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revision 1.1248 by jmc, Mon Apr 12 20:29:44 2010 UTC revision 1.1457 by heimbach, Fri Jun 17 13:33:55 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 adjoint monitor:
8     - Add adjoint monitor output for packages exf, seaice
9       and update relevant testreport output
10    o pkg/seaice:
11     - re-order diags inits so that they appear in order in available_diagnostics.log
12     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
13       area/heff/hsnow preceeding thermodynamic growth/melt.
14     - modified diag: SIdA; output actual effect, as the description states.
15     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
16     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
17       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
18        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
19     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
20     - added diagnostics for seaice genereic tracers (SItr*).
21     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
22     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
23    o pkg/diagnostics:
24      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
25      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
26        (was _RL, now integer) with option = 0 to retrieve all levels.
27      - add pieces of code to compute velocity potential at each level (new diagnostics
28        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
29        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
30    o model/src (rStar):
31      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
32        affect solution only if z* with full pressure in EOS;
33        update output of test-exp global_ocean.90x40x15.
34    o pkg/seaice:
35      - introduce siEps=1e-5 parameter
36      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
37      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
38      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
39        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
40        as well as ice cover age and ridging index (attached to AREA).
41        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
42        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
43        Up to SItrMaxNum=3 tracers can be used simultaneously.
44    o pkg/salt_plume:
45      -introduce SPsalFRAC run time parameter that sets the fraction of the
46       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
47       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
48    o model debug options:
49      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
50        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
51      - Refine debug-msg printing selection (3 new levels):
52        debugMode  : controls printing of debug messages (sequence of S/R calls).
53        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
54         debLevZero =  0 ; /* level of disabled aux. msg printing */
55         debLevA =  1 ; /* level of minimum  aux. msg printing */
56         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
57         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
58         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
59         debLevE =  5 ; /* level of extensive debug printing */
60        New debugLevel default: with default debugMode value (=F),
61          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
62          and if debugMode=T, default debugLevel = 4 (debLevD).
63        Relation with previous settings:
64         debLevB (=2) corresponds to former debLevA (=1)
65         debLevD (=4) corresponds to former debLevB (=2)
66        Note:
67         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
68         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
69            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
70      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
71        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
72    o pkg/obcs:
73      - change OBCSfixTopo default from True to False (should not change the results);
74        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
75    o pkg/thsice:
76      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
77        2nd layer seaice sublimation (unlikely to happen)
78      - use Interior mask for OBCS in thsice_advection.F (similar to what is
79        done in gad_advection & seaice_advection).
80    o adjoint:
81      bug fix spotted by Gael Forget:
82      seaice_advection and thsice_advection still had
83      legacy CPP options to avoid CS corner updates for adjoint
84    o pkg/seaice:
85      => Change some of the defaults (2011/05/29):
86         - change SEAICEuseFluxForm default (from False to True)
87         - change DIFF1 default (from 0.004 m/s to 0. m/s)
88         And print warnings if DIFF1 is not set in data.seaice and centered
89          avection scheme is used without any diffusion.
90      also:
91      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
92      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
93      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
94        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
95        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
96      update results of test exp.:
97         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
98             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
99             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
100         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
101         seaice_obcs: output (SEAICEuseFluxForm=T)
102      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
103          for standard fwd & AD lab_sea tests (to keep the same output).
104    o pkg/seaice/seaice_growth.F:
105      - use Ian Fenty's capping formulas for actual ice
106      thickness thoughout EVOLUTION branch.
107      - put treatment pathological case #2) in CPP brackets
108      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
109      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
110    o pkg/seaice:
111      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
112      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
113      also pass fac as a param, which can be 1. (to update the tendency
114      field) or the time step (to update the field itself).
115      - seaice_advdiff.F: for multidim, call seaice_diffusion with
116      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
117      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
118      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
119      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
120    o pkg/seaice:
121      diffusion with centered advection scheme (diffus.F & advect.F):
122      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
123        to just compute the laplacian of input-field.
124      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
125      - fix flux-form version in diffus.F to conserve tracer.
126      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
127       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
128    
129    checkpoint62y (2011/05/26)
130    o pkg/seaice:
131     - seaice_growth.F : in EVOLUTION branch, always include
132       a_QSWbyATM_cover in qnet (as it should be).
133     - verification/global_ocean.cs32x15 : update results accordingly
134       (output.seaice.txt output_adm.seaice.txt).
135    o pkg/seaice + obcs:
136     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
137       equivalent of assuming no tracer gradient outside the OB region.
138       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
139     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
140       after changes above);
141     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
142       only at OB location (instead of over a band of OLx width).
143    o pkg/seaice:
144     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
145       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
146    o pkg/obcs:
147      - split header file "OBCS.h" into 4 separated files:
148        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
149       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
150         (contain no conditional statement which depends on OBCS options).
