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revision 1.1240 by jmc, Wed Mar 24 02:12:51 2010 UTC revision 1.1486 by jmc, Wed Aug 3 00:32:26 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/mypackage:
8      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
9    
10    checkpoint63a (2011/08/02)
11    o pkg/diagnostics (velocity potential):
12      - fix velocity-potential calculation when using OBCS: balance net inflow
13        at each level (new S/R OBCS_DIAG_BALANCE).
14      - fix some of the problems with OBCS in stream-function calculation.
15    o pkg/exf/exf_readparms.F
16      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
17        EXF_NML_OBCS) more consistent, so that you need not have these lists
18        in data.exf when they are not used.
19    o optim/optim_readdata.F:
20      - add some output about obcs variables that might help debugging
21      - add a check about nvarlength
22    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
23    o pkg/diagnostics (velocity potential):
24      - fix mask for OBCS (still problems in stream-function with OBCS);
25      - add specific parameter (default = main code CG2D params) for solver;
26      - in case of poor convergence, use solution corresponding to lowest residual.
27    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
28      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
29      and should be avoided where possible.
30    o model/src (rStar):
31      - include r* effect on reference-state (PhiRef) in totPhiHyd
32        (so that it's really the potential anomaly at the cell center);
33        affect solution only if z* with full pressure in EOS.
34      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
35        update output (because of z* in totPhiHyd and viscA4 changes);
36      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
37        @ constant r) until interpolation at constant r is implemented.
38    o pkg/diagnostics
39      - fix RCENTER diagnostics in case cell center is not at interface middle
40    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
41      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
42      that THETA and SALT are "conservative temperature" and "absolute
43      salinity"
44    o pkg/ctrl
45      - fix computation of endrec in s/r ctrl_init_rec
46      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
47    o pkg/seaice/seaice_growth.F
48      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
49        remove then obsolete STORE directives
50      - fix STORE directives for tice and tices, so that only the
51        appropriate part of the fields are stored (and not the entire
52        field); update global_ocean.cs32x15.seaice AD output.
53      - cosmetic changes: adjust CPP flags and indentation for better
54        legibilty
55    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
56      Chris Wilson)
57    o pkg/gmredi:
58       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
59       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
60    
61    checkpoint63  (2011/07/11)
62    o pkg/exch2:
63     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
64     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
65       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
66       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
67    o pkg/diagnostics:
68     - deal with pairs of post-processed diags which are computed together; in
69       particular, re-order list of diags within 1 file to save 2nd computation.
70     - add S/R to compute velocity stream-function (called after velocity-potential
71       calculation) from divergence free transport -> new diagnostics "PsiVEL".
72     - add parameter to select grid-point location where PsiVEL == 0.
73    o eesupp/src:
74       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
75       (specific S/R needed with exch2 topology - for now, just print an error msg)
76    o pkg/shelfice
77     - Implement friction velocity-dependent transfer coefficients following
78       Holland and Jenkins, JPO, 1999
79       Original code by M. Losch with small modifs.
80       Enable with CPP option SHI_ALLOW_GAMMAFRICT
81       and runtime flag SHELFICEuseGammaFrict
82    o verification lab_sea & global_ocean.cs32x15:
83     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
84       does not miss some dependencies (but is slower) and also works with many files
85       (default makedepend limitation for AD built).
86     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
87    o pkg/diagnostics:
88     - add run-time parameter "useMissingValue" (def=False) to fill land-point
89        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
90       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
91     - Extend the use of "missing_value" setting from data.diagnostics for the case
92       of counter-diagnostics (where fraction-weight is zero). This applies both to
93       MNC and MDS output files.
94    o pkg/seaice/seaice_growth.F:
95      - add 'a priori' cap of latent heat flux based on actual mass considerations
96        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
97        non-legacy seaice_solve4temp.
98      - add diagnostic of the residual sublimation freshwater flux (the freshwater
99        flux taken from the ocean if the total actual latent heat fluxes exceed
100        the maximum)
101      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
102       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
103      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
104       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
105      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
106      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
107    o verification 1D_ocean_ice_column:
108       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
109       update results
110    o pkg/diagnostics:
111     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
112       which are not filled-up but computed from other diags ; In this case, the mate
113       diag points to the primary (filled-up) diag to used for post processing.
114     - Update Velocity-potential computation using post-processed diag framework.
115     ==> Change the ordering of fields and time-periods in MDS output file
116       when using periodic averaging: now writes one time record with the full set
117       of fields for this time period, then the next time reccord (it used to be
118       one field with the full set of time records then the next field).
119         Note: this is now similar to NetCDF (MNC) output file. <==
120    
121    checkpoint62z (2011/06/21)
122    o adjoint monitor:
123     - Add adjoint monitor output for packages exf, seaice
124       and update relevant testreport output
125    o pkg/seaice:
126     - re-order diags inits so that they appear in order in available_diagnostics.log
127     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
128       area/heff/hsnow preceeding thermodynamic growth/melt.
129     - modified diag: SIdA; output actual effect, as the description states.
130     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
131     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
132       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
133        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
134     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
135     - added diagnostics for seaice generic tracers (SItr*).
136     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
137     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
138     I. Fenty: 18-Jun-2011:
139     Minor changes to seaice package:
140     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
141        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
142       - Differentiated "regularization variables" from "floor variables"
143        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
144        * hiceMin became SEAICE_hice_reg (old hiceMin)
145          (with _reg meaning regularization variable)
146       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
147        so as to ensure energy conservation when going between phases
148      - A22 was not used anywhere
149     2) Changed regularization procedure for heffActual and hsnowActual to ensure
150        well-boundedness and smooth adjoint in seaice_growth.F
151     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
152        because the old regularization always set heffActual >= 0.05 cm
153     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
154        on AREA when HEFF > 0.
