130      - update output of exp. global_ocean.90x40x15
131    o pkg/mom_vecinv:
132      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
133    o update seaice exp.:
134      use more consistent parameter values (remove "backward compatability only":
135       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
136      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
137       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
138    o update test-exp global_ocean.90x40x15:
139      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
140      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
141      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
142      o turn on zStar & viscA4 in standard set-up (dir input/)
143        and update output files: output.txt & output.dwnslp.txt
144    o new AD-test experiment: obcs_ctrl
145      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
146    o pkg/dic:
147      fix two bugs in handling water vapour pressure in carbonate chemistry
148      and air-sea fluxes. Found by Val Bennington and Galen McKinley
149      (add DIC Option = WATERVAP_BUG to recover old results)
150      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
151    o adding allowInteriorFreezing option to check for water below freezing point
152      at depth and bring the negative heat anomaly to the surface level
153    o pkgs _fields_load:
154      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
155      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
156        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
157        rbcs to get interpolation weights and time reccord number.
158      - fix multi-threading in aim_fields_load.F
159      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
160    o external_fields_load:
161      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
162       interpolation weights) to use in a periodic time-series ; do not divide by
163       time-step to convert to integer:
164       - this fixes case where externForcingPeriod is not multiple of time-step
165          (Thanks to Christopher L. Wolfe)
166       - this fixes case where externForcingPeriod is an odd multiple of time-step
167         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
168      store index of time-record which is currently loaded:
169       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
170       - needed for the adjoint but not yet used because of extensive recomputations;
171         (to be fixed soon)
172    
173    checkpoint62v (2011/04/02)
174    o verification/1D_ocean_ice_column added to test Ian Fenty's
175      pkg/seaice_growth.F modifications for improving sea ice code differentiability
176    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
177      (new velocity statistics after changing maskInW & maskInS definition)
178    o pkg/generic_advdiff with OBCS:
179      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
180      equivalent to assumption of no tracer gradient outside the OB region.
181      This will affect the results if using obcs+biharmonic diffusion.
182      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
183    o pkg/obcs:
184      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
185      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
186      in Interior region. No impact on solution but affects Velocity monitor stats.
187    o pkg/ptracers (adjoint)
188      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
189      tape file for each tracer
190    o model/inc/src and pkg/autodiff: add parameters that allow to turn
191      of parts of the adjoint code at run time. For now, there are only
192      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
193      parameters are set in data.pkg.
194      This is the lazy coward's version of doing this, but still useful for
195      debugging. In order to do it right, everything needs to be moved to
196      pkg/autodiff.
197    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
198      the end; this fixes the adjoint balancing code for open boundaries.
199    o pkg/ctrl:
200      - change behavior of xx_${varname}period to be analogous to exf-conventions:
201        xx_${varname}period =   0.,  means time-independent control part
202        xx_${varname}period = -12., means one-year-periodic monthly control part
203      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
204        clean up ctrl_init a little, remove unused variables
205      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
206      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
207    
208    checkpoint62u (2011/03/15)
209    o model/src:
210      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
211        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
212      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
213        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
214    o pkg/ctrl/obcs/ecco:
215      - remove obsolete, unused, and partially broken code:
216        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
217        ALLOW_CTRL_OBCS_BALANCE
218      - put a stop statement into ecco/cost_obcsvol.F, but also add
219        cost_obcsvol to ecco_ad_diff.list
220    o pkg/ecco: fix counting cost function contributions for obcs (code
221      by Matt M.) and diffkr for diagnostics
222    o pkg/ecco, pkg/ctrl, pkg/grdchk:
223      add cost penalty terms for initial uvel, vvel, eta controls
224      and I/O for prior error files
225    o pkg/mdsio:
226       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
227       (new argument) to check for tiled file in mdsioLocalDir : this fix the
228       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
229    o pkg/ctrl:
230     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
231       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
232       unused and superfluous variables
233     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
234    o pkg/ecco
235     - enable adjoint of Stevens OB
236    o pkg/ctrl/ecco/grdchk:
237      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
238        Fortunately, we do not have any tests for the numerous cpp-flagged
239        option of "obcs as control parameters" so we will never know
240        if this is an improvement (but at least now things compile).