151      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
152        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
153    o ctrl, cost, grdchk & autodiff pkgs:
154      - make options file more standard (like other {PKG}_OPTIONS.h file but
155        with AD_CONFIG.h); clean-up some of the included header files.
156    o pkg/obcs:
157      - do not mask tracer when applying OB (tracer == 0 could generate problems)
158      - apply tracer OB values to tracer field only at OB location (instead of
159        over a band of OLx width)
160      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
161      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
162        obcs_apply_tloc.F & obcs_apply_sloc.F
163    o obcs in model/src:
164      - call OBCS_APPLY_W only if NonHydrostatic.
165      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
166      - reset dEtaHdt and wVel to zero outside OB interior region ;
167      - leave tracer unchanged outside OB interior region: This has no effect
168        on the solution but just to prevent unrealistic tracer value outside OB.
169      - zero out velocity outside OB interior region: This has no effect on
170        the solution but just to prevent unrealistic velocity outside OB.
171    o obcs and non-lin free-surf:
172       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
173       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
174       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
175       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
176       update results of test-exp. exp4(nlfs).
177    o exp4 (nlfs) test-exp:
178       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
179       with NonLin-FreeSurf); update output.nlfs.txt
180    o obcs and 2d/3d solver norm:
181       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
182       and outside OB interior region (will allow to place OB further inside the
183       domain). Depending on the domain, can affects cg2d-Norm (previous
184       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
185       and cg3d-Norm (previous Norm was computed before canceling OB terms),
186       e.g. in tutorial_plume_on_slope.
187      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
188    o pkg rbcs:
189      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
190      - add capability to apply relaxation to horizontal velocity uVel & vVel.
191    o pkg/grdchk: add gradient check for control variable xx_shifwflx
192    o pkg/shelfice/shelfice_init_fixed.F
193      fix CPP-flag combinations
194    o pkg/seaice: Merge iceage code of Pierre Rampal
195      * update/change/correct ice age calculations
196      * add age updates for pathological cases
197      Probably needs more testing...
198    
199    checkpoint62x (2011/05/13)
200    o pkg/mom_vecinv:
201       high-order vorticity scheme: use interior masks (maskInW & S)
202       to zero-out (outside OB) gradient of vorticity.
203    o verification exp.:
204       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
205       hs94.128x64x5 and seaice_obcs ; update results.
206    o pkg/obcs:
207      fix bug in OBeta for YZ sections in obcs_exf_load.F
208    o pkg/ctrl, pkg/shelfice, and optim:
209      - add new control variable xx_shifwflx (fresh water flux underneath ice
210        shelves). This is almost as tedious as obcs-ctrl, because the
211        variables needs its own mask.
212      - add a cost function term that penalizes the deviation of xx_shifwflx
213        from the first guess (zero) in analogy to other control variables
214    o pkg/shelfice:
215      - start basic adjoint
216    o pkg/ctrl:
217      - remove extra 2D field "for good measure" when initializing in
218        ctrl_set_globfld_[xy/xz/yz].F
219      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
220      - improve error messages in ctrl_set_unpack_*
221    o OBC implementation in momentum:
222       use interior masks (maskInC,W & S) in momentum S/R:
223       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
224       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
225       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
226       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
227       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
228        (and also with Leith/Smagorinsky harmonic-viscosity).
229       Update output of experiment dome and exp4 (+nlfs).
230    o exp4 test-exp:
231      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
232        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
233        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
234        time-varying OB at Western-side for wVel (NonHyd); update output.
235      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
236        and biharmonic-viscosity ; also use prescribed time varying OB.
237    o pkg/obcs:
238      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
239    o model/src:
240      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
241      - initialise startTime & nIter0 with unlikely values: allows to set one
242        from the other without ambiguity.
243    o seaice_obcs test-exp.:
244      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
245    o pkg/obcs:
246      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
247        no longer needed with maskInC,W,S in pkg/generic_advdiff.
248    o pkg/seaice:
249      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
250        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
251      - fixed bug in the initialization of sea ice salinity variable HSALT
252        in seaice_init_varia.F  (removed dependence on ICE2WATR)
253    o fizhi-cs test exp.:
254       switch reference output convention for these 2 non-standard test-exp,
255        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
256          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
257       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
258    o model/inc:
259      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
260        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
261    o pkg/seaice:
262      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
263    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
264      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
265        and initial HSALT
266    
267    checkpoint62w (2011/04/26)
268    o pkg/mom_fluxform:
269      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
270      - use parameter "sideDragFactor" in no-slip BC side-drag part.
