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revision 1.1314 by jmc, Sat Oct 16 17:23:12 2010 UTC revision 1.1462 by jmc, Wed Jun 22 19:17:36 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/diagnostics:
8     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
9       which are not filled-up but computed from other diags ; In this case, the mate
10       diag points to the primary (filled-up) diag to used for post processing.
11     - Update Velocity-potential computation using post-processed diag framework.
12     Change the ordering of fields and time-periods in MDS output file
13       when using periodic averaging: now writes one time record with the full set
14       of fields for this time period, then the next time reccord (it used to be
15       one field with the full set of time records then the next field).
16       Note: this is now similar to NetCDF (MNC) output file.
17    
18    checkpoint62z (2011/06/21)
19    o adjoint monitor:
20     - Add adjoint monitor output for packages exf, seaice
21       and update relevant testreport output
22    o pkg/seaice:
23     - re-order diags inits so that they appear in order in available_diagnostics.log
24     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
25       area/heff/hsnow preceeding thermodynamic growth/melt.
26     - modified diag: SIdA; output actual effect, as the description states.
27     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
28     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
29       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
30        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
31     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
32     - added diagnostics for seaice generic tracers (SItr*).
33     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
34     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
35     I. Fenty: 18-Jun-2011:
36     Minor changes to seaice package:
37     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
38        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
39       - Differentiated "regularization variables" from "floor variables"
40        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
41        * hiceMin became SEAICE_hice_reg (old hiceMin)
42          (with _reg meaning regularization variable)
43       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
44        so as to ensure energy conservation when going between phases
45      - A22 was not used anywhere
46     2) Changed regularization procedure for heffActual and hsnowActual to ensure
47        well-boundedness and smooth adjoint in seaice_growth.F
48     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
49        because the old regularization always set heffActual >= 0.05 cm
50     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
51        on AREA when HEFF > 0.
52      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
53        requiring that DISABLE_AREA_FLOOR *not* be defined
54     Affected verifications:
55      - 1D_ocean_ice_column (output.txt output_adm.txt)
56      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
57    o pkg/diagnostics:
58      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
59      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
60        (was _RL, now integer) with option = 0 to retrieve all levels.
61      - add pieces of code to compute velocity potential at each level (new diagnostics
62        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
63        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
64      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
65        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
66        and in diagnostics_fract_fill.F (do not need a valid pointer for the
67        diagnostics counter-mate); check that definition of counter-diagnostic
68        includes a valid counter-mate (in diagnostics_set_levels.F).
69    o model/src (rStar):
70      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
71        affect solution only if z* with full pressure in EOS;
72        update output of test-exp global_ocean.90x40x15.
73    o pkg/seaice:
74      - introduce siEps=1e-5 parameter
75      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
76      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
77      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
78        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
79        as well as ice cover age and ridging index (attached to AREA).
80        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
81        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
82        Up to SItrMaxNum=3 tracers can be used simultaneously.
83    o pkg/salt_plume:
84      -introduce SPsalFRAC run time parameter that sets the fraction of the
85       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
86       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
87    o model debug options:
88      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
89        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
90      - Refine debug-msg printing selection (3 new levels):
91        debugMode  : controls printing of debug messages (sequence of S/R calls).
92        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
93         debLevZero =  0 ; /* level of disabled aux. msg printing */
94         debLevA =  1 ; /* level of minimum  aux. msg printing */
95         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
96         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
97         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
98         debLevE =  5 ; /* level of extensive debug printing */
99        New debugLevel default: with default debugMode value (=F),
100          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
101          and if debugMode=T, default debugLevel = 4 (debLevD).
102        Relation with previous settings:
103         debLevB (=2) corresponds to former debLevA (=1)
104         debLevD (=4) corresponds to former debLevB (=2)
105        Note:
106         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
107         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
108            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
109      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
110        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
111    o pkg/obcs:
112      - change OBCSfixTopo default from True to False (should not change the results);
113        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
114    o pkg/thsice:
115      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
116        2nd layer seaice sublimation (unlikely to happen)
117      - use Interior mask for OBCS in thsice_advection.F (similar to what is
118        done in gad_advection & seaice_advection).