155      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
156        requiring that DISABLE_AREA_FLOOR *not* be defined
157     Affected verifications:
158      - 1D_ocean_ice_column (output.txt output_adm.txt)
159      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
160    o pkg/diagnostics:
161      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
162      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
163        (was _RL, now integer) with option = 0 to retrieve all levels.
164      - add pieces of code to compute velocity potential at each level (new diagnostics
165        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
166        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
167      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
168        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
169        and in diagnostics_fract_fill.F (do not need a valid pointer for the
170        diagnostics counter-mate); check that definition of counter-diagnostic
171        includes a valid counter-mate (in diagnostics_set_levels.F).
172    o model/src (rStar):
173      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
174        affect solution only if z* with full pressure in EOS;
175        update output of test-exp global_ocean.90x40x15.
176    o pkg/seaice:
177      - introduce siEps=1e-5 parameter
178      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
179      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
180      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
181        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
182        as well as ice cover age and ridging index (attached to AREA).
183        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
184        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
185        Up to SItrMaxNum=3 tracers can be used simultaneously.
186    o pkg/salt_plume:
187      -introduce SPsalFRAC run time parameter that sets the fraction of the
188       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
189       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
190    o model debug options:
191      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
192        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
193      - Refine debug-msg printing selection (3 new levels):
194        debugMode  : controls printing of debug messages (sequence of S/R calls).
195        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
196         debLevZero =  0 ; /* level of disabled aux. msg printing */
197         debLevA =  1 ; /* level of minimum  aux. msg printing */
198         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
199         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
200         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
201         debLevE =  5 ; /* level of extensive debug printing */
202        New debugLevel default: with default debugMode value (=F),
203          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
204          and if debugMode=T, default debugLevel = 4 (debLevD).
205        Relation with previous settings:
206         debLevB (=2) corresponds to former debLevA (=1)
207         debLevD (=4) corresponds to former debLevB (=2)
208        Note:
209         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
210         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
211            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
212      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
213        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
214    o pkg/obcs:
215      - change OBCSfixTopo default from True to False (should not change the results);
216        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
217    o pkg/thsice:
218      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
219        2nd layer seaice sublimation (unlikely to happen)
220      - use Interior mask for OBCS in thsice_advection.F (similar to what is
221        done in gad_advection & seaice_advection).
222    o adjoint:
223      bug fix spotted by Gael Forget:
224      seaice_advection and thsice_advection still had
225      legacy CPP options to avoid CS corner updates for adjoint
226    o pkg/seaice:
227      => Change some of the defaults (2011/05/29):
228         - change SEAICEuseFluxForm default (from False to True)
229         - change DIFF1 default (from 0.004 m/s to 0. m/s)
230         And print warnings if DIFF1 is not set in data.seaice and centered
231          avection scheme is used without any diffusion.
232      also:
233      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
234      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
235      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
236        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
237        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
238      update results of test exp.:
239         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
240             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
241             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
242         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
243         seaice_obcs: output (SEAICEuseFluxForm=T)
244      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
245          for standard fwd & AD lab_sea tests (to keep the same output).
246    o pkg/seaice/seaice_growth.F:
247      - use Ian Fenty's capping formulas for actual ice
248      thickness thoughout EVOLUTION branch.
249      - put treatment pathological case #2) in CPP brackets
250      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
251      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
252    o pkg/seaice:
253      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
254      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
255      also pass fac as a param, which can be 1. (to update the tendency
256      field) or the time step (to update the field itself).
257      - seaice_advdiff.F: for multidim, call seaice_diffusion with
258      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
259      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
260      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
261      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
262    o pkg/seaice:
263      diffusion with centered advection scheme (diffus.F & advect.F):
264      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
265        to just compute the laplacian of input-field.
266      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
267      - fix flux-form version in diffus.F to conserve tracer.
268      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
269       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
270    
271    checkpoint62y (2011/05/26)
272    o pkg/seaice:
273     - seaice_growth.F : in EVOLUTION branch, always include
274       a_QSWbyATM_cover in qnet (as it should be).
275     - verification/global_ocean.cs32x15 : update results accordingly
276       (output.seaice.txt output_adm.seaice.txt).
277    o pkg/seaice + obcs:
278     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
279       equivalent of assuming no tracer gradient outside the OB region.
280       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
281     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
282       after changes above);
283     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
284       only at OB location (instead of over a band of OLx width).
285    o pkg/seaice:
286     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
287       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
288    o pkg/obcs:
289      - split header file "OBCS.h" into 4 separated files:
290        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
291       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
292         (contain no conditional statement which depends on OBCS options).
293      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
294        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
295    o ctrl, cost, grdchk & autodiff pkgs:
296      - make options file more standard (like other {PKG}_OPTIONS.h file but
297        with AD_CONFIG.h); clean-up some of the included header files.
298    o pkg/obcs:
299      - do not mask tracer when applying OB (tracer == 0 could generate problems)
300      - apply tracer OB values to tracer field only at OB location (instead of
301        over a band of OLx width)
302      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
303      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
304        obcs_apply_tloc.F & obcs_apply_sloc.F
305    o obcs in model/src:
306      - call OBCS_APPLY_W only if NonHydrostatic.
307      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
308      - reset dEtaHdt and wVel to zero outside OB interior region ;
309      - leave tracer unchanged outside OB interior region: This has no effect
310        on the solution but just to prevent unrealistic tracer value outside OB.
311      - zero out velocity outside OB interior region: This has no effect on
312        the solution but just to prevent unrealistic velocity outside OB.
313    o obcs and non-lin free-surf:
314       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
315       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
316       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
317       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
318       update results of test-exp. exp4(nlfs).