241      - remove an obsolete initialization from ecco_cost_init_barfiles.F
242      - fix some problems within never used ifdefs to make the code compile
243    o pkg/obcs:
244     - Refine Interior mask definition to work with more complex OB (e.g.
245       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
246       read in Interior mask from file. Check if Interior mask is consistent
247       with OB list of indices.
248    o pkg/seaice
249     - beginning code for a seaice tracer package,
250       but currently only used for seaice age: SEAICE_AGE
251       SEAICE_num = 4
252       iTracer = 1: area-weighted ice age
253               = 2: volume-weighted ice age
254               = 3, 4: template for one-year vs. multi-year ice
255       data.seaice has new namelist SEAICE_PARM03 for arrays related to
256       SEAICE_num
257    
258    checkpoint62t (2011/03/05)
259    o pkg/obcs:
260     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
261       then normal component. This ensures that the normal component is set
262       correctly even when it conficts with tangential setting from an other OB.
263       Affects results of test-experiment seaice_obcs: update the output.txt
264    o pkg/obcs:
265     - add code to monitor statistics of dynamical fields at OB.
266     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
267       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
268       - change default: balance the Net inflow through all OB (instead of balancing
269         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
270     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
271       to match Nortern OB inflow (OBCS_balanceFacN=0).
272    o pkg/seaice:
273     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
274    o pkg/seaice (seaice_growth v 1.113):
275     - reverting seaice_growth to v 1.111 in order to have code with exact bit
276       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
277       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
278       runtime flag SEAICEareaFormula is kept but is inactive
279    o model/src:
280     - add new param to scale curvilinear grid distance and area when using
281       a different sphere radius from the grid-files.
282     - test/check multi-threads EXCH applied to local variable (cg2d_x)
283    o adjoint:
284     - enable adjoint of Stevens OB
285     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
286       (a bit delicate because of potentially modified adj. common block structure;
287       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
288    
289    checkpoint62s (2011/02/15)
290    o pkg/seaice (seaice_growth v 1.112):
291     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
292       computing the ice cover tendency from effective thickness tendencies. Include
293       Ian Fenty's formula.
294     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
295       SEAICEareaFormula.
296     - simplify notations for the various d_HEFF/d_AREA terms.
297    o pkg/gmredi:
298     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
299       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
300       add a verification test-run (front_relax.bvp) to test GM_useBVP.
301    o pkg/seaice (seaice_growth v 1.111):
302     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
303     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
304       also melt ice.
305    o pkg/seaice:
306     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
307     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
308    o pkg/cheapaml:
309     - from Nico Wienders: New version of this package.
310    o pkg/flt:
311     - add CPP options to prevent floats to re-enter the opposite side of
312       a periodic domain (default: keep periodicity)
313    o pkg/gmredi:
314     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
315       (needed for multi-dim advection).
316     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
317    o model/src:
318     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
319    o tutorial_tracer_adjsens
320     - extend to NLFS and replace maskC by hFacC
321       (change reference output accordingly)
322    
323    checkpoint62r (2011/01/24)
324    o testreport:
325     - add option -deloutp (-do) to remove output file after successful run
326     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
327       extract exact list of procs from this file ; adjust COMMAND by
328       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
329    o pkg/ecco: replace old ineffective way of penalizing deviations from
330      first guess (of obcs) with code by Matt Mazloff
331    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
332      exf/cal
333      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
334        and handle case of obcs?period == 0
335        Not affected by these changes: There is still an inconsistency in
336        the computation of start/endrec for the obcs variables for ALLOW_CAL
337        defined (see comment by Menemenlis, 7-Mar-2003)
338      - make S/R ctrl_get_gen_rec return something meaningful even if
339        ALLOW_CAL is not defined
340      - ctrl_getobcs?: simplify code so that it does not need to use
341                       S/R exf_swapfields
342    o testreport:
343       allow to test MPI with different number of processors for each experiment:
344       create file "SIZE.h.mpi" in each build dir.