271      - update output of exp. global_ocean.90x40x15
272    o pkg/mom_vecinv:
273      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
274    o update seaice exp.:
275      use more consistent parameter values (remove "backward compatability only":
276       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
277      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
278       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
279    o update test-exp global_ocean.90x40x15:
280      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
281      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
282      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
283      o turn on zStar & viscA4 in standard set-up (dir input/)
284        and update output files: output.txt & output.dwnslp.txt
285    o new AD-test experiment: obcs_ctrl
286      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
287    o pkg/dic:
288      fix two bugs in handling water vapour pressure in carbonate chemistry
289      and air-sea fluxes. Found by Val Bennington and Galen McKinley
290      (add DIC Option = WATERVAP_BUG to recover old results)
291      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
292    o adding allowInteriorFreezing option to check for water below freezing point
293      at depth and bring the negative heat anomaly to the surface level
294    o pkgs _fields_load:
295      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
296      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
297        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
298        rbcs to get interpolation weights and time reccord number.
299      - fix multi-threading in aim_fields_load.F
300      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
301    o external_fields_load:
302      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
303       interpolation weights) to use in a periodic time-series ; do not divide by
304       time-step to convert to integer:
305       - this fixes case where externForcingPeriod is not multiple of time-step
306          (Thanks to Christopher L. Wolfe)
307       - this fixes case where externForcingPeriod is an odd multiple of time-step
308         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
309      store index of time-record which is currently loaded:
310       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
311       - needed for the adjoint but not yet used because of extensive recomputations;
312         (to be fixed soon)
313    
314    checkpoint62v (2011/04/02)
315    o verification/1D_ocean_ice_column added to test Ian Fenty's
316      pkg/seaice_growth.F modifications for improving sea ice code differentiability
317    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
318      (new velocity statistics after changing maskInW & maskInS definition)
319    o pkg/generic_advdiff with OBCS:
320      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
321      equivalent to assumption of no tracer gradient outside the OB region.
322      This will affect the results if using obcs+biharmonic diffusion.
323      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
324    o pkg/obcs:
325      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
326      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
327      in Interior region. No impact on solution but affects Velocity monitor stats.
328    o pkg/ptracers (adjoint)
329      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
330      tape file for each tracer
331    o model/inc/src and pkg/autodiff: add parameters that allow to turn
332      of parts of the adjoint code at run time. For now, there are only
333      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
334      parameters are set in data.pkg.
335      This is the lazy coward's version of doing this, but still useful for
336      debugging. In order to do it right, everything needs to be moved to
337      pkg/autodiff.
338    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
339      the end; this fixes the adjoint balancing code for open boundaries.
340    o pkg/ctrl:
341      - change behavior of xx_${varname}period to be analogous to exf-conventions:
342        xx_${varname}period =   0.,  means time-independent control part
343        xx_${varname}period = -12., means one-year-periodic monthly control part
344      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
345        clean up ctrl_init a little, remove unused variables
346      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
347      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
348    
349    checkpoint62u (2011/03/15)
350    o model/src:
351      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
352        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
353      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
354        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
355    o pkg/ctrl/obcs/ecco:
356      - remove obsolete, unused, and partially broken code:
357        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
358        ALLOW_CTRL_OBCS_BALANCE
359      - put a stop statement into ecco/cost_obcsvol.F, but also add
360        cost_obcsvol to ecco_ad_diff.list
361    o pkg/ecco: fix counting cost function contributions for obcs (code
362      by Matt M.) and diffkr for diagnostics
363    o pkg/ecco, pkg/ctrl, pkg/grdchk:
364      add cost penalty terms for initial uvel, vvel, eta controls
365      and I/O for prior error files
366    o pkg/mdsio:
367       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
368       (new argument) to check for tiled file in mdsioLocalDir : this fix the
369       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
370    o pkg/ctrl:
371     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
372       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
373       unused and superfluous variables
374     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
375    o pkg/ecco
376     - enable adjoint of Stevens OB
377    o pkg/ctrl/ecco/grdchk:
378      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
379        Fortunately, we do not have any tests for the numerous cpp-flagged
380        option of "obcs as control parameters" so we will never know
381        if this is an improvement (but at least now things compile).
382      - remove an obsolete initialization from ecco_cost_init_barfiles.F
383      - fix some problems within never used ifdefs to make the code compile
384    o pkg/obcs:
385     - Refine Interior mask definition to work with more complex OB (e.g.
386       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
387       read in Interior mask from file. Check if Interior mask is consistent
388       with OB list of indices.
389    o pkg/seaice
390     - beginning code for a seaice tracer package,
391       but currently only used for seaice age: SEAICE_AGE
392       SEAICE_num = 4
393       iTracer = 1: area-weighted ice age
394               = 2: volume-weighted ice age
395               = 3, 4: template for one-year vs. multi-year ice
396       data.seaice has new namelist SEAICE_PARM03 for arrays related to
397       SEAICE_num
398    
399    checkpoint62t (2011/03/05)
400    o pkg/obcs:
401     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
402       then normal component. This ensures that the normal component is set
403       correctly even when it conficts with tangential setting from an other OB.
404       Affects results of test-experiment seaice_obcs: update the output.txt
405    o pkg/obcs:
406     - add code to monitor statistics of dynamical fields at OB.
