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revision 1.1245 by jmc, Thu Apr 1 15:32:08 2010 UTC revision 1.1483 by mlosch, Wed Jul 27 15:00:32 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/exf/exf_readparms.F
8      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
9        EXF_NML_OBCS) more consistent, so that you need not have these lists
10        in data.exf when they are not used.
11    o optim/optim_readdata.F:
12      - add some output about obcs variables that might help debugging
13      - add a check about nvarlength
14    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
15    o pkg/diagnostics (velocity potential):
16      - fix mask for OBCS (still problems in stream-function with OBCS);
17      - add specific parameter (default = main code CG2D params) for solver;
18      - in case of poor convergence, use solution corresponding to lowest residual.
19    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
20      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
21      and should be avoided where possible.
22    o model/src (rStar):
23      - include r* effect on reference-state (PhiRef) in totPhiHyd
24        (so that it's really the potential anomaly at the cell center);
25        affect solution only if z* with full pressure in EOS.
26      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
27        update output (because of z* in totPhiHyd and viscA4 changes);
28      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
29        @ constant r) until interpolation at constant r is implemented.
30    o pkg/diagnostics
31      - fix RCENTER diagnostics in case cell center is not at interface middle
32    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
33      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
34      that THETA and SALT are "conservative temperature" and "absolute
35      salinity"
36    o pkg/ctrl
37      - fix computation of endrec in s/r ctrl_init_rec
38      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
39    o pkg/seaice/seaice_growth.F
40      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
41        remove then obsolete STORE directives
42      - fix STORE directives for tice and tices, so that only the
43        appropriate part of the fields are stored (and not the entire
44        field); update global_ocean.cs32x15.seaice AD output.
45      - cosmetic changes: adjust CPP flags and indentation for better
46        legibilty
47    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
48      Chris Wilson)
49    o pkg/gmredi:
50       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
51       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
52    
53    checkpoint63 (2011/07/11)
54    o pkg/exch2:
55     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
56     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
57       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
58       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
59    o pkg/diagnostics:
60     - deal with pairs of post-processed diags which are computed together; in
61       particular, re-order list of diags within 1 file to save 2nd computation.
62     - add S/R to compute velocity stream-function (called after velocity-potential
63       calculation) from divergence free transport -> new diagnostics "PsiVEL".
64     - add parameter to select grid-point location where PsiVEL == 0.
65    o eesupp/src:
66       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
67       (specific S/R needed with exch2 topology - for now, just print an error msg)
68    o pkg/shelfice
69     - Implement friction velocity-dependent transfer coefficients following
70       Holland and Jenkins, JPO, 1999
71       Original code by M. Losch with small modifs.
72       Enable with CPP option SHI_ALLOW_GAMMAFRICT
73       and runtime flag SHELFICEuseGammaFrict
74    o verification lab_sea & global_ocean.cs32x15:
75     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
76       does not miss some dependencies (but is slower) and also works with many files
77       (default makedepend limitation for AD built).
78     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
79    o pkg/diagnostics:
80     - add run-time parameter "useMissingValue" (def=False) to fill land-point
81        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
82       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
83     - Extend the use of "missing_value" setting from data.diagnostics for the case
84       of counter-diagnostics (where fraction-weight is zero). This applies both to
85       MNC and MDS output files.
86    o pkg/seaice/seaice_growth.F:
87      - add 'a priori' cap of latent heat flux based on actual mass considerations
88        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
89        non-legacy seaice_solve4temp.
90      - add diagnostic of the residual sublimation freshwater flux (the freshwater
91        flux taken from the ocean if the total actual latent heat fluxes exceed
92        the maximum)
93      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
94       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
95      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
96       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
97      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
98      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
99    o verification 1D_ocean_ice_column:
100       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
101       update results
102    o pkg/diagnostics:
103     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
104       which are not filled-up but computed from other diags ; In this case, the mate
105       diag points to the primary (filled-up) diag to used for post processing.
106     - Update Velocity-potential computation using post-processed diag framework.
107     ==> Change the ordering of fields and time-periods in MDS output file
108       when using periodic averaging: now writes one time record with the full set
109       of fields for this time period, then the next time reccord (it used to be
110       one field with the full set of time records then the next field).
111         Note: this is now similar to NetCDF (MNC) output file. <==
112    
113    checkpoint62z (2011/06/21)
114    o adjoint monitor:
115     - Add adjoint monitor output for packages exf, seaice
116       and update relevant testreport output
117    o pkg/seaice:
118     - re-order diags inits so that they appear in order in available_diagnostics.log
119     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
120       area/heff/hsnow preceeding thermodynamic growth/melt.
121     - modified diag: SIdA; output actual effect, as the description states.
122     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
123     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
124       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
125        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
126     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
127     - added diagnostics for seaice generic tracers (SItr*).
128     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
129     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
130     I. Fenty: 18-Jun-2011:
131     Minor changes to seaice package:
132     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
133        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
134       - Differentiated "regularization variables" from "floor variables"
135        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
136        * hiceMin became SEAICE_hice_reg (old hiceMin)
137          (with _reg meaning regularization variable)
138       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
139        so as to ensure energy conservation when going between phases
140      - A22 was not used anywhere
141     2) Changed regularization procedure for heffActual and hsnowActual to ensure
142        well-boundedness and smooth adjoint in seaice_growth.F
143     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
144        because the old regularization always set heffActual >= 0.05 cm
145     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
146        on AREA when HEFF > 0.
