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revision 1.1226 by jmc, Tue Jan 26 16:13:21 2010 UTC revision 1.1477 by jmc, Wed Jul 20 13:45:05 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 model/src (rStar):
8      - include r* effect on reference-state (PhiRef) in totPhiHyd
9        (so that it's really the potential anomaly at the cell center);
10        affect solution only if z* with full pressure in EOS.
11      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
12        update output (because of z* in totPhiHyd and viscA4 changes);
13      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
14        @ constant r) until interpolation at constant r is implemented.
15    o pkg/diagnostics
16      - fix RCENTER diagnostics in case cell center is not at interface middle
17    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
18      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
19      that THETA and SALT are "conservative temperature" and "absolute
20      salinity"
21    o pkg/ctrl
22      - fix computation of endrec in s/r ctrl_init_rec
23      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
24    o pkg/seaice/seaice_growth.F
25      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
26        remove then obsolete STORE directives
27      - fix STORE directives for tice and tices, so that only the
28        appropriate part of the fields are stored (and not the entire
29        field); update global_ocean.cs32x15.seaice AD output.
30      - cosmetic changes: adjust CPP flags and indentation for better
31        legibilty
32    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
33      Chris Wilson)
34    o pkg/gmredi:
35       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
36       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
37    
38    checkpoint63 (2011/07/11)
39    o pkg/exch2:
40     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
41     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
42       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
43       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
44    o pkg/diagnostics:
45     - deal with pairs of post-processed diags which are computed together; in
46       particular, re-order list of diags within 1 file to save 2nd computation.
47     - add S/R to compute velocity stream-function (called after velocity-potential
48       calculation) from divergence free transport -> new diagnostics "PsiVEL".
49     - add parameter to select grid-point location where PsiVEL == 0.
50    o eesupp/src:
51       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
52       (specific S/R needed with exch2 topology - for now, just print an error msg)
53    o pkg/shelfice
54     - Implement friction velocity-dependent transfer coefficients following
55       Holland and Jenkins, JPO, 1999
56       Original code by M. Losch with small modifs.
57       Enable with CPP option SHI_ALLOW_GAMMAFRICT
58       and runtime flag SHELFICEuseGammaFrict
59    o verification lab_sea & global_ocean.cs32x15:
60     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
61       does not miss some dependencies (but is slower) and also works with many files
62       (default makedepend limitation for AD built).
63     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
64    o pkg/diagnostics:
65     - add run-time parameter "useMissingValue" (def=False) to fill land-point
66        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
67       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
68     - Extend the use of "missing_value" setting from data.diagnostics for the case
69       of counter-diagnostics (where fraction-weight is zero). This applies both to
70       MNC and MDS output files.
71    o pkg/seaice/seaice_growth.F:
72      - add 'a priori' cap of latent heat flux based on actual mass considerations
73        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
74        non-legacy seaice_solve4temp.
75      - add diagnostic of the residual sublimation freshwater flux (the freshwater
76        flux taken from the ocean if the total actual latent heat fluxes exceed
77        the maximum)
78      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
79       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
80      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
81       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
82      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
83      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
84    o verification 1D_ocean_ice_column:
85       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
86       update results
87    o pkg/diagnostics:
88     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
89       which are not filled-up but computed from other diags ; In this case, the mate
90       diag points to the primary (filled-up) diag to used for post processing.
91     - Update Velocity-potential computation using post-processed diag framework.
92     ==> Change the ordering of fields and time-periods in MDS output file
93       when using periodic averaging: now writes one time record with the full set
94       of fields for this time period, then the next time reccord (it used to be
95       one field with the full set of time records then the next field).
96         Note: this is now similar to NetCDF (MNC) output file. <==
97    
98    checkpoint62z (2011/06/21)
99    o adjoint monitor:
100     - Add adjoint monitor output for packages exf, seaice
101       and update relevant testreport output
102    o pkg/seaice:
103     - re-order diags inits so that they appear in order in available_diagnostics.log
104     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
105       area/heff/hsnow preceeding thermodynamic growth/melt.
106     - modified diag: SIdA; output actual effect, as the description states.
107     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
108     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
109       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
110        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
111     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
112     - added diagnostics for seaice generic tracers (SItr*).
113     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
114     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
115     I. Fenty: 18-Jun-2011:
116     Minor changes to seaice package:
117     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
118        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
119       - Differentiated "regularization variables" from "floor variables"
120        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
121        * hiceMin became SEAICE_hice_reg (old hiceMin)
122          (with _reg meaning regularization variable)
123       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
124        so as to ensure energy conservation when going between phases
125      - A22 was not used anywhere
126     2) Changed regularization procedure for heffActual and hsnowActual to ensure
127        well-boundedness and smooth adjoint in seaice_growth.F
128     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
129        because the old regularization always set heffActual >= 0.05 cm
130     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
131        on AREA when HEFF > 0.
132      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
133        requiring that DISABLE_AREA_FLOOR *not* be defined
134     Affected verifications:
135      - 1D_ocean_ice_column (output.txt output_adm.txt)
136      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
137    o pkg/diagnostics:
138      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
139      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
140        (was _RL, now integer) with option = 0 to retrieve all levels.
141      - add pieces of code to compute velocity potential at each level (new diagnostics
142        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
143        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
144      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
145        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
146        and in diagnostics_fract_fill.F (do not need a valid pointer for the
147        diagnostics counter-mate); check that definition of counter-diagnostic
148        includes a valid counter-mate (in diagnostics_set_levels.F).