319    o exp4 (nlfs) test-exp:
320       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
321       with NonLin-FreeSurf); update output.nlfs.txt
322    o obcs and 2d/3d solver norm:
323       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
324       and outside OB interior region (will allow to place OB further inside the
325       domain). Depending on the domain, can affects cg2d-Norm (previous
326       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
327       and cg3d-Norm (previous Norm was computed before canceling OB terms),
328       e.g. in tutorial_plume_on_slope.
329      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
330    o pkg rbcs:
331      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
332      - add capability to apply relaxation to horizontal velocity uVel & vVel.
333    o pkg/grdchk: add gradient check for control variable xx_shifwflx
334    o pkg/shelfice/shelfice_init_fixed.F
335      fix CPP-flag combinations
336    o pkg/seaice: Merge iceage code of Pierre Rampal
337      * update/change/correct ice age calculations
338      * add age updates for pathological cases
339      Probably needs more testing...
340    
341    checkpoint62x (2011/05/13)
342    o pkg/mom_vecinv:
343       high-order vorticity scheme: use interior masks (maskInW & S)
344       to zero-out (outside OB) gradient of vorticity.
345    o verification exp.:
346       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
347       hs94.128x64x5 and seaice_obcs ; update results.
348    o pkg/obcs:
349      fix bug in OBeta for YZ sections in obcs_exf_load.F
350    o pkg/ctrl, pkg/shelfice, and optim:
351      - add new control variable xx_shifwflx (fresh water flux underneath ice
352        shelves). This is almost as tedious as obcs-ctrl, because the
353        variables needs its own mask.
354      - add a cost function term that penalizes the deviation of xx_shifwflx
355        from the first guess (zero) in analogy to other control variables
356    o pkg/shelfice:
357      - start basic adjoint
358    o pkg/ctrl:
359      - remove extra 2D field "for good measure" when initializing in
360        ctrl_set_globfld_[xy/xz/yz].F
361      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
362      - improve error messages in ctrl_set_unpack_*
363    o OBC implementation in momentum:
364       use interior masks (maskInC,W & S) in momentum S/R:
365       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
366       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
367       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
368       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
369       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
370        (and also with Leith/Smagorinsky harmonic-viscosity).
371       Update output of experiment dome and exp4 (+nlfs).
372    o exp4 test-exp:
373      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
374        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
375        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
376        time-varying OB at Western-side for wVel (NonHyd); update output.
377      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
378        and biharmonic-viscosity ; also use prescribed time varying OB.
379    o pkg/obcs:
380      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
381    o model/src:
382      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
383      - initialise startTime & nIter0 with unlikely values: allows to set one
384        from the other without ambiguity.
385    o seaice_obcs test-exp.:
386      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
387    o pkg/obcs:
388      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
389        no longer needed with maskInC,W,S in pkg/generic_advdiff.
390    o pkg/seaice:
391      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
392        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
393      - fixed bug in the initialization of sea ice salinity variable HSALT
394        in seaice_init_varia.F  (removed dependence on ICE2WATR)
395    o fizhi-cs test exp.:
396       switch reference output convention for these 2 non-standard test-exp,
397        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
398          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
399       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
400    o model/inc:
401      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
402        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
403    o pkg/seaice:
404      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
405    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
406      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
407        and initial HSALT
408    
409    checkpoint62w (2011/04/26)
410    o pkg/mom_fluxform:
411      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
412      - use parameter "sideDragFactor" in no-slip BC side-drag part.
413      - update output of exp. global_ocean.90x40x15
414    o pkg/mom_vecinv:
415      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
416    o update seaice exp.:
417      use more consistent parameter values (remove "backward compatability only":
418       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
419      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
420       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
421    o update test-exp global_ocean.90x40x15:
422      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
423      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
424      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
425      o turn on zStar & viscA4 in standard set-up (dir input/)
426        and update output files: output.txt & output.dwnslp.txt
427    o new AD-test experiment: obcs_ctrl
428      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
429    o pkg/dic:
430      fix two bugs in handling water vapour pressure in carbonate chemistry
431      and air-sea fluxes. Found by Val Bennington and Galen McKinley
432      (add DIC Option = WATERVAP_BUG to recover old results)
433      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
434    o adding allowInteriorFreezing option to check for water below freezing point
435      at depth and bring the negative heat anomaly to the surface level
436    o pkgs _fields_load:
437      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
438      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
439        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
440        rbcs to get interpolation weights and time reccord number.
441      - fix multi-threading in aim_fields_load.F
442      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
443    o external_fields_load:
444      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
445       interpolation weights) to use in a periodic time-series ; do not divide by
446       time-step to convert to integer:
447       - this fixes case where externForcingPeriod is not multiple of time-step
448          (Thanks to Christopher L. Wolfe)
449       - this fixes case where externForcingPeriod is an odd multiple of time-step
450         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
451      store index of time-record which is currently loaded:
452       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
453       - needed for the adjoint but not yet used because of extensive recomputations;
454         (to be fixed soon)
455    
456    checkpoint62v (2011/04/02)
457    o verification/1D_ocean_ice_column added to test Ian Fenty's
458      pkg/seaice_growth.F modifications for improving sea ice code differentiability
459    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
460      (new velocity statistics after changing maskInW & maskInS definition)
461    o pkg/generic_advdiff with OBCS:
462      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
463      equivalent to assumption of no tracer gradient outside the OB region.
464      This will affect the results if using obcs+biharmonic diffusion.
465      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
466    o pkg/obcs:
467      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
468      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
469      in Interior region. No impact on solution but affects Velocity monitor stats.
470    o pkg/ptracers (adjoint)
471      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
472      tape file for each tracer
473    o model/inc/src and pkg/autodiff: add parameters that allow to turn
474      of parts of the adjoint code at run time. For now, there are only
475      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
476      parameters are set in data.pkg.