147      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
148        requiring that DISABLE_AREA_FLOOR *not* be defined
149     Affected verifications:
150      - 1D_ocean_ice_column (output.txt output_adm.txt)
151      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
152    o pkg/diagnostics:
153      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
154      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
155        (was _RL, now integer) with option = 0 to retrieve all levels.
156      - add pieces of code to compute velocity potential at each level (new diagnostics
157        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
158        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
159      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
160        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
161        and in diagnostics_fract_fill.F (do not need a valid pointer for the
162        diagnostics counter-mate); check that definition of counter-diagnostic
163        includes a valid counter-mate (in diagnostics_set_levels.F).
164    o model/src (rStar):
165      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
166        affect solution only if z* with full pressure in EOS;
167        update output of test-exp global_ocean.90x40x15.
168    o pkg/seaice:
169      - introduce siEps=1e-5 parameter
170      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
171      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
172      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
173        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
174        as well as ice cover age and ridging index (attached to AREA).
175        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
176        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
177        Up to SItrMaxNum=3 tracers can be used simultaneously.
178    o pkg/salt_plume:
179      -introduce SPsalFRAC run time parameter that sets the fraction of the
180       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
181       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
182    o model debug options:
183      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
184        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
185      - Refine debug-msg printing selection (3 new levels):
186        debugMode  : controls printing of debug messages (sequence of S/R calls).
187        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
188         debLevZero =  0 ; /* level of disabled aux. msg printing */
189         debLevA =  1 ; /* level of minimum  aux. msg printing */
190         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
191         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
192         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
193         debLevE =  5 ; /* level of extensive debug printing */
194        New debugLevel default: with default debugMode value (=F),
195          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
196          and if debugMode=T, default debugLevel = 4 (debLevD).
197        Relation with previous settings:
198         debLevB (=2) corresponds to former debLevA (=1)
199         debLevD (=4) corresponds to former debLevB (=2)
200        Note:
201         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
202         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
203            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
204      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
205        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
206    o pkg/obcs:
207      - change OBCSfixTopo default from True to False (should not change the results);
208        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
209    o pkg/thsice:
210      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
211        2nd layer seaice sublimation (unlikely to happen)
212      - use Interior mask for OBCS in thsice_advection.F (similar to what is
213        done in gad_advection & seaice_advection).
214    o adjoint:
215      bug fix spotted by Gael Forget:
216      seaice_advection and thsice_advection still had
217      legacy CPP options to avoid CS corner updates for adjoint
218    o pkg/seaice:
219      => Change some of the defaults (2011/05/29):
220         - change SEAICEuseFluxForm default (from False to True)
221         - change DIFF1 default (from 0.004 m/s to 0. m/s)
222         And print warnings if DIFF1 is not set in data.seaice and centered
223          avection scheme is used without any diffusion.
224      also:
225      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
226      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
227      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
228        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
229        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
230      update results of test exp.:
231         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
232             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
233             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
234         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
235         seaice_obcs: output (SEAICEuseFluxForm=T)
236      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
237          for standard fwd & AD lab_sea tests (to keep the same output).
238    o pkg/seaice/seaice_growth.F:
239      - use Ian Fenty's capping formulas for actual ice
240      thickness thoughout EVOLUTION branch.
241      - put treatment pathological case #2) in CPP brackets
242      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
243      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
244    o pkg/seaice:
245      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
246      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
247      also pass fac as a param, which can be 1. (to update the tendency
248      field) or the time step (to update the field itself).
249      - seaice_advdiff.F: for multidim, call seaice_diffusion with
250      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
251      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
252      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
253      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
254    o pkg/seaice:
255      diffusion with centered advection scheme (diffus.F & advect.F):
256      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
257        to just compute the laplacian of input-field.
258      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
259      - fix flux-form version in diffus.F to conserve tracer.
260      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
261       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
262    
263    checkpoint62y (2011/05/26)
264    o pkg/seaice:
265     - seaice_growth.F : in EVOLUTION branch, always include
266       a_QSWbyATM_cover in qnet (as it should be).
267     - verification/global_ocean.cs32x15 : update results accordingly
268       (output.seaice.txt output_adm.seaice.txt).
269    o pkg/seaice + obcs:
270     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
271       equivalent of assuming no tracer gradient outside the OB region.
272       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
273     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
274       after changes above);
275     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
276       only at OB location (instead of over a band of OLx width).
277    o pkg/seaice:
278     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
279       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
280    o pkg/obcs:
281      - split header file "OBCS.h" into 4 separated files:
282        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
283       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
284         (contain no conditional statement which depends on OBCS options).
285      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
286        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
287    o ctrl, cost, grdchk & autodiff pkgs:
288      - make options file more standard (like other {PKG}_OPTIONS.h file but
289        with AD_CONFIG.h); clean-up some of the included header files.
290    o pkg/obcs:
291      - do not mask tracer when applying OB (tracer == 0 could generate problems)
292      - apply tracer OB values to tracer field only at OB location (instead of
293        over a band of OLx width)
294      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
295      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
296        obcs_apply_tloc.F & obcs_apply_sloc.F
297    o obcs in model/src:
298      - call OBCS_APPLY_W only if NonHydrostatic.
299      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
300      - reset dEtaHdt and wVel to zero outside OB interior region ;
301      - leave tracer unchanged outside OB interior region: This has no effect
302        on the solution but just to prevent unrealistic tracer value outside OB.
303      - zero out velocity outside OB interior region: This has no effect on
304        the solution but just to prevent unrealistic velocity outside OB.
305    o obcs and non-lin free-surf:
306       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
307       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
308       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
309       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
310       update results of test-exp. exp4(nlfs).