119    o adjoint:
120      bug fix spotted by Gael Forget:
121      seaice_advection and thsice_advection still had
122      legacy CPP options to avoid CS corner updates for adjoint
123    o pkg/seaice:
124      => Change some of the defaults (2011/05/29):
125         - change SEAICEuseFluxForm default (from False to True)
126         - change DIFF1 default (from 0.004 m/s to 0. m/s)
127         And print warnings if DIFF1 is not set in data.seaice and centered
128          avection scheme is used without any diffusion.
129      also:
130      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
131      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
132      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
133        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
134        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
135      update results of test exp.:
136         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
137             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
138             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
139         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
140         seaice_obcs: output (SEAICEuseFluxForm=T)
141      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
142          for standard fwd & AD lab_sea tests (to keep the same output).
143    o pkg/seaice/seaice_growth.F:
144      - use Ian Fenty's capping formulas for actual ice
145      thickness thoughout EVOLUTION branch.
146      - put treatment pathological case #2) in CPP brackets
147      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
148      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
149    o pkg/seaice:
150      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
151      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
152      also pass fac as a param, which can be 1. (to update the tendency
153      field) or the time step (to update the field itself).
154      - seaice_advdiff.F: for multidim, call seaice_diffusion with
155      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
156      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
157      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
158      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
159    o pkg/seaice:
160      diffusion with centered advection scheme (diffus.F & advect.F):
161      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
162        to just compute the laplacian of input-field.
163      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
164      - fix flux-form version in diffus.F to conserve tracer.
165      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
166       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
167    
168    checkpoint62y (2011/05/26)
169    o pkg/seaice:
170     - seaice_growth.F : in EVOLUTION branch, always include
171       a_QSWbyATM_cover in qnet (as it should be).
172     - verification/global_ocean.cs32x15 : update results accordingly
173       (output.seaice.txt output_adm.seaice.txt).
174    o pkg/seaice + obcs:
175     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
176       equivalent of assuming no tracer gradient outside the OB region.
177       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
178     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
179       after changes above);
180     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
181       only at OB location (instead of over a band of OLx width).
182    o pkg/seaice:
183     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
184       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
185    o pkg/obcs:
186      - split header file "OBCS.h" into 4 separated files:
187        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
188       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
189         (contain no conditional statement which depends on OBCS options).
190      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
191        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
192    o ctrl, cost, grdchk & autodiff pkgs:
193      - make options file more standard (like other {PKG}_OPTIONS.h file but
194        with AD_CONFIG.h); clean-up some of the included header files.
195    o pkg/obcs:
196      - do not mask tracer when applying OB (tracer == 0 could generate problems)
197      - apply tracer OB values to tracer field only at OB location (instead of
198        over a band of OLx width)
199      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
200      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
201        obcs_apply_tloc.F & obcs_apply_sloc.F
202    o obcs in model/src:
203      - call OBCS_APPLY_W only if NonHydrostatic.
204      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
205      - reset dEtaHdt and wVel to zero outside OB interior region ;
206      - leave tracer unchanged outside OB interior region: This has no effect
207        on the solution but just to prevent unrealistic tracer value outside OB.
208      - zero out velocity outside OB interior region: This has no effect on
209        the solution but just to prevent unrealistic velocity outside OB.
210    o obcs and non-lin free-surf:
211       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
212       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
213       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
214       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
215       update results of test-exp. exp4(nlfs).
216    o exp4 (nlfs) test-exp:
217       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
218       with NonLin-FreeSurf); update output.nlfs.txt
219    o obcs and 2d/3d solver norm:
220       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
221       and outside OB interior region (will allow to place OB further inside the
222       domain). Depending on the domain, can affects cg2d-Norm (previous
223       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
224       and cg3d-Norm (previous Norm was computed before canceling OB terms),
225       e.g. in tutorial_plume_on_slope.
226      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
227    o pkg rbcs:
228      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
229      - add capability to apply relaxation to horizontal velocity uVel & vVel.
230    o pkg/grdchk: add gradient check for control variable xx_shifwflx
231    o pkg/shelfice/shelfice_init_fixed.F
232      fix CPP-flag combinations
233    o pkg/seaice: Merge iceage code of Pierre Rampal
234      * update/change/correct ice age calculations
235      * add age updates for pathological cases
236      Probably needs more testing...
237    
238    checkpoint62x (2011/05/13)
239    o pkg/mom_vecinv:
240       high-order vorticity scheme: use interior masks (maskInW & S)
241       to zero-out (outside OB) gradient of vorticity.