345       Note: update of "-command" argument not yet implemented.
346    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
347      alleviate the need for additional 3D tapes when using
348      the non-inear free surface in the adjoint. This is done
349      by adding an 'update' of hfacc etc. to their current
350      value at the beginning of forward_step.F.
351    o pkg/seaice
352      seaice_lsr: move stress-divergence computations out of outer pseudo-
353      timestepping loop
354    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
355      up, so that the calls of the ctrl_* subroutines are really at the end
356      of the routine.
357    o pkg/gmredi:
358      allow to specify a 2-D horizontal map and a 1-D vertical profil
359      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
360    o pkg/seaice:
361      move lsr iterations from seaice_dynsolver to seaice_lsr.
362    o pkg/seaice:
363      reduce memory footprint of seaice mutldim advection tapes,
364      by using a 2D tape independent of the generic_advdiff ones,
365      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
366    
367    checkpoint62q (2010/12/29)
368    o model/src:
369      - check horizontal grid-spacing for unset or zero/negative values.
370      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
371    o pkg/flt:
372      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
373      - precision of input and output files set according to readBinaryPrec
374        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
375      - initial float position from tiled file was not converted to index space
376        (looks like a bug): fixed to make it similar to initial pos. global file.
377    o global_ocean.cs32x15:
378       change SIZE.h of AD set-up to get same tiling as with MPI.
379       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
380    o model/src:
381       add flag to control printing of domain fields (bathymetry, hFac ...) in
382       ini_mask_etc (call to plot_fieds_xy*).
383    o pkg/thsice:
384       if useEXF, some forcing fields are not valid in overlap: fixed by computing
385       over the interior only + apply EXCH at the end (like with SEAICE advection).
386    o pkg/mdsio:
387      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
388        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
389      - change barrier call for safe multi-threads access to 3-D shared buffer.
390      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
391      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
392        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
393    o pkg/flt:
394      - add fourth-order Runge-Kutta integration
395      - add basic exch2 support (only 1 facet supported so far!)
396    o pkg/mdsio+rw:
397      new S/R to read local (or tile independent) vector (read counterpart of
398       mds_writevec_loc, and front-end write_glvec_rl/rs).
399    o global_ocean.cs32x15: additional input_ad.seaice experiment
400        that uses pkg/seaice rather than pkg/thsice.
401        (using multidim advection for seaice)
402    o towards more F95 syntax for array specification in namelist:
403      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
404        of all verification experiments.
405           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
406          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
407      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
408    o global_ocean.cs32x15: additional input.seaice experiment
409        that uses pkg/seaice rather than pkg/thsice.
410    
411    checkpoint62p (2010/12/17)
412    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
413        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
414    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
415        allow for use of multim. advection in seaice adjoint.
416    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
417      - first attempt to close budgets by taking into account the freshwater
418        flux implied by the sublimation of snow and ice. So far only the
419        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
420        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
421    o eesupp/src:
422      new S/R with new option (NML_EXTENDED_F77) to change array specification
423      from F95 standard to commonly accepted extended F77 form.
424      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
425      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
426      for less tolerant f77 compiler (e.g., pgf77, g77).
427    o globalFiles:
428      commented out in parameter file "data" since it's not safe with MPI
429      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
430      in this case); no longer commented out in restart test (tst_2+2).
431    o add adTapeDir to specify a special directory where adjoint tapes are
432      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
433      and cannot be used together with mdsioLocalDir.
434    o nesting pkgs:
435      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
436      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
437      - add parameter files + utils dir + output from short run on beagle.