477      This is the lazy coward's version of doing this, but still useful for
478      debugging. In order to do it right, everything needs to be moved to
479      pkg/autodiff.
480    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
481      the end; this fixes the adjoint balancing code for open boundaries.
482    o pkg/ctrl:
483      - change behavior of xx_${varname}period to be analogous to exf-conventions:
484        xx_${varname}period =   0.,  means time-independent control part
485        xx_${varname}period = -12., means one-year-periodic monthly control part
486      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
487        clean up ctrl_init a little, remove unused variables
488      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
489      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
490    
491    checkpoint62u (2011/03/15)
492    o model/src:
493      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
494        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
495      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
496        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
497    o pkg/ctrl/obcs/ecco:
498      - remove obsolete, unused, and partially broken code:
499        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
500        ALLOW_CTRL_OBCS_BALANCE
501      - put a stop statement into ecco/cost_obcsvol.F, but also add
502        cost_obcsvol to ecco_ad_diff.list
503    o pkg/ecco: fix counting cost function contributions for obcs (code
504      by Matt M.) and diffkr for diagnostics
505    o pkg/ecco, pkg/ctrl, pkg/grdchk:
506      add cost penalty terms for initial uvel, vvel, eta controls
507      and I/O for prior error files
508    o pkg/mdsio:
509       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
510       (new argument) to check for tiled file in mdsioLocalDir : this fix the
511       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
512    o pkg/ctrl:
513     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
514       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
515       unused and superfluous variables
516     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
517    o pkg/ecco
518     - enable adjoint of Stevens OB
519    o pkg/ctrl/ecco/grdchk:
520      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
521        Fortunately, we do not have any tests for the numerous cpp-flagged
522        option of "obcs as control parameters" so we will never know
523        if this is an improvement (but at least now things compile).
524      - remove an obsolete initialization from ecco_cost_init_barfiles.F
525      - fix some problems within never used ifdefs to make the code compile
526    o pkg/obcs:
527     - Refine Interior mask definition to work with more complex OB (e.g.
528       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
529       read in Interior mask from file. Check if Interior mask is consistent
530       with OB list of indices.
531    o pkg/seaice
532     - beginning code for a seaice tracer package,
533       but currently only used for seaice age: SEAICE_AGE
534       SEAICE_num = 4
535       iTracer = 1: area-weighted ice age
536               = 2: volume-weighted ice age
537               = 3, 4: template for one-year vs. multi-year ice
538       data.seaice has new namelist SEAICE_PARM03 for arrays related to
539       SEAICE_num
540    
541    checkpoint62t (2011/03/05)
542    o pkg/obcs:
543     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
544       then normal component. This ensures that the normal component is set
545       correctly even when it conficts with tangential setting from an other OB.
546       Affects results of test-experiment seaice_obcs: update the output.txt
547    o pkg/obcs:
548     - add code to monitor statistics of dynamical fields at OB.
549     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
550       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
551       - change default: balance the Net inflow through all OB (instead of balancing
552         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
553     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
554       to match Nortern OB inflow (OBCS_balanceFacN=0).
555    o pkg/seaice:
556     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
557    o pkg/seaice (seaice_growth v 1.113):
558     - reverting seaice_growth to v 1.111 in order to have code with exact bit
559       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
560       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
561       runtime flag SEAICEareaFormula is kept but is inactive
562    o model/src:
563     - add new param to scale curvilinear grid distance and area when using
564       a different sphere radius from the grid-files.
565     - test/check multi-threads EXCH applied to local variable (cg2d_x)
566    o adjoint:
567     - enable adjoint of Stevens OB
568     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
569       (a bit delicate because of potentially modified adj. common block structure;
570       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
571    
572    checkpoint62s (2011/02/15)
573    o pkg/seaice (seaice_growth v 1.112):
574     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
575       computing the ice cover tendency from effective thickness tendencies. Include
576       Ian Fenty's formula.
577     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
578       SEAICEareaFormula.
579     - simplify notations for the various d_HEFF/d_AREA terms.
580    o pkg/gmredi:
581     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
582       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
583       add a verification test-run (front_relax.bvp) to test GM_useBVP.
584    o pkg/seaice (seaice_growth v 1.111):
585     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
586     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
587       also melt ice.
588    o pkg/seaice:
589     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
590     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
591    o pkg/cheapaml:
592     - from Nico Wienders: New version of this package.
593    o pkg/flt:
594     - add CPP options to prevent floats to re-enter the opposite side of
595       a periodic domain (default: keep periodicity)
596    o pkg/gmredi:
597     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
598       (needed for multi-dim advection).
599     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
600    o model/src:
601     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
602    o tutorial_tracer_adjsens
603     - extend to NLFS and replace maskC by hFacC
604       (change reference output accordingly)
605    
606    checkpoint62r (2011/01/24)
607    o testreport:
608     - add option -deloutp (-do) to remove output file after successful run
609     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
610       extract exact list of procs from this file ; adjust COMMAND by
611       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
612    o pkg/ecco: replace old ineffective way of penalizing deviations from
613      first guess (of obcs) with code by Matt Mazloff
614    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
615      exf/cal
616      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
617        and handle case of obcs?period == 0
618        Not affected by these changes: There is still an inconsistency in
619        the computation of start/endrec for the obcs variables for ALLOW_CAL
620        defined (see comment by Menemenlis, 7-Mar-2003)
621      - make S/R ctrl_get_gen_rec return something meaningful even if
622        ALLOW_CAL is not defined
623      - ctrl_getobcs?: simplify code so that it does not need to use
624                       S/R exf_swapfields
625    o testreport:
626       allow to test MPI with different number of processors for each experiment:
627       create file "SIZE.h.mpi" in each build dir.