242    o verification exp.:
243       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
244       hs94.128x64x5 and seaice_obcs ; update results.
245    o pkg/obcs:
246      fix bug in OBeta for YZ sections in obcs_exf_load.F
247    o pkg/ctrl, pkg/shelfice, and optim:
248      - add new control variable xx_shifwflx (fresh water flux underneath ice
249        shelves). This is almost as tedious as obcs-ctrl, because the
250        variables needs its own mask.
251      - add a cost function term that penalizes the deviation of xx_shifwflx
252        from the first guess (zero) in analogy to other control variables
253    o pkg/shelfice:
254      - start basic adjoint
255    o pkg/ctrl:
256      - remove extra 2D field "for good measure" when initializing in
257        ctrl_set_globfld_[xy/xz/yz].F
258      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
259      - improve error messages in ctrl_set_unpack_*
260    o OBC implementation in momentum:
261       use interior masks (maskInC,W & S) in momentum S/R:
262       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
263       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
264       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
265       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
266       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
267        (and also with Leith/Smagorinsky harmonic-viscosity).
268       Update output of experiment dome and exp4 (+nlfs).
269    o exp4 test-exp:
270      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
271        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
272        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
273        time-varying OB at Western-side for wVel (NonHyd); update output.
274      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
275        and biharmonic-viscosity ; also use prescribed time varying OB.
276    o pkg/obcs:
277      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
278    o model/src:
279      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
280      - initialise startTime & nIter0 with unlikely values: allows to set one
281        from the other without ambiguity.
282    o seaice_obcs test-exp.:
283      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
284    o pkg/obcs:
285      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
286        no longer needed with maskInC,W,S in pkg/generic_advdiff.
287    o pkg/seaice:
288      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
289        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
290      - fixed bug in the initialization of sea ice salinity variable HSALT
291        in seaice_init_varia.F  (removed dependence on ICE2WATR)
292    o fizhi-cs test exp.:
293       switch reference output convention for these 2 non-standard test-exp,
294        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
295          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
296       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
297    o model/inc:
298      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
299        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
300    o pkg/seaice:
301      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
302    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
303      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
304        and initial HSALT
305    
306    checkpoint62w (2011/04/26)
307    o pkg/mom_fluxform:
308      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
309      - use parameter "sideDragFactor" in no-slip BC side-drag part.
310      - update output of exp. global_ocean.90x40x15
311    o pkg/mom_vecinv:
312      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
313    o update seaice exp.:
314      use more consistent parameter values (remove "backward compatability only":
315       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
316      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
317       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
318    o update test-exp global_ocean.90x40x15:
319      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
320      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
321      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
322      o turn on zStar & viscA4 in standard set-up (dir input/)
323        and update output files: output.txt & output.dwnslp.txt
324    o new AD-test experiment: obcs_ctrl
325      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
326    o pkg/dic:
327      fix two bugs in handling water vapour pressure in carbonate chemistry
328      and air-sea fluxes. Found by Val Bennington and Galen McKinley
329      (add DIC Option = WATERVAP_BUG to recover old results)
330      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
331    o adding allowInteriorFreezing option to check for water below freezing point
332      at depth and bring the negative heat anomaly to the surface level
333    o pkgs _fields_load:
334      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
335      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
336        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
337        rbcs to get interpolation weights and time reccord number.
338      - fix multi-threading in aim_fields_load.F
339      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
340    o external_fields_load:
341      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
342       interpolation weights) to use in a periodic time-series ; do not divide by
343       time-step to convert to integer:
344       - this fixes case where externForcingPeriod is not multiple of time-step
345          (Thanks to Christopher L. Wolfe)
346       - this fixes case where externForcingPeriod is an odd multiple of time-step
347         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
348      store index of time-record which is currently loaded:
349       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
350       - needed for the adjoint but not yet used because of extensive recomputations;
351         (to be fixed soon)
352    
353    checkpoint62v (2011/04/02)
354    o verification/1D_ocean_ice_column added to test Ian Fenty's
355      pkg/seaice_growth.F modifications for improving sea ice code differentiability
356    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
357      (new velocity statistics after changing maskInW & maskInS definition)
358    o pkg/generic_advdiff with OBCS:
359      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
360      equivalent to assumption of no tracer gradient outside the OB region.