438    o pkg/seaice:
439        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
440    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
441      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
442    
443    checkpoint62o (2010/11/25)
444    o pkg/exf:
445      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
446    o pkg/seaice:
447      - seaice_ocean_stress: split a loop for better vectorization of the
448        adjoint code
449      - seaice_growth.F: fix bug in conservation of freshwater connected to
450        capping of heff, put contribution into d_HEFFbyNEG
451      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
452        by something more sensible (parameters that are what their name implies)
453      - change some defaults, so that by default exf-parameters are used for
454        things like rhoAir, cpAir,latent/sensible heat parameters, in order
455        to reproduce the old results, many data.seaice now contain funny values
456        for cpAir and latent heat of sublimation
457    o packages_readparms.F: move exf_readparms up in line so that
458        exf-parameters are visible for other packages (e.g. seaice)
459    o debugMode & debugLevel=2:
460      - differentiate between debugMode & debugLevel=2:
461        debugMode: controls printing of debug messages (sequence of S/R calls).
462        debugLevel: controls printing of algorithm intermediate results and stats.
463      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
464        => allows to print debug-stats without all sequence of call messages.
465      - switch control of debug print from debugLevel to debugMode in many S/R.
466    o pkg/obcs (obcs-sponge):
467        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
468        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
469    o pkg/generic_advdiff:
470      - record overlap minimum size for each advection scheme;
471      - refine criteria on overlap minimum size;
472      - check and stop (in gad_check) if overlap size is too small.
473    o pkg/obcs:
474      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
475        once, in ptracers_implicit.F)
476      - with seaice: remove test on empty file name in obcs_apply_seaice (always
477        apply OB values when tile has OB)
478    o model/src, coriolis setting:
479      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
480        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
481        files (selectCoriMap=3) with any grid.
482      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
483    o pkg/seaice/seaice_growth.F:
484        a few cosmetic changes that reduce the number of lines of code
485    o pkg/obcs: add boundary conditions following Stevens (1990)
486      - the code follows old MOM/NAOSIM code
487      - so far it is only implemented for the eastern and western boundaries
488        and NOT for pTracers
489    o pkg/rbcs:
490      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
491        beginning of the first rbcs forcing period.
492      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
493        offline package, i.e., one file per time, labeled by iteration number;
494        deltaTrbcs sets the timestep with which the data was generated;
495        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
496      - rbcsForcingCycle=0 makes forcing non-cyclic.
497      - make arithmetic safe for negative times and odd forcing periods.
498    
499    checkpoint62n (2010/11/09)
500    o pkg/seaice:
501        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
502    o pkg/obcs:
503       New S/R to copy tracer value from the OB location to narrow band region
504        (width = same as overlap) beyond the OB: preserve OB value (needed for
505        high-order scheme) which were overwritten by EXCH call if in overlap
506        region. Applied to theta, salt, ptracer and advected seaice variables.
507       With seaice: use maskInC in similar way as in gad_advection.F,
508        in seaice_advection.F and advect.F.
509       Update output of experiment seaice_obcs and change exp4 to test OBCS with
510        4th order Adv.Scheme. for pasive salt and ptracer.
511    o tools/genmake2:
512      - when looking for an optfile (not specified), only search for Fortran compiler
513        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
514      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
515        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
516      - set default for CPP to "cpp -traditional -P" (was the case without specifying
517        an optfile, but otherwise default was just "cpp".
518      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
519      - when "CC" is not set in the optfile, look for possible C compiler
520        (instead of just setting CC=cc)
521      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
522        => add a ".F" to ".o" rule for source files with no "#include" (such as
523           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
524      - move gfortran before g77 in list of possible Fortran compiler (consistent
525        with reference compiler switch from g77 to gfortran)
526    o pkg/seaice:
527      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
528        seaice_check that stops the model, when the CPP flag is used.
529      o seaice_growth.F: make capping of ice volume conserving by returning the
530        capped ice as freshwater to EmPmR. This does not change the verification
531        experiments but will change runs where the capping is acutally active
532    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
533      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
534         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
535         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
536    o tools/genmake2:
537      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
538      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
539      - clean previous genmake log files before anything else.