311    o exp4 (nlfs) test-exp:
312       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
313       with NonLin-FreeSurf); update output.nlfs.txt
314    o obcs and 2d/3d solver norm:
315       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
316       and outside OB interior region (will allow to place OB further inside the
317       domain). Depending on the domain, can affects cg2d-Norm (previous
318       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
319       and cg3d-Norm (previous Norm was computed before canceling OB terms),
320       e.g. in tutorial_plume_on_slope.
321      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
322    o pkg rbcs:
323      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
324      - add capability to apply relaxation to horizontal velocity uVel & vVel.
325    o pkg/grdchk: add gradient check for control variable xx_shifwflx
326    o pkg/shelfice/shelfice_init_fixed.F
327      fix CPP-flag combinations
328    o pkg/seaice: Merge iceage code of Pierre Rampal
329      * update/change/correct ice age calculations
330      * add age updates for pathological cases
331      Probably needs more testing...
332    
333    checkpoint62x (2011/05/13)
334    o pkg/mom_vecinv:
335       high-order vorticity scheme: use interior masks (maskInW & S)
336       to zero-out (outside OB) gradient of vorticity.
337    o verification exp.:
338       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
339       hs94.128x64x5 and seaice_obcs ; update results.
340    o pkg/obcs:
341      fix bug in OBeta for YZ sections in obcs_exf_load.F
342    o pkg/ctrl, pkg/shelfice, and optim:
343      - add new control variable xx_shifwflx (fresh water flux underneath ice
344        shelves). This is almost as tedious as obcs-ctrl, because the
345        variables needs its own mask.
346      - add a cost function term that penalizes the deviation of xx_shifwflx
347        from the first guess (zero) in analogy to other control variables
348    o pkg/shelfice:
349      - start basic adjoint
350    o pkg/ctrl:
351      - remove extra 2D field "for good measure" when initializing in
352        ctrl_set_globfld_[xy/xz/yz].F
353      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
354      - improve error messages in ctrl_set_unpack_*
355    o OBC implementation in momentum:
356       use interior masks (maskInC,W & S) in momentum S/R:
357       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
358       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
359       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
360       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
361       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
362        (and also with Leith/Smagorinsky harmonic-viscosity).
363       Update output of experiment dome and exp4 (+nlfs).
364    o exp4 test-exp:
365      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
366        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
367        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
368        time-varying OB at Western-side for wVel (NonHyd); update output.
369      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
370        and biharmonic-viscosity ; also use prescribed time varying OB.
371    o pkg/obcs:
372      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
373    o model/src:
374      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
375      - initialise startTime & nIter0 with unlikely values: allows to set one
376        from the other without ambiguity.
377    o seaice_obcs test-exp.:
378      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
379    o pkg/obcs:
380      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
381        no longer needed with maskInC,W,S in pkg/generic_advdiff.
382    o pkg/seaice:
383      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
384        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
385      - fixed bug in the initialization of sea ice salinity variable HSALT
386        in seaice_init_varia.F  (removed dependence on ICE2WATR)
387    o fizhi-cs test exp.:
388       switch reference output convention for these 2 non-standard test-exp,
389        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
390          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
391       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
392    o model/inc:
393      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
394        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
395    o pkg/seaice:
396      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
397    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
398      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
399        and initial HSALT
400    
401    checkpoint62w (2011/04/26)
402    o pkg/mom_fluxform:
403      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
404      - use parameter "sideDragFactor" in no-slip BC side-drag part.
405      - update output of exp. global_ocean.90x40x15
406    o pkg/mom_vecinv:
407      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
408    o update seaice exp.:
409      use more consistent parameter values (remove "backward compatability only":
410       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
411      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
412       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
413    o update test-exp global_ocean.90x40x15:
414      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
415      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
416      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
417      o turn on zStar & viscA4 in standard set-up (dir input/)
418        and update output files: output.txt & output.dwnslp.txt
419    o new AD-test experiment: obcs_ctrl
420      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
421    o pkg/dic:
422      fix two bugs in handling water vapour pressure in carbonate chemistry
423      and air-sea fluxes. Found by Val Bennington and Galen McKinley
424      (add DIC Option = WATERVAP_BUG to recover old results)
425      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
426    o adding allowInteriorFreezing option to check for water below freezing point
427      at depth and bring the negative heat anomaly to the surface level
428    o pkgs _fields_load:
429      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
430      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
431        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
432        rbcs to get interpolation weights and time reccord number.
433      - fix multi-threading in aim_fields_load.F
434      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
435    o external_fields_load:
436      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
437       interpolation weights) to use in a periodic time-series ; do not divide by
438       time-step to convert to integer:
439       - this fixes case where externForcingPeriod is not multiple of time-step
440          (Thanks to Christopher L. Wolfe)
441       - this fixes case where externForcingPeriod is an odd multiple of time-step
442         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
443      store index of time-record which is currently loaded:
444       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
445       - needed for the adjoint but not yet used because of extensive recomputations;
446         (to be fixed soon)
447    
448    checkpoint62v (2011/04/02)
449    o verification/1D_ocean_ice_column added to test Ian Fenty's
450      pkg/seaice_growth.F modifications for improving sea ice code differentiability
451    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
452      (new velocity statistics after changing maskInW & maskInS definition)
453    o pkg/generic_advdiff with OBCS:
454      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
455      equivalent to assumption of no tracer gradient outside the OB region.
456      This will affect the results if using obcs+biharmonic diffusion.
457      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
458    o pkg/obcs:
459      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
460      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
461      in Interior region. No impact on solution but affects Velocity monitor stats.