361      This will affect the results if using obcs+biharmonic diffusion.
362      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
363    o pkg/obcs:
364      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
365      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
366      in Interior region. No impact on solution but affects Velocity monitor stats.
367    o pkg/ptracers (adjoint)
368      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
369      tape file for each tracer
370    o model/inc/src and pkg/autodiff: add parameters that allow to turn
371      of parts of the adjoint code at run time. For now, there are only
372      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
373      parameters are set in data.pkg.
374      This is the lazy coward's version of doing this, but still useful for
375      debugging. In order to do it right, everything needs to be moved to
376      pkg/autodiff.
377    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
378      the end; this fixes the adjoint balancing code for open boundaries.
379    o pkg/ctrl:
380      - change behavior of xx_${varname}period to be analogous to exf-conventions:
381        xx_${varname}period =   0.,  means time-independent control part
382        xx_${varname}period = -12., means one-year-periodic monthly control part
383      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
384        clean up ctrl_init a little, remove unused variables
385      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
386      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
387    
388    checkpoint62u (2011/03/15)
389    o model/src:
390      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
391        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
392      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
393        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
394    o pkg/ctrl/obcs/ecco:
395      - remove obsolete, unused, and partially broken code:
396        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
397        ALLOW_CTRL_OBCS_BALANCE
398      - put a stop statement into ecco/cost_obcsvol.F, but also add
399        cost_obcsvol to ecco_ad_diff.list
400    o pkg/ecco: fix counting cost function contributions for obcs (code
401      by Matt M.) and diffkr for diagnostics
402    o pkg/ecco, pkg/ctrl, pkg/grdchk:
403      add cost penalty terms for initial uvel, vvel, eta controls
404      and I/O for prior error files
405    o pkg/mdsio:
406       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
407       (new argument) to check for tiled file in mdsioLocalDir : this fix the
408       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
409    o pkg/ctrl:
410     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
411       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
412       unused and superfluous variables
413     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
414    o pkg/ecco
415     - enable adjoint of Stevens OB
416    o pkg/ctrl/ecco/grdchk:
417      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
418        Fortunately, we do not have any tests for the numerous cpp-flagged
419        option of "obcs as control parameters" so we will never know
420        if this is an improvement (but at least now things compile).
421      - remove an obsolete initialization from ecco_cost_init_barfiles.F
422      - fix some problems within never used ifdefs to make the code compile
423    o pkg/obcs:
424     - Refine Interior mask definition to work with more complex OB (e.g.
425       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
426       read in Interior mask from file. Check if Interior mask is consistent
427       with OB list of indices.
428    o pkg/seaice
429     - beginning code for a seaice tracer package,
430       but currently only used for seaice age: SEAICE_AGE
431       SEAICE_num = 4
432       iTracer = 1: area-weighted ice age
433               = 2: volume-weighted ice age
434               = 3, 4: template for one-year vs. multi-year ice
435       data.seaice has new namelist SEAICE_PARM03 for arrays related to
436       SEAICE_num
437    
438    checkpoint62t (2011/03/05)
439    o pkg/obcs:
440     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
441       then normal component. This ensures that the normal component is set
442       correctly even when it conficts with tangential setting from an other OB.
443       Affects results of test-experiment seaice_obcs: update the output.txt
444    o pkg/obcs:
445     - add code to monitor statistics of dynamical fields at OB.
446     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
447       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
448       - change default: balance the Net inflow through all OB (instead of balancing
449         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
450     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
451       to match Nortern OB inflow (OBCS_balanceFacN=0).
452    o pkg/seaice:
453     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
454    o pkg/seaice (seaice_growth v 1.113):
455     - reverting seaice_growth to v 1.111 in order to have code with exact bit
456       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
457       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
458       runtime flag SEAICEareaFormula is kept but is inactive
459    o model/src:
460     - add new param to scale curvilinear grid distance and area when using
461       a different sphere radius from the grid-files.