628       Note: update of "-command" argument not yet implemented.
629    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
630      alleviate the need for additional 3D tapes when using
631      the non-inear free surface in the adjoint. This is done
632      by adding an 'update' of hfacc etc. to their current
633      value at the beginning of forward_step.F.
634    o pkg/seaice
635      seaice_lsr: move stress-divergence computations out of outer pseudo-
636      timestepping loop
637    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
638      up, so that the calls of the ctrl_* subroutines are really at the end
639      of the routine.
640    o pkg/gmredi:
641      allow to specify a 2-D horizontal map and a 1-D vertical profil
642      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
643    o pkg/seaice:
644      move lsr iterations from seaice_dynsolver to seaice_lsr.
645    o pkg/seaice:
646      reduce memory footprint of seaice mutldim advection tapes,
647      by using a 2D tape independent of the generic_advdiff ones,
648      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
649    
650    checkpoint62q (2010/12/29)
651    o model/src:
652      - check horizontal grid-spacing for unset or zero/negative values.
653      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
654    o pkg/flt:
655      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
656      - precision of input and output files set according to readBinaryPrec
657        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
658      - initial float position from tiled file was not converted to index space
659        (looks like a bug): fixed to make it similar to initial pos. global file.
660    o global_ocean.cs32x15:
661       change SIZE.h of AD set-up to get same tiling as with MPI.
662       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
663    o model/src:
664       add flag to control printing of domain fields (bathymetry, hFac ...) in
665       ini_mask_etc (call to plot_fieds_xy*).
666    o pkg/thsice:
667       if useEXF, some forcing fields are not valid in overlap: fixed by computing
668       over the interior only + apply EXCH at the end (like with SEAICE advection).
669    o pkg/mdsio:
670      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
671        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
672      - change barrier call for safe multi-threads access to 3-D shared buffer.
673      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
674      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
675        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
676    o pkg/flt:
677      - add fourth-order Runge-Kutta integration
678      - add basic exch2 support (only 1 facet supported so far!)
679    o pkg/mdsio+rw:
680      new S/R to read local (or tile independent) vector (read counterpart of
681       mds_writevec_loc, and front-end write_glvec_rl/rs).
682    o global_ocean.cs32x15: additional input_ad.seaice experiment
683        that uses pkg/seaice rather than pkg/thsice.
684        (using multidim advection for seaice)
685    o towards more F95 syntax for array specification in namelist:
686      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
687        of all verification experiments.
688           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
689          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
690      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
691    o global_ocean.cs32x15: additional input.seaice experiment
692        that uses pkg/seaice rather than pkg/thsice.
693    
694    checkpoint62p (2010/12/17)
695    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
696        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
697    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
698        allow for use of multim. advection in seaice adjoint.
699    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
700      - first attempt to close budgets by taking into account the freshwater
701        flux implied by the sublimation of snow and ice. So far only the
702        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
703        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
704    o eesupp/src:
705      new S/R with new option (NML_EXTENDED_F77) to change array specification
706      from F95 standard to commonly accepted extended F77 form.
707      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
708      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
709      for less tolerant f77 compiler (e.g., pgf77, g77).
710    o globalFiles:
711      commented out in parameter file "data" since it's not safe with MPI
712      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
713      in this case); no longer commented out in restart test (tst_2+2).
714    o add adTapeDir to specify a special directory where adjoint tapes are
715      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
716      and cannot be used together with mdsioLocalDir.
717    o nesting pkgs:
718      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
719      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
720      - add parameter files + utils dir + output from short run on beagle.
721    o pkg/seaice:
722        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
723    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
724      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
725    
726    checkpoint62o (2010/11/25)
727    o pkg/exf:
728      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
729    o pkg/seaice:
730      - seaice_ocean_stress: split a loop for better vectorization of the
731        adjoint code
732      - seaice_growth.F: fix bug in conservation of freshwater connected to
733        capping of heff, put contribution into d_HEFFbyNEG
734      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
735        by something more sensible (parameters that are what their name implies)
736      - change some defaults, so that by default exf-parameters are used for
737        things like rhoAir, cpAir,latent/sensible heat parameters, in order
738        to reproduce the old results, many data.seaice now contain funny values
739        for cpAir and latent heat of sublimation
740    o packages_readparms.F: move exf_readparms up in line so that
741        exf-parameters are visible for other packages (e.g. seaice)
742    o debugMode & debugLevel=2:
743      - differentiate between debugMode & debugLevel=2:
744        debugMode: controls printing of debug messages (sequence of S/R calls).
745        debugLevel: controls printing of algorithm intermediate results and stats.
746      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
747        => allows to print debug-stats without all sequence of call messages.
748      - switch control of debug print from debugLevel to debugMode in many S/R.
749    o pkg/obcs (obcs-sponge):
750        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
751        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
752    o pkg/generic_advdiff:
753      - record overlap minimum size for each advection scheme;
754      - refine criteria on overlap minimum size;
755      - check and stop (in gad_check) if overlap size is too small.
756    o pkg/obcs:
757      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
758        once, in ptracers_implicit.F)
759      - with seaice: remove test on empty file name in obcs_apply_seaice (always
760        apply OB values when tile has OB)
761    o model/src, coriolis setting:
762      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
763        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
764        files (selectCoriMap=3) with any grid.
765      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
766    o pkg/seaice/seaice_growth.F:
767        a few cosmetic changes that reduce the number of lines of code
768    o pkg/obcs: add boundary conditions following Stevens (1990)
769      - the code follows old MOM/NAOSIM code
770      - so far it is only implemented for the eastern and western boundaries
771        and NOT for pTracers
772    o pkg/rbcs:
773      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
774        beginning of the first rbcs forcing period.