462    o pkg/ptracers (adjoint)
463      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
464      tape file for each tracer
465    o model/inc/src and pkg/autodiff: add parameters that allow to turn
466      of parts of the adjoint code at run time. For now, there are only
467      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
468      parameters are set in data.pkg.
469      This is the lazy coward's version of doing this, but still useful for
470      debugging. In order to do it right, everything needs to be moved to
471      pkg/autodiff.
472    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
473      the end; this fixes the adjoint balancing code for open boundaries.
474    o pkg/ctrl:
475      - change behavior of xx_${varname}period to be analogous to exf-conventions:
476        xx_${varname}period =   0.,  means time-independent control part
477        xx_${varname}period = -12., means one-year-periodic monthly control part
478      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
479        clean up ctrl_init a little, remove unused variables
480      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
481      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
482    
483    checkpoint62u (2011/03/15)
484    o model/src:
485      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
486        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
487      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
488        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
489    o pkg/ctrl/obcs/ecco:
490      - remove obsolete, unused, and partially broken code:
491        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
492        ALLOW_CTRL_OBCS_BALANCE
493      - put a stop statement into ecco/cost_obcsvol.F, but also add
494        cost_obcsvol to ecco_ad_diff.list
495    o pkg/ecco: fix counting cost function contributions for obcs (code
496      by Matt M.) and diffkr for diagnostics
497    o pkg/ecco, pkg/ctrl, pkg/grdchk:
498      add cost penalty terms for initial uvel, vvel, eta controls
499      and I/O for prior error files
500    o pkg/mdsio:
501       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
502       (new argument) to check for tiled file in mdsioLocalDir : this fix the
503       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
504    o pkg/ctrl:
505     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
506       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
507       unused and superfluous variables
508     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
509    o pkg/ecco
510     - enable adjoint of Stevens OB
511    o pkg/ctrl/ecco/grdchk:
512      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
513        Fortunately, we do not have any tests for the numerous cpp-flagged
514        option of "obcs as control parameters" so we will never know
515        if this is an improvement (but at least now things compile).
516      - remove an obsolete initialization from ecco_cost_init_barfiles.F
517      - fix some problems within never used ifdefs to make the code compile
518    o pkg/obcs:
519     - Refine Interior mask definition to work with more complex OB (e.g.
520       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
521       read in Interior mask from file. Check if Interior mask is consistent
522       with OB list of indices.
523    o pkg/seaice
524     - beginning code for a seaice tracer package,
525       but currently only used for seaice age: SEAICE_AGE
526       SEAICE_num = 4
527       iTracer = 1: area-weighted ice age
528               = 2: volume-weighted ice age
529               = 3, 4: template for one-year vs. multi-year ice
530       data.seaice has new namelist SEAICE_PARM03 for arrays related to
531       SEAICE_num
532    
533    checkpoint62t (2011/03/05)
534    o pkg/obcs:
535     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
536       then normal component. This ensures that the normal component is set
537       correctly even when it conficts with tangential setting from an other OB.
538       Affects results of test-experiment seaice_obcs: update the output.txt
539    o pkg/obcs:
540     - add code to monitor statistics of dynamical fields at OB.
541     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
542       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
543       - change default: balance the Net inflow through all OB (instead of balancing
544         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
545     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
546       to match Nortern OB inflow (OBCS_balanceFacN=0).
547    o pkg/seaice:
548     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
549    o pkg/seaice (seaice_growth v 1.113):
550     - reverting seaice_growth to v 1.111 in order to have code with exact bit
551       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
552       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
553       runtime flag SEAICEareaFormula is kept but is inactive
554    o model/src:
555     - add new param to scale curvilinear grid distance and area when using
556       a different sphere radius from the grid-files.
557     - test/check multi-threads EXCH applied to local variable (cg2d_x)
558    o adjoint:
559     - enable adjoint of Stevens OB
560     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
561       (a bit delicate because of potentially modified adj. common block structure;
562       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
563    
564    checkpoint62s (2011/02/15)
565    o pkg/seaice (seaice_growth v 1.112):
566     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
567       computing the ice cover tendency from effective thickness tendencies. Include
568       Ian Fenty's formula.
569     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
570       SEAICEareaFormula.
571     - simplify notations for the various d_HEFF/d_AREA terms.
572    o pkg/gmredi:
573     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
574       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
575       add a verification test-run (front_relax.bvp) to test GM_useBVP.
576    o pkg/seaice (seaice_growth v 1.111):
577     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
578     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
579       also melt ice.
580    o pkg/seaice:
581     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
582     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
583    o pkg/cheapaml:
584     - from Nico Wienders: New version of this package.
585    o pkg/flt:
586     - add CPP options to prevent floats to re-enter the opposite side of
587       a periodic domain (default: keep periodicity)
588    o pkg/gmredi:
589     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
590       (needed for multi-dim advection).
591     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
592    o model/src:
593     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
594    o tutorial_tracer_adjsens
595     - extend to NLFS and replace maskC by hFacC
596       (change reference output accordingly)
597    
598    checkpoint62r (2011/01/24)
599    o testreport:
600     - add option -deloutp (-do) to remove output file after successful run
601     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
602       extract exact list of procs from this file ; adjust COMMAND by
603       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
604    o pkg/ecco: replace old ineffective way of penalizing deviations from
605      first guess (of obcs) with code by Matt Mazloff
606    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
607      exf/cal
608      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
609        and handle case of obcs?period == 0
610        Not affected by these changes: There is still an inconsistency in
611        the computation of start/endrec for the obcs variables for ALLOW_CAL
612        defined (see comment by Menemenlis, 7-Mar-2003)
613      - make S/R ctrl_get_gen_rec return something meaningful even if
614        ALLOW_CAL is not defined
615      - ctrl_getobcs?: simplify code so that it does not need to use
616                       S/R exf_swapfields
617    o testreport:
618       allow to test MPI with different number of processors for each experiment:
619       create file "SIZE.h.mpi" in each build dir.