540      - change Makefile to remove testreport log files (*.tr_log) and genmake log
541        files only with "CLEAN" target (instead of "Clean");
542    o pkg/generic_advdiff:
543      Change OBCS in multiDim advection (gad_advection.F):
544       Use maskInC to prevent intermediate update of tracer-field in OB regions,
545       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
546       which were applying future time-step OB values.
547      This way, all explicit calculations use current-time-step OB values
548       (simpler and more consistent).
549      Affects results when set-up uses time-varying OBC and multi-dim advection;
550       update output of experiment seaice_obcs.
551    o pkg/seaice:
552      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
553       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
554         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
555      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
556       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
557       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
558    o pkg aim (2010/10/26):
559      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
560        formulation with obliquity, eccentricity, ... as run-time parameters,
561      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
562        upward shortwave radition at the surface (all-sky and clear-sky).
563    o pkg/obcs:
564      - writing sections with globalFiles=T does not work: switch to tiled-files
565        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
566      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
567      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
568    
569    checkpoint62m (2010/10/21)
570    o pkg/seaice: vectorize seaice_solve4temp.F
571      - move iterations loops outside of i/j-loops
572      - requires 2D arrays for TB and effConduct
573      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
574        modified in this routine
575      - a little bit of clean up, adjusting indentation, etc.
576      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
577        performance and '**TWO' by '**2' (because TWO is a float),
578        replaced ONE, ZERO
579    o eesupp/src:
580       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
581    o pkg/seaice/seaice_growth.F
582      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
583      merging process. The merged routine has two branches, and one activates the 'evolution'
584      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
585      In summary, here is what the '10/10 revision' did consist of
586        part 1: seaice_growth.F revisions 1.71 to 1.75
587          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
588            The emphasis here was on improving readability (e.g. by trying to use meaningful
589            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
590        part 1.5:
591          - revising the lab_sea experiment to make it a more useful (i.e. stable
592            and representative of an actual model run). This was done by generating a
593            (winter) pickup to start from, switching back the main experiment dynamic
594            solver from evp to lsr, having one of the experiments use the free drift solution.
595        part 2: seaice_growth.F revisions 1.76 to 1.85
596          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
597          - Sorting out the various fields units and sign (set early on and reset at the end)
598            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
599            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
600          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
601            and simplifying logical expressions to further improve readibility.
602        part 3: seaice_growth.F revisions 1.86 to 1.89
603          - Re-organize the blocks of code more logically.
604          - Merging the '_if.F' pieces that add something new.
605    o pkg/thsice:
606      - vectorize thsice_solve4temp and thsice_get_exf.
607        Problem: thsice_solve4temp has an unvectorizable statement that
608        might also be problematic for TAF
609      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
610        does not change the verifcation experiment, but will change all
611        experiments that have this flag undefined (not tested in verification);
612        a little reorganization to save a few 2D fields and recomputations
613      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
614      - 2nd step:  fix some store dirs
615        o seems to work somewhat, i.e. using ifort but not g77
616        o likely cause are incomplete init. or recomputation
617        o start verification/global_ocean.cs32x15/input_ad.thsice
618    o pkg/obcs: add support for exch2
619      - the position of the boundary and prescribed values are specified using
620        a global domain with exch2 facets stacked
621        - in x for N,S boundaries (like W2_mapIO=-1)
622        - in y for E,W boundaries (so E,W boundaries do not overlap)
623    o pkg/mdsio: add support for writing global sections with exch2
624        file layout is as for obcs described above:
625        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
626        - for y-z sections, facets are stacked in y
627    o pkg/thsice:
628       - change a few routines for better vectorization: thsice_albedo.F,
629         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
630         not affected, but in particular the latter routine has changed
631         dramatically (not necessarily easier to read now).
632       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
633       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
634    o verification/lab_sea:
635      - overhaul of the forward model experiments. The main motivation
636        for this revision is that lab_sea has proven quite fragile (when
637        changing the sea-ice code, and switching platforms) to a point
638        when failures were very hard to attribute to specific code problems.
639      - the suspected reason for this fragility is noise amplification by evp so,
640        to start with, we decided to replace evp with lsr in the main experiment.