775      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
776        offline package, i.e., one file per time, labeled by iteration number;
777        deltaTrbcs sets the timestep with which the data was generated;
778        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
779      - rbcsForcingCycle=0 makes forcing non-cyclic.
780      - make arithmetic safe for negative times and odd forcing periods.
781    
782    checkpoint62n (2010/11/09)
783    o pkg/seaice:
784        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
785    o pkg/obcs:
786       New S/R to copy tracer value from the OB location to narrow band region
787        (width = same as overlap) beyond the OB: preserve OB value (needed for
788        high-order scheme) which were overwritten by EXCH call if in overlap
789        region. Applied to theta, salt, ptracer and advected seaice variables.
790       With seaice: use maskInC in similar way as in gad_advection.F,
791        in seaice_advection.F and advect.F.
792       Update output of experiment seaice_obcs and change exp4 to test OBCS with
793        4th order Adv.Scheme. for pasive salt and ptracer.
794    o tools/genmake2:
795      - when looking for an optfile (not specified), only search for Fortran compiler
796        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
797      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
798        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
799      - set default for CPP to "cpp -traditional -P" (was the case without specifying
800        an optfile, but otherwise default was just "cpp".
801      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
802      - when "CC" is not set in the optfile, look for possible C compiler
803        (instead of just setting CC=cc)
804      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
805        => add a ".F" to ".o" rule for source files with no "#include" (such as
806           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
807      - move gfortran before g77 in list of possible Fortran compiler (consistent
808        with reference compiler switch from g77 to gfortran)
809    o pkg/seaice:
810      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
811        seaice_check that stops the model, when the CPP flag is used.
812      o seaice_growth.F: make capping of ice volume conserving by returning the
813        capped ice as freshwater to EmPmR. This does not change the verification
814        experiments but will change runs where the capping is acutally active
815    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
816      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
817         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
818         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
819    o tools/genmake2:
820      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
821      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
822      - clean previous genmake log files before anything else.
823      - change Makefile to remove testreport log files (*.tr_log) and genmake log
824        files only with "CLEAN" target (instead of "Clean");
825    o pkg/generic_advdiff:
826      Change OBCS in multiDim advection (gad_advection.F):
827       Use maskInC to prevent intermediate update of tracer-field in OB regions,
828       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
829       which were applying future time-step OB values.
830      This way, all explicit calculations use current-time-step OB values
831       (simpler and more consistent).
832      Affects results when set-up uses time-varying OBC and multi-dim advection;
833       update output of experiment seaice_obcs.
834    o pkg/seaice:
835      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
836       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
837         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
838      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
839       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
840       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
841    o pkg aim (2010/10/26):
842      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
843        formulation with obliquity, eccentricity, ... as run-time parameters,
844      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
845        upward shortwave radition at the surface (all-sky and clear-sky).
846    o pkg/obcs:
847      - writing sections with globalFiles=T does not work: switch to tiled-files
848        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
849      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
850      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
851    
852    checkpoint62m (2010/10/21)
853    o pkg/seaice: vectorize seaice_solve4temp.F
854      - move iterations loops outside of i/j-loops
855      - requires 2D arrays for TB and effConduct
856      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
857        modified in this routine
858      - a little bit of clean up, adjusting indentation, etc.
859      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
860        performance and '**TWO' by '**2' (because TWO is a float),
861        replaced ONE, ZERO
862    o eesupp/src:
863       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
864    o pkg/seaice/seaice_growth.F
865      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
866      merging process. The merged routine has two branches, and one activates the 'evolution'
867      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
868      In summary, here is what the '10/10 revision' did consist of
869        part 1: seaice_growth.F revisions 1.71 to 1.75
870          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
871            The emphasis here was on improving readability (e.g. by trying to use meaningful
872            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
873        part 1.5:
874          - revising the lab_sea experiment to make it a more useful (i.e. stable
875            and representative of an actual model run). This was done by generating a
876            (winter) pickup to start from, switching back the main experiment dynamic
877            solver from evp to lsr, having one of the experiments use the free drift solution.
878        part 2: seaice_growth.F revisions 1.76 to 1.85
879          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
880          - Sorting out the various fields units and sign (set early on and reset at the end)
881            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
882            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
883          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
884            and simplifying logical expressions to further improve readibility.
885        part 3: seaice_growth.F revisions 1.86 to 1.89
886          - Re-organize the blocks of code more logically.
887          - Merging the '_if.F' pieces that add something new.
888    o pkg/thsice:
889      - vectorize thsice_solve4temp and thsice_get_exf.
890        Problem: thsice_solve4temp has an unvectorizable statement that
891        might also be problematic for TAF
892      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
893        does not change the verifcation experiment, but will change all
894        experiments that have this flag undefined (not tested in verification);
895        a little reorganization to save a few 2D fields and recomputations
896      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
897      - 2nd step:  fix some store dirs
898        o seems to work somewhat, i.e. using ifort but not g77
899        o likely cause are incomplete init. or recomputation
900        o start verification/global_ocean.cs32x15/input_ad.thsice
901    o pkg/obcs: add support for exch2
902      - the position of the boundary and prescribed values are specified using
903        a global domain with exch2 facets stacked
904        - in x for N,S boundaries (like W2_mapIO=-1)
905        - in y for E,W boundaries (so E,W boundaries do not overlap)
906    o pkg/mdsio: add support for writing global sections with exch2
907        file layout is as for obcs described above:
908        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
909        - for y-z sections, facets are stacked in y
910    o pkg/thsice:
911       - change a few routines for better vectorization: thsice_albedo.F,
912         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
913         not affected, but in particular the latter routine has changed
914         dramatically (not necessarily easier to read now).