407     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
408       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
409       - change default: balance the Net inflow through all OB (instead of balancing
410         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
411     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
412       to match Nortern OB inflow (OBCS_balanceFacN=0).
413    o pkg/seaice:
414     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
415    o pkg/seaice (seaice_growth v 1.113):
416     - reverting seaice_growth to v 1.111 in order to have code with exact bit
417       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
418       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
419       runtime flag SEAICEareaFormula is kept but is inactive
420    o model/src:
421     - add new param to scale curvilinear grid distance and area when using
422       a different sphere radius from the grid-files.
423     - test/check multi-threads EXCH applied to local variable (cg2d_x)
424    o adjoint:
425     - enable adjoint of Stevens OB
426     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
427       (a bit delicate because of potentially modified adj. common block structure;
428       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
429    
430    checkpoint62s (2011/02/15)
431    o pkg/seaice (seaice_growth v 1.112):
432     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
433       computing the ice cover tendency from effective thickness tendencies. Include
434       Ian Fenty's formula.
435     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
436       SEAICEareaFormula.
437     - simplify notations for the various d_HEFF/d_AREA terms.
438    o pkg/gmredi:
439     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
440       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
441       add a verification test-run (front_relax.bvp) to test GM_useBVP.
442    o pkg/seaice (seaice_growth v 1.111):
443     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
444     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
445       also melt ice.
446    o pkg/seaice:
447     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
448     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
449    o pkg/cheapaml:
450     - from Nico Wienders: New version of this package.
451    o pkg/flt:
452     - add CPP options to prevent floats to re-enter the opposite side of
453       a periodic domain (default: keep periodicity)
454    o pkg/gmredi:
455     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
456       (needed for multi-dim advection).
457     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
458    o model/src:
459     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
460    o tutorial_tracer_adjsens
461     - extend to NLFS and replace maskC by hFacC
462       (change reference output accordingly)
463    
464    checkpoint62r (2011/01/24)
465    o testreport:
466     - add option -deloutp (-do) to remove output file after successful run
467     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
468       extract exact list of procs from this file ; adjust COMMAND by
469       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
470    o pkg/ecco: replace old ineffective way of penalizing deviations from
471      first guess (of obcs) with code by Matt Mazloff
472    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
473      exf/cal
474      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
475        and handle case of obcs?period == 0
476        Not affected by these changes: There is still an inconsistency in
477        the computation of start/endrec for the obcs variables for ALLOW_CAL
478        defined (see comment by Menemenlis, 7-Mar-2003)
479      - make S/R ctrl_get_gen_rec return something meaningful even if
480        ALLOW_CAL is not defined
481      - ctrl_getobcs?: simplify code so that it does not need to use
482                       S/R exf_swapfields
483    o testreport:
484       allow to test MPI with different number of processors for each experiment:
485       create file "SIZE.h.mpi" in each build dir.
486       Note: update of "-command" argument not yet implemented.
487    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
488      alleviate the need for additional 3D tapes when using
489      the non-inear free surface in the adjoint. This is done
490      by adding an 'update' of hfacc etc. to their current
491      value at the beginning of forward_step.F.
492    o pkg/seaice
493      seaice_lsr: move stress-divergence computations out of outer pseudo-
494      timestepping loop
495    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
496      up, so that the calls of the ctrl_* subroutines are really at the end
497      of the routine.
498    o pkg/gmredi:
499      allow to specify a 2-D horizontal map and a 1-D vertical profil
500      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
501    o pkg/seaice:
502      move lsr iterations from seaice_dynsolver to seaice_lsr.
503    o pkg/seaice:
504      reduce memory footprint of seaice mutldim advection tapes,
505      by using a 2D tape independent of the generic_advdiff ones,
506      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
507    
508    checkpoint62q (2010/12/29)
509    o model/src:
510      - check horizontal grid-spacing for unset or zero/negative values.
511      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
512    o pkg/flt:
513      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
514      - precision of input and output files set according to readBinaryPrec
515        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
516      - initial float position from tiled file was not converted to index space
517        (looks like a bug): fixed to make it similar to initial pos. global file.
518    o global_ocean.cs32x15:
519       change SIZE.h of AD set-up to get same tiling as with MPI.
520       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
521    o model/src:
522       add flag to control printing of domain fields (bathymetry, hFac ...) in
523       ini_mask_etc (call to plot_fieds_xy*).
524    o pkg/thsice:
525       if useEXF, some forcing fields are not valid in overlap: fixed by computing
526       over the interior only + apply EXCH at the end (like with SEAICE advection).
527    o pkg/mdsio:
528      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
529        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
530      - change barrier call for safe multi-threads access to 3-D shared buffer.
531      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
532      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
533        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
534    o pkg/flt:
535      - add fourth-order Runge-Kutta integration
536      - add basic exch2 support (only 1 facet supported so far!)
537    o pkg/mdsio+rw:
538      new S/R to read local (or tile independent) vector (read counterpart of
539       mds_writevec_loc, and front-end write_glvec_rl/rs).