620       Note: update of "-command" argument not yet implemented.
621    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
622      alleviate the need for additional 3D tapes when using
623      the non-inear free surface in the adjoint. This is done
624      by adding an 'update' of hfacc etc. to their current
625      value at the beginning of forward_step.F.
626    o pkg/seaice
627      seaice_lsr: move stress-divergence computations out of outer pseudo-
628      timestepping loop
629    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
630      up, so that the calls of the ctrl_* subroutines are really at the end
631      of the routine.
632    o pkg/gmredi:
633      allow to specify a 2-D horizontal map and a 1-D vertical profil
634      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
635    o pkg/seaice:
636      move lsr iterations from seaice_dynsolver to seaice_lsr.
637    o pkg/seaice:
638      reduce memory footprint of seaice mutldim advection tapes,
639      by using a 2D tape independent of the generic_advdiff ones,
640      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
641    
642    checkpoint62q (2010/12/29)
643    o model/src:
644      - check horizontal grid-spacing for unset or zero/negative values.
645      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
646    o pkg/flt:
647      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
648      - precision of input and output files set according to readBinaryPrec
649        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
650      - initial float position from tiled file was not converted to index space
651        (looks like a bug): fixed to make it similar to initial pos. global file.
652    o global_ocean.cs32x15:
653       change SIZE.h of AD set-up to get same tiling as with MPI.
654       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
655    o model/src:
656       add flag to control printing of domain fields (bathymetry, hFac ...) in
657       ini_mask_etc (call to plot_fieds_xy*).
658    o pkg/thsice:
659       if useEXF, some forcing fields are not valid in overlap: fixed by computing
660       over the interior only + apply EXCH at the end (like with SEAICE advection).
661    o pkg/mdsio:
662      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
663        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
664      - change barrier call for safe multi-threads access to 3-D shared buffer.
665      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
666      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
667        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
668    o pkg/flt:
669      - add fourth-order Runge-Kutta integration
670      - add basic exch2 support (only 1 facet supported so far!)
671    o pkg/mdsio+rw:
672      new S/R to read local (or tile independent) vector (read counterpart of
673       mds_writevec_loc, and front-end write_glvec_rl/rs).
674    o global_ocean.cs32x15: additional input_ad.seaice experiment
675        that uses pkg/seaice rather than pkg/thsice.
676        (using multidim advection for seaice)
677    o towards more F95 syntax for array specification in namelist:
678      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
679        of all verification experiments.
680           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
681          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
682      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
683    o global_ocean.cs32x15: additional input.seaice experiment
684        that uses pkg/seaice rather than pkg/thsice.
685    
686    checkpoint62p (2010/12/17)
687    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
688        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
689    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
690        allow for use of multim. advection in seaice adjoint.
691    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
692      - first attempt to close budgets by taking into account the freshwater
693        flux implied by the sublimation of snow and ice. So far only the
694        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
695        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
696    o eesupp/src:
697      new S/R with new option (NML_EXTENDED_F77) to change array specification
698      from F95 standard to commonly accepted extended F77 form.
699      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
700      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
701      for less tolerant f77 compiler (e.g., pgf77, g77).
702    o globalFiles:
703      commented out in parameter file "data" since it's not safe with MPI
704      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
705      in this case); no longer commented out in restart test (tst_2+2).
706    o add adTapeDir to specify a special directory where adjoint tapes are
707      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
708      and cannot be used together with mdsioLocalDir.
709    o nesting pkgs:
710      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
711      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
712      - add parameter files + utils dir + output from short run on beagle.
713    o pkg/seaice:
714        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
715    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
716      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
717    
718    checkpoint62o (2010/11/25)
719    o pkg/exf:
720      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
721    o pkg/seaice:
722      - seaice_ocean_stress: split a loop for better vectorization of the
723        adjoint code
724      - seaice_growth.F: fix bug in conservation of freshwater connected to
725        capping of heff, put contribution into d_HEFFbyNEG
726      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
727        by something more sensible (parameters that are what their name implies)
728      - change some defaults, so that by default exf-parameters are used for
729        things like rhoAir, cpAir,latent/sensible heat parameters, in order
730        to reproduce the old results, many data.seaice now contain funny values
731        for cpAir and latent heat of sublimation
732    o packages_readparms.F: move exf_readparms up in line so that
733        exf-parameters are visible for other packages (e.g. seaice)
734    o debugMode & debugLevel=2:
735      - differentiate between debugMode & debugLevel=2:
736        debugMode: controls printing of debug messages (sequence of S/R calls).
737        debugLevel: controls printing of algorithm intermediate results and stats.
738      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
739        => allows to print debug-stats without all sequence of call messages.
740      - switch control of debug print from debugLevel to debugMode in many S/R.
741    o pkg/obcs (obcs-sponge):
742        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
743        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
744    o pkg/generic_advdiff:
745      - record overlap minimum size for each advection scheme;
746      - refine criteria on overlap minimum size;
747      - check and stop (in gad_check) if overlap size is too small.
748    o pkg/obcs:
749      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
750        once, in ptracers_implicit.F)
751      - with seaice: remove test on empty file name in obcs_apply_seaice (always
752        apply OB values when tile has OB)
753    o model/src, coriolis setting:
754      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
755        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
756        files (selectCoriMap=3) with any grid.