915       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
916       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
917    o verification/lab_sea:
918      - overhaul of the forward model experiments. The main motivation
919        for this revision is that lab_sea has proven quite fragile (when
920        changing the sea-ice code, and switching platforms) to a point
921        when failures were very hard to attribute to specific code problems.
922      - the suspected reason for this fragility is noise amplification by evp so,
923        to start with, we decided to replace evp with lsr in the main experiment.
924      - the input.lsr experiment thus became obsolete and was removed.
925      - it was replaced with the input.fd experiment that uses an
926        analytical "free drift" solution as the ice velocity field.
927      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
928        will hopefully allow us to discriminate problems due to dynamic solvers
929        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
930        us to test additional options, along with the salt plume package.
931      - Finally a pickup was generated (at the end of a one year run) to
932        make the tests more representative of an actual model run. Previously
933        the tests starting point was a 1m thickness of ice everywhere.
934    o pkg/seaice:
935      - introducing S\R seaice_freedrift.F that compute the
936        analytical solution to an approximate ice momentum
937        equation (i.e. the simple stress/coriolis balance).
938      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
939        of the free drift velocity field, and enable its use.
940        To actually use the free drift solution as the model ice
941        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
942    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
943    
944    checkpoint62l (2010/10/04)
945    o pkg/seaice:
946      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
947      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
948       version (with USE_ORIGINAL_SBI undef);
949    o add hooks for new packages OASIS, the package will follow
950      (hooks exclude the seaice pkg for now)
951    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
952      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
953      rather than mdsio_readvector.F/mdsio_writevector.F, within
954      adread_adwrite.F to read/write adjoint-related tapes to disk.
955    o eesupp and pkg/mdsio: ALLOW_WHIO
956      Option to write/read 2D fields to files including tiles halos.
957      The main purpose is for adjoint related "tape I/O".
958      The secondary purpose is for debugging phases.
959      A word on those rather specifically intended purposes.
960      The code was meant to be stripped down to the bare minimum.
961      Typically, there is a unique and basic mapping to the global
962      buffer (tile by tile, then proc by proc, then level by level), and
963      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
964      meant to generate user friendly outputs of various shapes and forms.
965      Rather it is intended, for the knowledgeabale developers,
966      to be largely independent of the many mdsio options, to allow
967      outputs of tiles+halos in debugging phases and in adjoint runs,
968      and to allow some flexibility in tuning (adoint) I/O depending on each
969      file system behavior. With regard to tuning, most of the potential knobs
970      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
971      to specify directories, to specify the typical size of I/O calls, etc.)
972      are not yet included, and will be added if they prove useful.
973    o pkg/seaice:
974       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
975    o pkg/seaice:
976       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
977       code (seaice_budget_ice_if.F) which enable to recover old standard
978       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
979       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
980    o model/src (rStar):
981       use simple average (not area weighted) of rStarFac at U,V point when using
982       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
983       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
984    
985    checkpoint62k (2010/09/17)
986    o adjoint
987       * changed verification/global_ocean.cs32x15 ; adjoint now tests
988         Adams-Bashforth 3 + NLFS + RSTAR
989       * some more modifs required for ECCO-GODAE v4
990    o pkg/seaice
991       add SEAICE_AGE_VOL option to use volume instead of area for
992       integrating SEAICE_AGE
993    o model/src:
994       first check-in of sigma & hybrid-sigma coordinate code ; also includes
995       non-linear free-surface parts ; but pressure-gradient not yet coded.
996    o pkg/ptracers:
997       option for ptracer to convert Salt Relax into additional EmP.
998        tested in exp. global_ocean.90x40x15.dwnslp (update output)
999    
1000    checkpoint62j (2010/08/25)
1001    o pkg/ggl90:
1002       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1003    o pkg/dic: car_flux.F, phos_flux.F
1004      - reduce number of exp-calls in order to improve performance
1005      - clean up a little (replace fields by their macros, etc., fix
1006        typo in CPP-flag)
1007    o pkg/ggl90: minor changes
1008      - GGL90diffKrS was removed --> always use GGL90diffKr
1009      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1010      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1011        (commented out for now)
1012      - change in max/min operations to ensure that smoothing is ok
1013      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1014      - always use diffKrNrT as background profile (i.e. never use diffKr field)
1015    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1016    o pkg/dic:
1017      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1018        vectorization
1019      - small bug fix in insol for the unlikely case of a cartesian grid
1020      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1021        + now vectorize, which also removes adjoint recomputations;
1022        + replace integer maksp1 by _RL maskp1
1023        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1024    
1025    checkpoint62i (2010/07/21)
1026    o pkg/flt:
1027      - with OBCS: stop floats which enter the OB region
1028    o model/src:
1029      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1030        for implicit vertical advection.
1031    o pkg/seaice:
1032     - account for melting in seaice age evolution.
1033     - remove double counting of seaice ridging effect on seaice age.
1034    
1035    checkpoint62h (2010/06/18)
1036    o pkg/exch2:
1037     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1038    o tools/genmake2
1039      - remove "-pdefault" option: redundant with the use of "packages.conf";
1040      - remove file pkg/pkg_default : set the default as a pkg group
1041        ("default_pkg_list") defined in pkg/pkg_groups;
1042      - fix for case pkg/pkg_depend is missing (was hanging before);
1043      - add option "-pgroups" to specify a different pkg_groups than the default.
1044    o verification/adjustment.cs-32x32x1:
1045       add a "minimal" set-up test (code_min & input_min) which only compiles
1046       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1047    o tools/genmake2
1048      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1049      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1050    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1051      files are nearly the same anyway.