540    o global_ocean.cs32x15: additional input_ad.seaice experiment
541        that uses pkg/seaice rather than pkg/thsice.
542        (using multidim advection for seaice)
543    o towards more F95 syntax for array specification in namelist:
544      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
545        of all verification experiments.
546           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
547          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
548      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
549    o global_ocean.cs32x15: additional input.seaice experiment
550        that uses pkg/seaice rather than pkg/thsice.
551    
552    checkpoint62p (2010/12/17)
553    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
554        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
555    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
556        allow for use of multim. advection in seaice adjoint.
557    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
558      - first attempt to close budgets by taking into account the freshwater
559        flux implied by the sublimation of snow and ice. So far only the
560        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
561        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
562    o eesupp/src:
563      new S/R with new option (NML_EXTENDED_F77) to change array specification
564      from F95 standard to commonly accepted extended F77 form.
565      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
566      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
567      for less tolerant f77 compiler (e.g., pgf77, g77).
568    o globalFiles:
569      commented out in parameter file "data" since it's not safe with MPI
570      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
571      in this case); no longer commented out in restart test (tst_2+2).
572    o add adTapeDir to specify a special directory where adjoint tapes are
573      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
574      and cannot be used together with mdsioLocalDir.
575    o nesting pkgs:
576      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
577      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
578      - add parameter files + utils dir + output from short run on beagle.
579    o pkg/seaice:
580        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
581    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
582      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
583    
584    checkpoint62o (2010/11/25)
585    o pkg/exf:
586      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
587    o pkg/seaice:
588      - seaice_ocean_stress: split a loop for better vectorization of the
589        adjoint code
590      - seaice_growth.F: fix bug in conservation of freshwater connected to
591        capping of heff, put contribution into d_HEFFbyNEG
592      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
593        by something more sensible (parameters that are what their name implies)
594      - change some defaults, so that by default exf-parameters are used for
595        things like rhoAir, cpAir,latent/sensible heat parameters, in order
596        to reproduce the old results, many data.seaice now contain funny values
597        for cpAir and latent heat of sublimation
598    o packages_readparms.F: move exf_readparms up in line so that
599        exf-parameters are visible for other packages (e.g. seaice)
600    o debugMode & debugLevel=2:
601      - differentiate between debugMode & debugLevel=2:
602        debugMode: controls printing of debug messages (sequence of S/R calls).
603        debugLevel: controls printing of algorithm intermediate results and stats.
604      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
605        => allows to print debug-stats without all sequence of call messages.
606      - switch control of debug print from debugLevel to debugMode in many S/R.
607    o pkg/obcs (obcs-sponge):
608        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
609        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
610    o pkg/generic_advdiff:
611      - record overlap minimum size for each advection scheme;
612      - refine criteria on overlap minimum size;
613      - check and stop (in gad_check) if overlap size is too small.
614    o pkg/obcs:
615      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
616        once, in ptracers_implicit.F)
617      - with seaice: remove test on empty file name in obcs_apply_seaice (always
618        apply OB values when tile has OB)
619    o model/src, coriolis setting:
620      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
621        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
622        files (selectCoriMap=3) with any grid.
623      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
624    o pkg/seaice/seaice_growth.F:
625        a few cosmetic changes that reduce the number of lines of code
626    o pkg/obcs: add boundary conditions following Stevens (1990)
627      - the code follows old MOM/NAOSIM code
628      - so far it is only implemented for the eastern and western boundaries
629        and NOT for pTracers
630    o pkg/rbcs:
631      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
632        beginning of the first rbcs forcing period.
633      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
634        offline package, i.e., one file per time, labeled by iteration number;
635        deltaTrbcs sets the timestep with which the data was generated;
636        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
637      - rbcsForcingCycle=0 makes forcing non-cyclic.
638      - make arithmetic safe for negative times and odd forcing periods.
639    
640    checkpoint62n (2010/11/09)
641    o pkg/seaice:
642        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
643    o pkg/obcs:
644       New S/R to copy tracer value from the OB location to narrow band region
645        (width = same as overlap) beyond the OB: preserve OB value (needed for
646        high-order scheme) which were overwritten by EXCH call if in overlap
647        region. Applied to theta, salt, ptracer and advected seaice variables.
648       With seaice: use maskInC in similar way as in gad_advection.F,
649        in seaice_advection.F and advect.F.
650       Update output of experiment seaice_obcs and change exp4 to test OBCS with
651        4th order Adv.Scheme. for pasive salt and ptracer.
652    o tools/genmake2:
653      - when looking for an optfile (not specified), only search for Fortran compiler
654        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
655      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
656        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
657      - set default for CPP to "cpp -traditional -P" (was the case without specifying
658        an optfile, but otherwise default was just "cpp".