757      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
758    o pkg/seaice/seaice_growth.F:
759        a few cosmetic changes that reduce the number of lines of code
760    o pkg/obcs: add boundary conditions following Stevens (1990)
761      - the code follows old MOM/NAOSIM code
762      - so far it is only implemented for the eastern and western boundaries
763        and NOT for pTracers
764    o pkg/rbcs:
765      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
766        beginning of the first rbcs forcing period.
767      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
768        offline package, i.e., one file per time, labeled by iteration number;
769        deltaTrbcs sets the timestep with which the data was generated;
770        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
771      - rbcsForcingCycle=0 makes forcing non-cyclic.
772      - make arithmetic safe for negative times and odd forcing periods.
773    
774    checkpoint62n (2010/11/09)
775    o pkg/seaice:
776        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
777    o pkg/obcs:
778       New S/R to copy tracer value from the OB location to narrow band region
779        (width = same as overlap) beyond the OB: preserve OB value (needed for
780        high-order scheme) which were overwritten by EXCH call if in overlap
781        region. Applied to theta, salt, ptracer and advected seaice variables.
782       With seaice: use maskInC in similar way as in gad_advection.F,
783        in seaice_advection.F and advect.F.
784       Update output of experiment seaice_obcs and change exp4 to test OBCS with
785        4th order Adv.Scheme. for pasive salt and ptracer.
786    o tools/genmake2:
787      - when looking for an optfile (not specified), only search for Fortran compiler
788        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
789      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
790        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
791      - set default for CPP to "cpp -traditional -P" (was the case without specifying
792        an optfile, but otherwise default was just "cpp".
793      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
794      - when "CC" is not set in the optfile, look for possible C compiler
795        (instead of just setting CC=cc)
796      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
797        => add a ".F" to ".o" rule for source files with no "#include" (such as
798           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
799      - move gfortran before g77 in list of possible Fortran compiler (consistent
800        with reference compiler switch from g77 to gfortran)
801    o pkg/seaice:
802      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
803        seaice_check that stops the model, when the CPP flag is used.
804      o seaice_growth.F: make capping of ice volume conserving by returning the
805        capped ice as freshwater to EmPmR. This does not change the verification
806        experiments but will change runs where the capping is acutally active
807    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
808      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
809         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
810         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
811    o tools/genmake2:
812      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
813      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
814      - clean previous genmake log files before anything else.
815      - change Makefile to remove testreport log files (*.tr_log) and genmake log
816        files only with "CLEAN" target (instead of "Clean");
817    o pkg/generic_advdiff:
818      Change OBCS in multiDim advection (gad_advection.F):
819       Use maskInC to prevent intermediate update of tracer-field in OB regions,
820       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
821       which were applying future time-step OB values.
822      This way, all explicit calculations use current-time-step OB values
823       (simpler and more consistent).
824      Affects results when set-up uses time-varying OBC and multi-dim advection;
825       update output of experiment seaice_obcs.
826    o pkg/seaice:
827      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
828       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
829         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
830      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
831       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
832       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
833    o pkg aim (2010/10/26):
834      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
835        formulation with obliquity, eccentricity, ... as run-time parameters,
836      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
837        upward shortwave radition at the surface (all-sky and clear-sky).
838    o pkg/obcs:
839      - writing sections with globalFiles=T does not work: switch to tiled-files
840        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
841      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
842      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
843    
844    checkpoint62m (2010/10/21)
845    o pkg/seaice: vectorize seaice_solve4temp.F
846      - move iterations loops outside of i/j-loops
847      - requires 2D arrays for TB and effConduct
848      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
849        modified in this routine
850      - a little bit of clean up, adjusting indentation, etc.
851      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
852        performance and '**TWO' by '**2' (because TWO is a float),
853        replaced ONE, ZERO
854    o eesupp/src:
855       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
856    o pkg/seaice/seaice_growth.F
857      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
858      merging process. The merged routine has two branches, and one activates the 'evolution'
859      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
860      In summary, here is what the '10/10 revision' did consist of
861        part 1: seaice_growth.F revisions 1.71 to 1.75
862          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
863            The emphasis here was on improving readability (e.g. by trying to use meaningful
864            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
865        part 1.5:
866          - revising the lab_sea experiment to make it a more useful (i.e. stable
867            and representative of an actual model run). This was done by generating a
868            (winter) pickup to start from, switching back the main experiment dynamic
869            solver from evp to lsr, having one of the experiments use the free drift solution.
870        part 2: seaice_growth.F revisions 1.76 to 1.85
871          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
872          - Sorting out the various fields units and sign (set early on and reset at the end)
873            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
874            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
875          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
876            and simplifying logical expressions to further improve readibility.
877        part 3: seaice_growth.F revisions 1.86 to 1.89
878          - Re-organize the blocks of code more logically.
879          - Merging the '_if.F' pieces that add something new.
880    o pkg/thsice:
881      - vectorize thsice_solve4temp and thsice_get_exf.
882        Problem: thsice_solve4temp has an unvectorizable statement that
883        might also be problematic for TAF
884      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
885        does not change the verifcation experiment, but will change all
886        experiments that have this flag undefined (not tested in verification);
887        a little reorganization to save a few 2D fields and recomputations
888      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
889      - 2nd step:  fix some store dirs
890        o seems to work somewhat, i.e. using ifort but not g77
891        o likely cause are incomplete init. or recomputation
892        o start verification/global_ocean.cs32x15/input_ad.thsice
893    o pkg/obcs: add support for exch2
894      - the position of the boundary and prescribed values are specified using
895        a global domain with exch2 facets stacked
896        - in x for N,S boundaries (like W2_mapIO=-1)
897        - in y for E,W boundaries (so E,W boundaries do not overlap)
898    o pkg/mdsio: add support for writing global sections with exch2
899        file layout is as for obcs described above:
900        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
901        - for y-z sections, facets are stacked in y
902    o pkg/thsice:
903       - change a few routines for better vectorization: thsice_albedo.F,
904         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
905         not affected, but in particular the latter routine has changed
906         dramatically (not necessarily easier to read now).