1052      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1053       - redefinition of tau(i,i) (by a factor of ustar)
1054       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1055       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1056       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1057       - replace
1058         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1059         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1060         by
1061         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1062         (changes results)
1063       -> exf_bulkformulae v1.22,
1064          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1065          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1066                    output.txt 1.63
1067           offline_exf_seaice: output.seaicetd.txt 1.7
1068           seaice_obcs: output.txt 1.10)
1069      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1070       -> exf_bulkformulae v1.23,
1071          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1072          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1073      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1074    o adjoint of exch-1:
1075     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1076       (note: was already like this when using EXCH-2) and remove flow dir
1077       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1078     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1079     - update pkg/exch2 diff list.
1080    
1081    checkpoint62g (2010/05/19)
1082    o eesupp/src (exch-1):
1083     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1084       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1085       (renamed to exch1_*rx_cube.F).
1086     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1087       to call new exch1 S/R ; update Makefile and .cvsignore.
1088     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1089       exch2_xy_rx later)
1090      Note: after updating your code, need to run "make clean" in eesupp/src
1091    o test experiment bottom_ctrl_5x5:
1092       new output_adm.txt with fewer grdchk & less monitor output.
1093    o model/src:
1094      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1095       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1096       beeing treated in the same way (ini_grid is not called a 2nd time).
1097    o pkg/exf:
1098      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1099      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1100      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1101      - cosmetic changes to exf_bulkformulae.F to make it look more like
1102        exf_bulk_largeyeager04.F
1103    o eesupp/src (exch-1):
1104      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1105      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1106        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1107        (even without using MPI).
1108      - Message mode: move RecvAck setting (indicator of buffer being ready)
1109        from send_put to recv_get S/R (was useless before, but not sure if
1110        it's much more useful now);
1111      - Switch the order of sync: MPI-proc 1rst and then threads;
1112      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1113      - fix AD code for communication mode ='get' (but not used).
1114    o model/src:
1115      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1116      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1117    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1118    o pkg/ctrl: require a specific set of control variables and exf-flags for
1119      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1120    o model/src:
1121     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1122       1rst forward sweep, to avoid over-writing output files during recomputations
1123       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1124     b) 2nd version:
1125      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1126      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1127         writePickupAtEnd) + seaice & ptracers output;
1128      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1129    o model/src:
1130      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1131    o pkg/exch2:
1132      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1133      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1134    o pkg/autodiff & exch2:
1135      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1136      (for now, only if ALLOW_EXCH2 is defined).
1137    o pkg/autodiff:
1138      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1139        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1140       + clean-up comments (_RS is not always real*4)
1141      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1142      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1143        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1144    o testreport (AD-tests):
1145      no longer link files from dir "../input" (1rst link files from
1146      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1147    
1148    checkpoint62f (2010/04/29)
1149    o model/src/the_main_loop.F:
1150      adjust store directives for seaice evp and multicategory according to
1151      pkg/ecco/the_main_loop.F
1152    o adjoint:
1153      global_sum_ad was incomplete (noted many times by many people ;)
1154      nice description by Jean U. as follows:
1155      * allreduce(var) in global_sum.F can be interpreted as
1156        reduce(sum) followed by broadcast of sum.
1157      * The adjoint of that is
1158        sum(adjoint) followed by broadcast(summed adjoint value)
1159        or in other words, allreduce(sum, adjoint vars)
1160      We were missing the sum(adjoint)!
1161      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1162      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1163      The fix should produce 16-digit accuracy between
1164      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1165      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1166      We'll probably change this yet again shortly
1167    o eesupp/src:
1168      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1169    o pkg/icefront
1170      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1171        specification of addmass array based on a 2D field, which is added
1172        at bottommost wet level at each horizontal location.
1173    o model/src:
1174     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1175     layout; (not always compatible with delX,delY setting; commented out for now).
1176    o pkg/exch2:
1177     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1178     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1179    
1180    checkpoint62e (2010/04/15)
1181    o pkg/obcs:
1182      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1183    o pkg/dic:
1184      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1185        (note: not presently tested in any forward verification exp.)
1186       update tutorial_global_oce_biogeo AD output file.
1187    o pkg/exf:
1188      - account for the variation of albedo as a function of zenith angle
1189        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1190    o build_options:
1191     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1192    o pkg/dic:
1193      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1194      - use binary pickup file for restart;
1195      - initialise atmos-CO2 box from dic_pCO2 parameter;
1196      - fix multi-threaded.
1197    o pkg/rbcs:
1198     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1199       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1200     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1201       and update output.txt
1202    o pkg/kpp:
1203     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1204     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1205       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1206       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1207     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1208       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1209    o pkg/offline:
1210      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1211      (bug was added in version 1.10 on 2007-08-23).
1212    o pkg/offline:
1213      - no need to specify periodicExternalForcing, etc ... to use offline pack
1214      - offline input files no longer just single prec --> parameter offlineLoadPrec
1215    o verification/lab_sea:
1216      change AD test to multi-tile setup and update all 4 AD output.
1217      NOTE: while cost function values remain very similar,
1218      gradients are very different, although gradient checks are self-consistent
1219      Should try to get to the bottom of this (cost function summation order?)
1220    o pkg/dic:
1221      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1222      a weakness of TAF that drops part of double precision in log10 derivative.
1223      <= changes removed since problem has been fixed in current TAF version 1.9.71
1224      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1225  o pkg/ecco:  o pkg/ecco:
1226    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1227    update all 4 lab_sea AD output.    update all 4 lab_sea AD output.
# Line 41  o tools/build_options: Line 1259  o tools/build_options:
1259      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1260  o pkg/ecco  o pkg/ecco
1261    - allow user defined cost function contributions    - allow user defined cost function contributions
1262          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1263          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1264    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1265        the two options are complementary.        the two options are complementary.
1266  o pkg/smooth  o pkg/smooth
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