462     - test/check multi-threads EXCH applied to local variable (cg2d_x)
463    o adjoint:
464     - enable adjoint of Stevens OB
465     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
466       (a bit delicate because of potentially modified adj. common block structure;
467       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
468    
469    checkpoint62s (2011/02/15)
470    o pkg/seaice (seaice_growth v 1.112):
471     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
472       computing the ice cover tendency from effective thickness tendencies. Include
473       Ian Fenty's formula.
474     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
475       SEAICEareaFormula.
476     - simplify notations for the various d_HEFF/d_AREA terms.
477    o pkg/gmredi:
478     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
479       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
480       add a verification test-run (front_relax.bvp) to test GM_useBVP.
481    o pkg/seaice (seaice_growth v 1.111):
482     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
483     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
484       also melt ice.
485    o pkg/seaice:
486     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
487     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
488    o pkg/cheapaml:
489     - from Nico Wienders: New version of this package.
490    o pkg/flt:
491     - add CPP options to prevent floats to re-enter the opposite side of
492       a periodic domain (default: keep periodicity)
493    o pkg/gmredi:
494     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
495       (needed for multi-dim advection).
496     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
497    o model/src:
498     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
499    o tutorial_tracer_adjsens
500     - extend to NLFS and replace maskC by hFacC
501       (change reference output accordingly)
502    
503    checkpoint62r (2011/01/24)
504    o testreport:
505     - add option -deloutp (-do) to remove output file after successful run
506     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
507       extract exact list of procs from this file ; adjust COMMAND by
508       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
509    o pkg/ecco: replace old ineffective way of penalizing deviations from
510      first guess (of obcs) with code by Matt Mazloff
511    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
512      exf/cal
513      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
514        and handle case of obcs?period == 0
515        Not affected by these changes: There is still an inconsistency in
516        the computation of start/endrec for the obcs variables for ALLOW_CAL
517        defined (see comment by Menemenlis, 7-Mar-2003)
518      - make S/R ctrl_get_gen_rec return something meaningful even if
519        ALLOW_CAL is not defined
520      - ctrl_getobcs?: simplify code so that it does not need to use
521                       S/R exf_swapfields
522    o testreport:
523       allow to test MPI with different number of processors for each experiment:
524       create file "SIZE.h.mpi" in each build dir.
525       Note: update of "-command" argument not yet implemented.
526    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
527      alleviate the need for additional 3D tapes when using
528      the non-inear free surface in the adjoint. This is done
529      by adding an 'update' of hfacc etc. to their current
530      value at the beginning of forward_step.F.
531    o pkg/seaice
532      seaice_lsr: move stress-divergence computations out of outer pseudo-
533      timestepping loop
534    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
535      up, so that the calls of the ctrl_* subroutines are really at the end
536      of the routine.
537    o pkg/gmredi:
538      allow to specify a 2-D horizontal map and a 1-D vertical profil
539      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
540    o pkg/seaice:
541      move lsr iterations from seaice_dynsolver to seaice_lsr.
542    o pkg/seaice:
543      reduce memory footprint of seaice mutldim advection tapes,
544      by using a 2D tape independent of the generic_advdiff ones,
545      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
546    
547    checkpoint62q (2010/12/29)
548    o model/src:
549      - check horizontal grid-spacing for unset or zero/negative values.
550      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
551    o pkg/flt:
552      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
553      - precision of input and output files set according to readBinaryPrec
554        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
555      - initial float position from tiled file was not converted to index space
556        (looks like a bug): fixed to make it similar to initial pos. global file.
557    o global_ocean.cs32x15:
558       change SIZE.h of AD set-up to get same tiling as with MPI.
559       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
560    o model/src:
561       add flag to control printing of domain fields (bathymetry, hFac ...) in
562       ini_mask_etc (call to plot_fieds_xy*).
563    o pkg/thsice:
564       if useEXF, some forcing fields are not valid in overlap: fixed by computing
565       over the interior only + apply EXCH at the end (like with SEAICE advection).
566    o pkg/mdsio:
567      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
568        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
569      - change barrier call for safe multi-threads access to 3-D shared buffer.
570      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
571      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
572        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
573    o pkg/flt:
574      - add fourth-order Runge-Kutta integration
575      - add basic exch2 support (only 1 facet supported so far!)