641      - the input.lsr experiment thus became obsolete and was removed.
642      - it was replaced with the input.fd experiment that uses an
643        analytical "free drift" solution as the ice velocity field.
644      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
645        will hopefully allow us to discriminate problems due to dynamic solvers
646        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
647        us to test additional options, along with the salt plume package.
648      - Finally a pickup was generated (at the end of a one year run) to
649        make the tests more representative of an actual model run. Previously
650        the tests starting point was a 1m thickness of ice everywhere.
651    o pkg/seaice:
652      - introducing S\R seaice_freedrift.F that compute the
653        analytical solution to an approximate ice momentum
654        equation (i.e. the simple stress/coriolis balance).
655      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
656        of the free drift velocity field, and enable its use.
657        To actually use the free drift solution as the model ice
658        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
659    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
660    
661    checkpoint62l (2010/10/04)
662    o pkg/seaice:
663      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
664      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
665       version (with USE_ORIGINAL_SBI undef);
666    o add hooks for new packages OASIS, the package will follow
667      (hooks exclude the seaice pkg for now)
668    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
669      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
670      rather than mdsio_readvector.F/mdsio_writevector.F, within
671      adread_adwrite.F to read/write adjoint-related tapes to disk.
672    o eesupp and pkg/mdsio: ALLOW_WHIO
673      Option to write/read 2D fields to files including tiles halos.
674      The main purpose is for adjoint related "tape I/O".
675      The secondary purpose is for debugging phases.
676      A word on those rather specifically intended purposes.
677      The code was meant to be stripped down to the bare minimum.
678      Typically, there is a unique and basic mapping to the global
679      buffer (tile by tile, then proc by proc, then level by level), and
680      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
681      meant to generate user friendly outputs of various shapes and forms.
682      Rather it is intended, for the knowledgeabale developers,
683      to be largely independent of the many mdsio options, to allow
684      outputs of tiles+halos in debugging phases and in adjoint runs,
685      and to allow some flexibility in tuning (adoint) I/O depending on each
686      file system behavior. With regard to tuning, most of the potential knobs
687      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
688      to specify directories, to specify the typical size of I/O calls, etc.)
689      are not yet included, and will be added if they prove useful.
690    o pkg/seaice:
691       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
692    o pkg/seaice:
693       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
694       code (seaice_budget_ice_if.F) which enable to recover old standard
695       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
696       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
697    o model/src (rStar):
698       use simple average (not area weighted) of rStarFac at U,V point when using
699       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
700       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
701    
702    checkpoint62k (2010/09/17)
703    o adjoint
704       * changed verification/global_ocean.cs32x15 ; adjoint now tests
705         Adams-Bashforth 3 + NLFS + RSTAR
706       * some more modifs required for ECCO-GODAE v4
707    o pkg/seaice
708       add SEAICE_AGE_VOL option to use volume instead of area for
709       integrating SEAICE_AGE
710    o model/src:
711       first check-in of sigma & hybrid-sigma coordinate code ; also includes
712       non-linear free-surface parts ; but pressure-gradient not yet coded.
713    o pkg/ptracers:
714       option for ptracer to convert Salt Relax into additional EmP.
715        tested in exp. global_ocean.90x40x15.dwnslp (update output)
716    
717    checkpoint62j (2010/08/25)
718    o pkg/ggl90:
719       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
720    o pkg/dic: car_flux.F, phos_flux.F
721      - reduce number of exp-calls in order to improve performance
722      - clean up a little (replace fields by their macros, etc., fix
723        typo in CPP-flag)
724    o pkg/ggl90: minor changes
725      - GGL90diffKrS was removed --> always use GGL90diffKr
726      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
727      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
728        (commented out for now)
729      - change in max/min operations to ensure that smoothing is ok
730      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
731      - always use diffKrNrT as background profile (i.e. never use diffKr field)
732    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
733    o pkg/dic:
734      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
735        vectorization
736      - small bug fix in insol for the unlikely case of a cartesian grid
737      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
738        + now vectorize, which also removes adjoint recomputations;
739        + replace integer maksp1 by _RL maskp1
740        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
741    
742    checkpoint62i (2010/07/21)
743    o pkg/flt:
744      - with OBCS: stop floats which enter the OB region
745    o model/src:
746      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
747        for implicit vertical advection.