907       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
908       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
909    o verification/lab_sea:
910      - overhaul of the forward model experiments. The main motivation
911        for this revision is that lab_sea has proven quite fragile (when
912        changing the sea-ice code, and switching platforms) to a point
913        when failures were very hard to attribute to specific code problems.
914      - the suspected reason for this fragility is noise amplification by evp so,
915        to start with, we decided to replace evp with lsr in the main experiment.
916      - the input.lsr experiment thus became obsolete and was removed.
917      - it was replaced with the input.fd experiment that uses an
918        analytical "free drift" solution as the ice velocity field.
919      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
920        will hopefully allow us to discriminate problems due to dynamic solvers
921        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
922        us to test additional options, along with the salt plume package.
923      - Finally a pickup was generated (at the end of a one year run) to
924        make the tests more representative of an actual model run. Previously
925        the tests starting point was a 1m thickness of ice everywhere.
926    o pkg/seaice:
927      - introducing S\R seaice_freedrift.F that compute the
928        analytical solution to an approximate ice momentum
929        equation (i.e. the simple stress/coriolis balance).
930      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
931        of the free drift velocity field, and enable its use.
932        To actually use the free drift solution as the model ice
933        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
934    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
935    
936    checkpoint62l (2010/10/04)
937    o pkg/seaice:
938      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
939      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
940       version (with USE_ORIGINAL_SBI undef);
941    o add hooks for new packages OASIS, the package will follow
942      (hooks exclude the seaice pkg for now)
943    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
944      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
945      rather than mdsio_readvector.F/mdsio_writevector.F, within
946      adread_adwrite.F to read/write adjoint-related tapes to disk.
947    o eesupp and pkg/mdsio: ALLOW_WHIO
948      Option to write/read 2D fields to files including tiles halos.
949      The main purpose is for adjoint related "tape I/O".
950      The secondary purpose is for debugging phases.
951      A word on those rather specifically intended purposes.
952      The code was meant to be stripped down to the bare minimum.
953      Typically, there is a unique and basic mapping to the global
954      buffer (tile by tile, then proc by proc, then level by level), and
955      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
956      meant to generate user friendly outputs of various shapes and forms.
957      Rather it is intended, for the knowledgeabale developers,
958      to be largely independent of the many mdsio options, to allow
959      outputs of tiles+halos in debugging phases and in adjoint runs,
960      and to allow some flexibility in tuning (adoint) I/O depending on each
961      file system behavior. With regard to tuning, most of the potential knobs
962      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
963      to specify directories, to specify the typical size of I/O calls, etc.)
964      are not yet included, and will be added if they prove useful.
965    o pkg/seaice:
966       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
967    o pkg/seaice:
968       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
969       code (seaice_budget_ice_if.F) which enable to recover old standard
970       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
971       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
972    o model/src (rStar):
973       use simple average (not area weighted) of rStarFac at U,V point when using
974       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
975       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
976    
977    checkpoint62k (2010/09/17)
978    o adjoint
979       * changed verification/global_ocean.cs32x15 ; adjoint now tests
980         Adams-Bashforth 3 + NLFS + RSTAR
981       * some more modifs required for ECCO-GODAE v4
982    o pkg/seaice
983       add SEAICE_AGE_VOL option to use volume instead of area for
984       integrating SEAICE_AGE
985    o model/src:
986       first check-in of sigma & hybrid-sigma coordinate code ; also includes
987       non-linear free-surface parts ; but pressure-gradient not yet coded.
988    o pkg/ptracers:
989       option for ptracer to convert Salt Relax into additional EmP.
990        tested in exp. global_ocean.90x40x15.dwnslp (update output)
991    
992    checkpoint62j (2010/08/25)
993    o pkg/ggl90:
994       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
995    o pkg/dic: car_flux.F, phos_flux.F
996      - reduce number of exp-calls in order to improve performance
997      - clean up a little (replace fields by their macros, etc., fix
998        typo in CPP-flag)
999    o pkg/ggl90: minor changes
1000      - GGL90diffKrS was removed --> always use GGL90diffKr
1001      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1002      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1003        (commented out for now)
1004      - change in max/min operations to ensure that smoothing is ok
1005      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1006      - always use diffKrNrT as background profile (i.e. never use diffKr field)
1007    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1008    o pkg/dic:
1009      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1010        vectorization
1011      - small bug fix in insol for the unlikely case of a cartesian grid
1012      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1013        + now vectorize, which also removes adjoint recomputations;
1014        + replace integer maksp1 by _RL maskp1
1015        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1016    
1017    checkpoint62i (2010/07/21)
1018    o pkg/flt:
1019      - with OBCS: stop floats which enter the OB region
1020    o model/src:
1021      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1022        for implicit vertical advection.
1023    o pkg/seaice:
1024     - account for melting in seaice age evolution.
1025     - remove double counting of seaice ridging effect on seaice age.
1026    
1027    checkpoint62h (2010/06/18)
1028    o pkg/exch2:
1029     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1030    o tools/genmake2
1031      - remove "-pdefault" option: redundant with the use of "packages.conf";
1032      - remove file pkg/pkg_default : set the default as a pkg group
1033        ("default_pkg_list") defined in pkg/pkg_groups;
1034      - fix for case pkg/pkg_depend is missing (was hanging before);
1035      - add option "-pgroups" to specify a different pkg_groups than the default.