659      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
660      - when "CC" is not set in the optfile, look for possible C compiler
661        (instead of just setting CC=cc)
662      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
663        => add a ".F" to ".o" rule for source files with no "#include" (such as
664           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
665      - move gfortran before g77 in list of possible Fortran compiler (consistent
666        with reference compiler switch from g77 to gfortran)
667    o pkg/seaice:
668      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
669        seaice_check that stops the model, when the CPP flag is used.
670      o seaice_growth.F: make capping of ice volume conserving by returning the
671        capped ice as freshwater to EmPmR. This does not change the verification
672        experiments but will change runs where the capping is acutally active
673    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
674      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
675         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
676         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
677    o tools/genmake2:
678      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
679      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
680      - clean previous genmake log files before anything else.
681      - change Makefile to remove testreport log files (*.tr_log) and genmake log
682        files only with "CLEAN" target (instead of "Clean");
683    o pkg/generic_advdiff:
684      Change OBCS in multiDim advection (gad_advection.F):
685       Use maskInC to prevent intermediate update of tracer-field in OB regions,
686       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
687       which were applying future time-step OB values.
688      This way, all explicit calculations use current-time-step OB values
689       (simpler and more consistent).
690      Affects results when set-up uses time-varying OBC and multi-dim advection;
691       update output of experiment seaice_obcs.
692    o pkg/seaice:
693      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
694       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
695         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
696      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
697       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
698       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
699    o pkg aim (2010/10/26):
700      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
701        formulation with obliquity, eccentricity, ... as run-time parameters,
702      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
703        upward shortwave radition at the surface (all-sky and clear-sky).
704    o pkg/obcs:
705      - writing sections with globalFiles=T does not work: switch to tiled-files
706        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
707      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
708      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
709    
710    checkpoint62m (2010/10/21)
711    o pkg/seaice: vectorize seaice_solve4temp.F
712      - move iterations loops outside of i/j-loops
713      - requires 2D arrays for TB and effConduct
714      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
715        modified in this routine
716      - a little bit of clean up, adjusting indentation, etc.
717      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
718        performance and '**TWO' by '**2' (because TWO is a float),
719        replaced ONE, ZERO
720    o eesupp/src:
721       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
722    o pkg/seaice/seaice_growth.F
723      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
724      merging process. The merged routine has two branches, and one activates the 'evolution'
725      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
726      In summary, here is what the '10/10 revision' did consist of
727        part 1: seaice_growth.F revisions 1.71 to 1.75
728          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
729            The emphasis here was on improving readability (e.g. by trying to use meaningful
730            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
731        part 1.5:
732          - revising the lab_sea experiment to make it a more useful (i.e. stable
733            and representative of an actual model run). This was done by generating a
734            (winter) pickup to start from, switching back the main experiment dynamic
735            solver from evp to lsr, having one of the experiments use the free drift solution.
736        part 2: seaice_growth.F revisions 1.76 to 1.85
737          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
738          - Sorting out the various fields units and sign (set early on and reset at the end)
739            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
740            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
741          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
742            and simplifying logical expressions to further improve readibility.
743        part 3: seaice_growth.F revisions 1.86 to 1.89
744          - Re-organize the blocks of code more logically.
745          - Merging the '_if.F' pieces that add something new.
746    o pkg/thsice:
747      - vectorize thsice_solve4temp and thsice_get_exf.
748        Problem: thsice_solve4temp has an unvectorizable statement that
749        might also be problematic for TAF
750      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
751        does not change the verifcation experiment, but will change all
752        experiments that have this flag undefined (not tested in verification);
753        a little reorganization to save a few 2D fields and recomputations
754      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
755      - 2nd step:  fix some store dirs
756        o seems to work somewhat, i.e. using ifort but not g77
757        o likely cause are incomplete init. or recomputation
758        o start verification/global_ocean.cs32x15/input_ad.thsice
759    o pkg/obcs: add support for exch2
760      - the position of the boundary and prescribed values are specified using
761        a global domain with exch2 facets stacked
762        - in x for N,S boundaries (like W2_mapIO=-1)
763        - in y for E,W boundaries (so E,W boundaries do not overlap)
764    o pkg/mdsio: add support for writing global sections with exch2
765        file layout is as for obcs described above:
766        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
767        - for y-z sections, facets are stacked in y
768    o pkg/thsice:
769       - change a few routines for better vectorization: thsice_albedo.F,
770         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
771         not affected, but in particular the latter routine has changed
772         dramatically (not necessarily easier to read now).
773       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
774       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
775    o verification/lab_sea:
776      - overhaul of the forward model experiments. The main motivation
777        for this revision is that lab_sea has proven quite fragile (when
778        changing the sea-ice code, and switching platforms) to a point
779        when failures were very hard to attribute to specific code problems.
780      - the suspected reason for this fragility is noise amplification by evp so,
781        to start with, we decided to replace evp with lsr in the main experiment.
782      - the input.lsr experiment thus became obsolete and was removed.