748    o pkg/seaice:
749     - account for melting in seaice age evolution.
750     - remove double counting of seaice ridging effect on seaice age.
751    
752    checkpoint62h (2010/06/18)
753    o pkg/exch2:
754     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
755    o tools/genmake2
756      - remove "-pdefault" option: redundant with the use of "packages.conf";
757      - remove file pkg/pkg_default : set the default as a pkg group
758        ("default_pkg_list") defined in pkg/pkg_groups;
759      - fix for case pkg/pkg_depend is missing (was hanging before);
760      - add option "-pgroups" to specify a different pkg_groups than the default.
761    o verification/adjustment.cs-32x32x1:
762       add a "minimal" set-up test (code_min & input_min) which only compiles
763       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
764    o tools/genmake2
765      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
766      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
767    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
768      files are nearly the same anyway.
769      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
770       - redefinition of tau(i,i) (by a factor of ustar)
771       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
772       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
773       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
774       - replace
775         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
776         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
777         by
778         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
779         (changes results)
780       -> exf_bulkformulae v1.22,
781          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
782          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
783                    output.txt 1.63
784           offline_exf_seaice: output.seaicetd.txt 1.7
785           seaice_obcs: output.txt 1.10)
786      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
787       -> exf_bulkformulae v1.23,
788          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
789          and global_ocean.cs32x15.icedyn (only 11 matching digits)
790      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
791    o adjoint of exch-1:
792     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
793       (note: was already like this when using EXCH-2) and remove flow dir
794       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
795     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
796     - update pkg/exch2 diff list.
797    
798    checkpoint62g (2010/05/19)
799    o eesupp/src (exch-1):
800     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
801       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
802       (renamed to exch1_*rx_cube.F).
803     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
804       to call new exch1 S/R ; update Makefile and .cvsignore.
805     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
806       exch2_xy_rx later)
807      Note: after updating your code, need to run "make clean" in eesupp/src
808    o test experiment bottom_ctrl_5x5:
809       new output_adm.txt with fewer grdchk & less monitor output.
810    o model/src:
811      remove the call to ini_cori in initialise_varia.F (just keep the usual one
812       in initialise_fixed.F). More consistent with coriolis & horizontal grid
813       beeing treated in the same way (ini_grid is not called a 2nd time).
814    o pkg/exf:
815      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
816      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
817      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
818      - cosmetic changes to exf_bulkformulae.F to make it look more like
819        exf_bulk_largeyeager04.F
820    o eesupp/src (exch-1):
821      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
822      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
823        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
824        (even without using MPI).
825      - Message mode: move RecvAck setting (indicator of buffer being ready)
826        from send_put to recv_get S/R (was useless before, but not sure if
827        it's much more useful now);
828      - Switch the order of sync: MPI-proc 1rst and then threads;
829      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
830      - fix AD code for communication mode ='get' (but not used).
831    o model/src:
832      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
833      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
834    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
835    o pkg/ctrl: require a specific set of control variables and exf-flags for
836      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
837    o model/src:
838     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
839       1rst forward sweep, to avoid over-writing output files during recomputations
840       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
841     b) 2nd version:
842      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
843      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
844         writePickupAtEnd) + seaice & ptracers output;
845      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
846    o model/src:
847      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
848    o pkg/exch2:
849      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
850      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
851    o pkg/autodiff & exch2:
852      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
853      (for now, only if ALLOW_EXCH2 is defined).