1036    o verification/adjustment.cs-32x32x1:
1037       add a "minimal" set-up test (code_min & input_min) which only compiles
1038       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1039    o tools/genmake2
1040      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1041      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1042    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1043      files are nearly the same anyway.
1044      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1045       - redefinition of tau(i,i) (by a factor of ustar)
1046       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1047       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1048       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1049       - replace
1050         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1051         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1052         by
1053         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1054         (changes results)
1055       -> exf_bulkformulae v1.22,
1056          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1057          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1058                    output.txt 1.63
1059           offline_exf_seaice: output.seaicetd.txt 1.7
1060           seaice_obcs: output.txt 1.10)
1061      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1062       -> exf_bulkformulae v1.23,
1063          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1064          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1065      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1066    o adjoint of exch-1:
1067     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1068       (note: was already like this when using EXCH-2) and remove flow dir
1069       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1070     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1071     - update pkg/exch2 diff list.
1072    
1073    checkpoint62g (2010/05/19)
1074    o eesupp/src (exch-1):
1075     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1076       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1077       (renamed to exch1_*rx_cube.F).
1078     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1079       to call new exch1 S/R ; update Makefile and .cvsignore.
1080     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1081       exch2_xy_rx later)
1082      Note: after updating your code, need to run "make clean" in eesupp/src
1083    o test experiment bottom_ctrl_5x5:
1084       new output_adm.txt with fewer grdchk & less monitor output.
1085    o model/src:
1086      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1087       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1088       beeing treated in the same way (ini_grid is not called a 2nd time).
1089    o pkg/exf:
1090      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1091      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1092      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1093      - cosmetic changes to exf_bulkformulae.F to make it look more like
1094        exf_bulk_largeyeager04.F
1095    o eesupp/src (exch-1):
1096      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1097      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1098        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1099        (even without using MPI).
1100      - Message mode: move RecvAck setting (indicator of buffer being ready)
1101        from send_put to recv_get S/R (was useless before, but not sure if
1102        it's much more useful now);
1103      - Switch the order of sync: MPI-proc 1rst and then threads;
1104      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1105      - fix AD code for communication mode ='get' (but not used).
1106    o model/src:
1107      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1108      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1109    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1110    o pkg/ctrl: require a specific set of control variables and exf-flags for
1111      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1112    o model/src:
1113     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1114       1rst forward sweep, to avoid over-writing output files during recomputations
1115       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1116     b) 2nd version:
1117      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1118      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1119         writePickupAtEnd) + seaice & ptracers output;
1120      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1121    o model/src:
1122      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1123    o pkg/exch2:
1124      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1125      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1126    o pkg/autodiff & exch2:
1127      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1128      (for now, only if ALLOW_EXCH2 is defined).
1129    o pkg/autodiff:
1130      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1131        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1132       + clean-up comments (_RS is not always real*4)
1133      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1134      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1135        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1136    o testreport (AD-tests):
1137      no longer link files from dir "../input" (1rst link files from
1138      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1139    
1140    checkpoint62f (2010/04/29)
1141    o model/src/the_main_loop.F:
1142      adjust store directives for seaice evp and multicategory according to
1143      pkg/ecco/the_main_loop.F
1144    o adjoint:
1145      global_sum_ad was incomplete (noted many times by many people ;)
1146      nice description by Jean U. as follows:
1147      * allreduce(var) in global_sum.F can be interpreted as
1148        reduce(sum) followed by broadcast of sum.
1149      * The adjoint of that is
1150        sum(adjoint) followed by broadcast(summed adjoint value)
1151        or in other words, allreduce(sum, adjoint vars)
1152      We were missing the sum(adjoint)!
1153      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1154      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1155      The fix should produce 16-digit accuracy between
1156      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1157      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1158      We'll probably change this yet again shortly
1159    o eesupp/src:
1160      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1161    o pkg/icefront
1162      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1163        specification of addmass array based on a 2D field, which is added
1164        at bottommost wet level at each horizontal location.
1165    o model/src:
1166     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1167     layout; (not always compatible with delX,delY setting; commented out for now).
1168    o pkg/exch2:
1169     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1170     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1171    
1172    checkpoint62e (2010/04/15)
1173    o pkg/obcs:
1174      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1175    o pkg/dic:
1176      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1177        (note: not presently tested in any forward verification exp.)
1178       update tutorial_global_oce_biogeo AD output file.
1179    o pkg/exf:
1180      - account for the variation of albedo as a function of zenith angle
1181        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1182    o build_options:
1183     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1184    o pkg/dic:
1185      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1186      - use binary pickup file for restart;
1187      - initialise atmos-CO2 box from dic_pCO2 parameter;
1188      - fix multi-threaded.
1189    o pkg/rbcs:
1190     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1191       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1192     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1193       and update output.txt
1194    o pkg/kpp:
1195     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1196     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1197       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1198       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1199     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1200       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1201  o pkg/offline:  o pkg/offline:
1202    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1203    (bug was added in version 1.10 on 2007-08-23).    (bug was added in version 1.10 on 2007-08-23).
# Line 57  o tools/build_options: Line 1251  o tools/build_options:
1251      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1252  o pkg/ecco  o pkg/ecco
1253    - allow user defined cost function contributions    - allow user defined cost function contributions
1254          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1255          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1256    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1257        the two options are complementary.        the two options are complementary.
1258  o pkg/smooth  o pkg/smooth
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