783      - it was replaced with the input.fd experiment that uses an
784        analytical "free drift" solution as the ice velocity field.
785      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
786        will hopefully allow us to discriminate problems due to dynamic solvers
787        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
788        us to test additional options, along with the salt plume package.
789      - Finally a pickup was generated (at the end of a one year run) to
790        make the tests more representative of an actual model run. Previously
791        the tests starting point was a 1m thickness of ice everywhere.
792    o pkg/seaice:
793      - introducing S\R seaice_freedrift.F that compute the
794        analytical solution to an approximate ice momentum
795        equation (i.e. the simple stress/coriolis balance).
796      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
797        of the free drift velocity field, and enable its use.
798        To actually use the free drift solution as the model ice
799        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
800    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
801    
802    checkpoint62l (2010/10/04)
803    o pkg/seaice:
804      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
805      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
806       version (with USE_ORIGINAL_SBI undef);
807    o add hooks for new packages OASIS, the package will follow
808      (hooks exclude the seaice pkg for now)
809    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
810      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
811      rather than mdsio_readvector.F/mdsio_writevector.F, within
812      adread_adwrite.F to read/write adjoint-related tapes to disk.
813    o eesupp and pkg/mdsio: ALLOW_WHIO
814      Option to write/read 2D fields to files including tiles halos.
815      The main purpose is for adjoint related "tape I/O".
816      The secondary purpose is for debugging phases.
817      A word on those rather specifically intended purposes.
818      The code was meant to be stripped down to the bare minimum.
819      Typically, there is a unique and basic mapping to the global
820      buffer (tile by tile, then proc by proc, then level by level), and
821      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
822      meant to generate user friendly outputs of various shapes and forms.
823      Rather it is intended, for the knowledgeabale developers,
824      to be largely independent of the many mdsio options, to allow
825      outputs of tiles+halos in debugging phases and in adjoint runs,
826      and to allow some flexibility in tuning (adoint) I/O depending on each
827      file system behavior. With regard to tuning, most of the potential knobs
828      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
829      to specify directories, to specify the typical size of I/O calls, etc.)
830      are not yet included, and will be added if they prove useful.
831    o pkg/seaice:
832       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
833    o pkg/seaice:
834       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
835       code (seaice_budget_ice_if.F) which enable to recover old standard
836       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
837       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
838    o model/src (rStar):
839       use simple average (not area weighted) of rStarFac at U,V point when using
840       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
841       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
842    
843    checkpoint62k (2010/09/17)
844    o adjoint
845       * changed verification/global_ocean.cs32x15 ; adjoint now tests
846         Adams-Bashforth 3 + NLFS + RSTAR
847       * some more modifs required for ECCO-GODAE v4
848    o pkg/seaice
849       add SEAICE_AGE_VOL option to use volume instead of area for
850       integrating SEAICE_AGE
851    o model/src:
852       first check-in of sigma & hybrid-sigma coordinate code ; also includes
853       non-linear free-surface parts ; but pressure-gradient not yet coded.
854    o pkg/ptracers:
855       option for ptracer to convert Salt Relax into additional EmP.
856        tested in exp. global_ocean.90x40x15.dwnslp (update output)
857    
858    checkpoint62j (2010/08/25)
859    o pkg/ggl90:
860       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
861    o pkg/dic: car_flux.F, phos_flux.F
862      - reduce number of exp-calls in order to improve performance
863      - clean up a little (replace fields by their macros, etc., fix
864        typo in CPP-flag)
865    o pkg/ggl90: minor changes
866      - GGL90diffKrS was removed --> always use GGL90diffKr
867      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
868      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
869        (commented out for now)
870      - change in max/min operations to ensure that smoothing is ok
871      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
872      - always use diffKrNrT as background profile (i.e. never use diffKr field)
873    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
874    o pkg/dic:
875      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
876        vectorization
877      - small bug fix in insol for the unlikely case of a cartesian grid
878      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
879        + now vectorize, which also removes adjoint recomputations;
880        + replace integer maksp1 by _RL maskp1
881        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
882    
883    checkpoint62i (2010/07/21)
884    o pkg/flt:
885      - with OBCS: stop floats which enter the OB region
886    o model/src:
887      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
888        for implicit vertical advection.
889    o pkg/seaice:
890     - account for melting in seaice age evolution.
891     - remove double counting of seaice ridging effect on seaice age.
892    
893    checkpoint62h (2010/06/18)
894    o pkg/exch2:
895     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
896    o tools/genmake2
897      - remove "-pdefault" option: redundant with the use of "packages.conf";
898      - remove file pkg/pkg_default : set the default as a pkg group
899        ("default_pkg_list") defined in pkg/pkg_groups;
900      - fix for case pkg/pkg_depend is missing (was hanging before);
901      - add option "-pgroups" to specify a different pkg_groups than the default.