854    o pkg/autodiff:
855      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
856        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
857       + clean-up comments (_RS is not always real*4)
858      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
859      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
860        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
861    o testreport (AD-tests):
862      no longer link files from dir "../input" (1rst link files from
863      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
864    
865    checkpoint62f (2010/04/29)
866    o model/src/the_main_loop.F:
867      adjust store directives for seaice evp and multicategory according to
868      pkg/ecco/the_main_loop.F
869    o adjoint:
870      global_sum_ad was incomplete (noted many times by many people ;)
871      nice description by Jean U. as follows:
872      * allreduce(var) in global_sum.F can be interpreted as
873        reduce(sum) followed by broadcast of sum.
874      * The adjoint of that is
875        sum(adjoint) followed by broadcast(summed adjoint value)
876        or in other words, allreduce(sum, adjoint vars)
877      We were missing the sum(adjoint)!
878      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
879      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
880      The fix should produce 16-digit accuracy between
881      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
882      multi-CPU single-tile (e.g. nSx=1, nPx-2)
883      We'll probably change this yet again shortly
884    o eesupp/src:
885      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
886    o pkg/icefront
887      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
888        specification of addmass array based on a 2D field, which is added
889        at bottommost wet level at each horizontal location.
890    o model/src:
891     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
892     layout; (not always compatible with delX,delY setting; commented out for now).
893    o pkg/exch2:
894     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
895     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
896    
897    checkpoint62e (2010/04/15)
898    o pkg/obcs:
899      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
900    o pkg/dic:
901      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
902        (note: not presently tested in any forward verification exp.)
903       update tutorial_global_oce_biogeo AD output file.
904    o pkg/exf:
905      - account for the variation of albedo as a function of zenith angle
906        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
907    o build_options:
908     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
909    o pkg/dic:
910      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
911      - use binary pickup file for restart;
912      - initialise atmos-CO2 box from dic_pCO2 parameter;
913      - fix multi-threaded.
914    o pkg/rbcs:
915     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
916       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
917     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
918       and update output.txt
919    o pkg/kpp:
920     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
921     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
922       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
923       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
924     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
925       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
926    o pkg/offline:
927      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
928      (bug was added in version 1.10 on 2007-08-23).
929    o pkg/offline:
930      - no need to specify periodicExternalForcing, etc ... to use offline pack
931      - offline input files no longer just single prec --> parameter offlineLoadPrec
932    o verification/lab_sea:
933      change AD test to multi-tile setup and update all 4 AD output.
934      NOTE: while cost function values remain very similar,
935      gradients are very different, although gradient checks are self-consistent
936      Should try to get to the bottom of this (cost function summation order?)
937    o pkg/dic:
938      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
939      a weakness of TAF that drops part of double precision in log10 derivative.
940      <= changes removed since problem has been fixed in current TAF version 1.9.71
941      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
942    o pkg/ecco:
943      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
944      update all 4 lab_sea AD output.
945    
946    checkpoint62d (2010/03/22)
947    o build_options:
948      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
949    o remove unbalanced quote (single or double) in commented line of source code
950      (may cause some warning with some preprocessor/makedepend versions).
951    o pkg/seaice:
952      fix seaice_model.F for adjoint (gael) and update AD results of experiments
953       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
954    o testreport:
955      add option '-runonly' (short: '-ro') to just do the run part (without make).
956    o eesupp: remove JAM communication code (obsolete).
957    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
958      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
959      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
960      (update also the output).
961    
962    checkpoint62c (2010/03/02)
963    o tools/build_options :
964       move (some) old optfiles from build_options/ to build_options/unsupported/
965  o model/src and pkg/exf  o model/src and pkg/exf
966     surface relaxation -- separating data and data.exf options     surface relaxation -- separating data and data.exf options
967     The point is to ensure that we specify the surface relaxation     The point is to ensure that we specify the surface relaxation
# Line 18  o tools/build_options: Line 976  o tools/build_options:
976      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
977  o pkg/ecco  o pkg/ecco
978    - allow user defined cost function contributions    - allow user defined cost function contributions
979          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
980          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
981    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
982        the two options are complementary.        the two options are complementary.
983  o pkg/smooth  o pkg/smooth
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