576    o pkg/mdsio+rw:
577      new S/R to read local (or tile independent) vector (read counterpart of
578       mds_writevec_loc, and front-end write_glvec_rl/rs).
579    o global_ocean.cs32x15: additional input_ad.seaice experiment
580        that uses pkg/seaice rather than pkg/thsice.
581        (using multidim advection for seaice)
582    o towards more F95 syntax for array specification in namelist:
583      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
584        of all verification experiments.
585           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
586          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
587      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
588    o global_ocean.cs32x15: additional input.seaice experiment
589        that uses pkg/seaice rather than pkg/thsice.
590    
591    checkpoint62p (2010/12/17)
592    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
593        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
594    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
595        allow for use of multim. advection in seaice adjoint.
596    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
597      - first attempt to close budgets by taking into account the freshwater
598        flux implied by the sublimation of snow and ice. So far only the
599        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
600        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
601    o eesupp/src:
602      new S/R with new option (NML_EXTENDED_F77) to change array specification
603      from F95 standard to commonly accepted extended F77 form.
604      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
605      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
606      for less tolerant f77 compiler (e.g., pgf77, g77).
607    o globalFiles:
608      commented out in parameter file "data" since it's not safe with MPI
609      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
610      in this case); no longer commented out in restart test (tst_2+2).
611    o add adTapeDir to specify a special directory where adjoint tapes are
612      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
613      and cannot be used together with mdsioLocalDir.
614    o nesting pkgs:
615      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
616      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
617      - add parameter files + utils dir + output from short run on beagle.
618    o pkg/seaice:
619        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
620    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
621      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
622    
623    checkpoint62o (2010/11/25)
624    o pkg/exf:
625      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
626    o pkg/seaice:
627      - seaice_ocean_stress: split a loop for better vectorization of the
628        adjoint code
629      - seaice_growth.F: fix bug in conservation of freshwater connected to
630        capping of heff, put contribution into d_HEFFbyNEG
631      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
632        by something more sensible (parameters that are what their name implies)
633      - change some defaults, so that by default exf-parameters are used for
634        things like rhoAir, cpAir,latent/sensible heat parameters, in order
635        to reproduce the old results, many data.seaice now contain funny values
636        for cpAir and latent heat of sublimation
637    o packages_readparms.F: move exf_readparms up in line so that
638        exf-parameters are visible for other packages (e.g. seaice)
639    o debugMode & debugLevel=2:
640      - differentiate between debugMode & debugLevel=2:
641        debugMode: controls printing of debug messages (sequence of S/R calls).
642        debugLevel: controls printing of algorithm intermediate results and stats.
643      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
644        => allows to print debug-stats without all sequence of call messages.
645      - switch control of debug print from debugLevel to debugMode in many S/R.
646    o pkg/obcs (obcs-sponge):
647        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
648        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
649    o pkg/generic_advdiff:
650      - record overlap minimum size for each advection scheme;
651      - refine criteria on overlap minimum size;
652      - check and stop (in gad_check) if overlap size is too small.
653    o pkg/obcs:
654      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
655        once, in ptracers_implicit.F)
656      - with seaice: remove test on empty file name in obcs_apply_seaice (always
657        apply OB values when tile has OB)
658    o model/src, coriolis setting:
659      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
660        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
661        files (selectCoriMap=3) with any grid.
662      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
663    o pkg/seaice/seaice_growth.F:
664        a few cosmetic changes that reduce the number of lines of code
665    o pkg/obcs: add boundary conditions following Stevens (1990)
666      - the code follows old MOM/NAOSIM code
667      - so far it is only implemented for the eastern and western boundaries
668        and NOT for pTracers
669    o pkg/rbcs:
670      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
671        beginning of the first rbcs forcing period.
672      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
673        offline package, i.e., one file per time, labeled by iteration number;
674        deltaTrbcs sets the timestep with which the data was generated;
675        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
676      - rbcsForcingCycle=0 makes forcing non-cyclic.
677      - make arithmetic safe for negative times and odd forcing periods.
678    
679    checkpoint62n (2010/11/09)
680    o pkg/seaice:
681        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
682    o pkg/obcs:
683       New S/R to copy tracer value from the OB location to narrow band region
684        (width = same as overlap) beyond the OB: preserve OB value (needed for
685        high-order scheme) which were overwritten by EXCH call if in overlap
686        region. Applied to theta, salt, ptracer and advected seaice variables.