902    o verification/adjustment.cs-32x32x1:
903       add a "minimal" set-up test (code_min & input_min) which only compiles
904       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
905    o tools/genmake2
906      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
907      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
908    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
909      files are nearly the same anyway.
910      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
911       - redefinition of tau(i,i) (by a factor of ustar)
912       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
913       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
914       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
915       - replace
916         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
917         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
918         by
919         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
920         (changes results)
921       -> exf_bulkformulae v1.22,
922          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
923          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
924                    output.txt 1.63
925           offline_exf_seaice: output.seaicetd.txt 1.7
926           seaice_obcs: output.txt 1.10)
927      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
928       -> exf_bulkformulae v1.23,
929          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
930          and global_ocean.cs32x15.icedyn (only 11 matching digits)
931      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
932    o adjoint of exch-1:
933     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
934       (note: was already like this when using EXCH-2) and remove flow dir
935       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
936     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
937     - update pkg/exch2 diff list.
938    
939    checkpoint62g (2010/05/19)
940    o eesupp/src (exch-1):
941     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
942       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
943       (renamed to exch1_*rx_cube.F).
944     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
945       to call new exch1 S/R ; update Makefile and .cvsignore.
946     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
947       exch2_xy_rx later)
948      Note: after updating your code, need to run "make clean" in eesupp/src
949    o test experiment bottom_ctrl_5x5:
950       new output_adm.txt with fewer grdchk & less monitor output.
951    o model/src:
952      remove the call to ini_cori in initialise_varia.F (just keep the usual one
953       in initialise_fixed.F). More consistent with coriolis & horizontal grid
954       beeing treated in the same way (ini_grid is not called a 2nd time).
955    o pkg/exf:
956      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
957      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
958      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
959      - cosmetic changes to exf_bulkformulae.F to make it look more like
960        exf_bulk_largeyeager04.F
961    o eesupp/src (exch-1):
962      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
963      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
964        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
965        (even without using MPI).
966      - Message mode: move RecvAck setting (indicator of buffer being ready)
967        from send_put to recv_get S/R (was useless before, but not sure if
968        it's much more useful now);
969      - Switch the order of sync: MPI-proc 1rst and then threads;
970      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
971      - fix AD code for communication mode ='get' (but not used).
972    o model/src:
973      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
974      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
975    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
976    o pkg/ctrl: require a specific set of control variables and exf-flags for
977      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
978    o model/src:
979     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
980       1rst forward sweep, to avoid over-writing output files during recomputations
981       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
982     b) 2nd version:
983      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
984      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
985         writePickupAtEnd) + seaice & ptracers output;
986      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
987    o model/src:
988      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
989    o pkg/exch2:
990      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
991      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
992    o pkg/autodiff & exch2:
993      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
994      (for now, only if ALLOW_EXCH2 is defined).
995    o pkg/autodiff:
996      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
997        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
998       + clean-up comments (_RS is not always real*4)
999      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1000      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1001        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1002    o testreport (AD-tests):
1003      no longer link files from dir "../input" (1rst link files from
1004      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1005    
1006    checkpoint62f (2010/04/29)
1007    o model/src/the_main_loop.F:
1008      adjust store directives for seaice evp and multicategory according to
1009      pkg/ecco/the_main_loop.F
1010    o adjoint:
1011      global_sum_ad was incomplete (noted many times by many people ;)
1012      nice description by Jean U. as follows:
1013      * allreduce(var) in global_sum.F can be interpreted as
1014        reduce(sum) followed by broadcast of sum.
1015      * The adjoint of that is
1016        sum(adjoint) followed by broadcast(summed adjoint value)
1017        or in other words, allreduce(sum, adjoint vars)
1018      We were missing the sum(adjoint)!
1019      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1020      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1021      The fix should produce 16-digit accuracy between
1022      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1023      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1024      We'll probably change this yet again shortly
1025    o eesupp/src:
1026      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1027    o pkg/icefront
1028      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1029        specification of addmass array based on a 2D field, which is added
1030        at bottommost wet level at each horizontal location.
1031    o model/src:
1032     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1033     layout; (not always compatible with delX,delY setting; commented out for now).
1034    o pkg/exch2:
1035     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1036     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1037    
1038    checkpoint62e (2010/04/15)
1039    o pkg/obcs:
1040      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1041    o pkg/dic:
1042      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1043        (note: not presently tested in any forward verification exp.)
1044       update tutorial_global_oce_biogeo AD output file.
1045    o pkg/exf:
1046      - account for the variation of albedo as a function of zenith angle
1047        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1048  o build_options:  o build_options:
1049   - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"   - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1050  o pkg/dic:  o pkg/dic:
# Line 76  o tools/build_options: Line 1117  o tools/build_options:
1117      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1118  o pkg/ecco  o pkg/ecco
1119    - allow user defined cost function contributions    - allow user defined cost function contributions
1120          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1121          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1122    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1123        the two options are complementary.        the two options are complementary.
1124  o pkg/smooth  o pkg/smooth
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