687       With seaice: use maskInC in similar way as in gad_advection.F,
688        in seaice_advection.F and advect.F.
689       Update output of experiment seaice_obcs and change exp4 to test OBCS with
690        4th order Adv.Scheme. for pasive salt and ptracer.
691    o tools/genmake2:
692      - when looking for an optfile (not specified), only search for Fortran compiler
693        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
694      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
695        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
696      - set default for CPP to "cpp -traditional -P" (was the case without specifying
697        an optfile, but otherwise default was just "cpp".
698      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
699      - when "CC" is not set in the optfile, look for possible C compiler
700        (instead of just setting CC=cc)
701      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
702        => add a ".F" to ".o" rule for source files with no "#include" (such as
703           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
704      - move gfortran before g77 in list of possible Fortran compiler (consistent
705        with reference compiler switch from g77 to gfortran)
706    o pkg/seaice:
707      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
708        seaice_check that stops the model, when the CPP flag is used.
709      o seaice_growth.F: make capping of ice volume conserving by returning the
710        capped ice as freshwater to EmPmR. This does not change the verification
711        experiments but will change runs where the capping is acutally active
712    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
713      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
714         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
715         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
716    o tools/genmake2:
717      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
718      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
719      - clean previous genmake log files before anything else.
720      - change Makefile to remove testreport log files (*.tr_log) and genmake log
721        files only with "CLEAN" target (instead of "Clean");
722    o pkg/generic_advdiff:
723      Change OBCS in multiDim advection (gad_advection.F):
724       Use maskInC to prevent intermediate update of tracer-field in OB regions,
725       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
726       which were applying future time-step OB values.
727      This way, all explicit calculations use current-time-step OB values
728       (simpler and more consistent).
729      Affects results when set-up uses time-varying OBC and multi-dim advection;
730       update output of experiment seaice_obcs.
731    o pkg/seaice:
732      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
733       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
734         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
735      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
736       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
737       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
738    o pkg aim (2010/10/26):
739      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
740        formulation with obliquity, eccentricity, ... as run-time parameters,
741      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
742        upward shortwave radition at the surface (all-sky and clear-sky).
743    o pkg/obcs:
744      - writing sections with globalFiles=T does not work: switch to tiled-files
745        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
746      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
747      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
748    
749    checkpoint62m (2010/10/21)
750    o pkg/seaice: vectorize seaice_solve4temp.F
751      - move iterations loops outside of i/j-loops
752      - requires 2D arrays for TB and effConduct
753      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
754        modified in this routine
755      - a little bit of clean up, adjusting indentation, etc.
756      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
757        performance and '**TWO' by '**2' (because TWO is a float),
758        replaced ONE, ZERO
759  o eesupp/src:  o eesupp/src:
760     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
761  o pkg/seaice/seaice_growth.F  o pkg/seaice/seaice_growth.F
# Line 38  o pkg/thsice: Line 790  o pkg/thsice:
790      does not change the verifcation experiment, but will change all      does not change the verifcation experiment, but will change all
791      experiments that have this flag undefined (not tested in verification);      experiments that have this flag undefined (not tested in verification);
792      a little reorganization to save a few 2D fields and recomputations      a little reorganization to save a few 2D fields and recomputations
793      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
794      - 2nd step:  fix some store dirs
795        o seems to work somewhat, i.e. using ifort but not g77
796        o likely cause are incomplete init. or recomputation
797        o start verification/global_ocean.cs32x15/input_ad.thsice
798  o pkg/obcs: add support for exch2  o pkg/obcs: add support for exch2
799    - the position of the boundary and prescribed values are specified using    - the position of the boundary and prescribed values are specified using
800      a global domain with exch2 facets stacked      a global domain with exch2 facets stacked
# Line 399  o tools/build_options: Line 1156  o tools/build_options:
1156      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1157  o pkg/ecco  o pkg/ecco
1158    - allow user defined cost function contributions    - allow user defined cost function contributions
1159          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1160          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1161    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1162        the two options are complementary.        the two options are complementary.
1163  o pkg/smooth  o pkg/smooth
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