149    o model/src (rStar):
150      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
151        affect solution only if z* with full pressure in EOS;
152        update output of test-exp global_ocean.90x40x15.
153    o pkg/seaice:
154      - introduce siEps=1e-5 parameter
155      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
156      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
157      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
158        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
159        as well as ice cover age and ridging index (attached to AREA).
160        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
161        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
162        Up to SItrMaxNum=3 tracers can be used simultaneously.
163    o pkg/salt_plume:
164      -introduce SPsalFRAC run time parameter that sets the fraction of the
165       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
166       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
167    o model debug options:
168      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
169        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
170      - Refine debug-msg printing selection (3 new levels):
171        debugMode  : controls printing of debug messages (sequence of S/R calls).
172        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
173         debLevZero =  0 ; /* level of disabled aux. msg printing */
174         debLevA =  1 ; /* level of minimum  aux. msg printing */
175         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
176         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
177         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
178         debLevE =  5 ; /* level of extensive debug printing */
179        New debugLevel default: with default debugMode value (=F),
180          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
181          and if debugMode=T, default debugLevel = 4 (debLevD).
182        Relation with previous settings:
183         debLevB (=2) corresponds to former debLevA (=1)
184         debLevD (=4) corresponds to former debLevB (=2)
185        Note:
186         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
187         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
188            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
189      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
190        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
191    o pkg/obcs:
192      - change OBCSfixTopo default from True to False (should not change the results);
193        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
194    o pkg/thsice:
195      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
196        2nd layer seaice sublimation (unlikely to happen)
197      - use Interior mask for OBCS in thsice_advection.F (similar to what is
198        done in gad_advection & seaice_advection).
199    o adjoint:
200      bug fix spotted by Gael Forget:
201      seaice_advection and thsice_advection still had
202      legacy CPP options to avoid CS corner updates for adjoint
203    o pkg/seaice:
204      => Change some of the defaults (2011/05/29):
205         - change SEAICEuseFluxForm default (from False to True)
206         - change DIFF1 default (from 0.004 m/s to 0. m/s)
207         And print warnings if DIFF1 is not set in data.seaice and centered
208          avection scheme is used without any diffusion.
209      also:
210      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
211      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
212      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
213        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
214        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
215      update results of test exp.:
216         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
217             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
218             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
219         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
220         seaice_obcs: output (SEAICEuseFluxForm=T)
221      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
222          for standard fwd & AD lab_sea tests (to keep the same output).
223    o pkg/seaice/seaice_growth.F:
224      - use Ian Fenty's capping formulas for actual ice
225      thickness thoughout EVOLUTION branch.
226      - put treatment pathological case #2) in CPP brackets
227      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
228      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
229    o pkg/seaice:
230      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
231      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
232      also pass fac as a param, which can be 1. (to update the tendency
233      field) or the time step (to update the field itself).
234      - seaice_advdiff.F: for multidim, call seaice_diffusion with
235      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
236      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
237      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
238      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
239    o pkg/seaice:
240      diffusion with centered advection scheme (diffus.F & advect.F):
241      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
242        to just compute the laplacian of input-field.
243      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
244      - fix flux-form version in diffus.F to conserve tracer.
245      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
246       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
247    
248    checkpoint62y (2011/05/26)
249    o pkg/seaice:
250     - seaice_growth.F : in EVOLUTION branch, always include
251       a_QSWbyATM_cover in qnet (as it should be).
252     - verification/global_ocean.cs32x15 : update results accordingly
253       (output.seaice.txt output_adm.seaice.txt).
254    o pkg/seaice + obcs:
255     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
256       equivalent of assuming no tracer gradient outside the OB region.
257       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
258     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
259       after changes above);
260     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
261       only at OB location (instead of over a band of OLx width).
262    o pkg/seaice:
263     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
264       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
265    o pkg/obcs:
266      - split header file "OBCS.h" into 4 separated files:
267        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
268       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
269         (contain no conditional statement which depends on OBCS options).
270      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
271        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
272    o ctrl, cost, grdchk & autodiff pkgs:
273      - make options file more standard (like other {PKG}_OPTIONS.h file but
274        with AD_CONFIG.h); clean-up some of the included header files.
275    o pkg/obcs:
276      - do not mask tracer when applying OB (tracer == 0 could generate problems)
277      - apply tracer OB values to tracer field only at OB location (instead of
278        over a band of OLx width)
279      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
280      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
281        obcs_apply_tloc.F & obcs_apply_sloc.F
282    o obcs in model/src:
283      - call OBCS_APPLY_W only if NonHydrostatic.
284      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
285      - reset dEtaHdt and wVel to zero outside OB interior region ;
286      - leave tracer unchanged outside OB interior region: This has no effect
287        on the solution but just to prevent unrealistic tracer value outside OB.
288      - zero out velocity outside OB interior region: This has no effect on
289        the solution but just to prevent unrealistic velocity outside OB.
290    o obcs and non-lin free-surf:
291       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
292       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
293       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
294       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
295       update results of test-exp. exp4(nlfs).
296    o exp4 (nlfs) test-exp:
297       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
298       with NonLin-FreeSurf); update output.nlfs.txt
299    o obcs and 2d/3d solver norm:
300       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
301       and outside OB interior region (will allow to place OB further inside the
302       domain). Depending on the domain, can affects cg2d-Norm (previous
303       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
304       and cg3d-Norm (previous Norm was computed before canceling OB terms),
305       e.g. in tutorial_plume_on_slope.
306      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
307    o pkg rbcs:
308      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
309      - add capability to apply relaxation to horizontal velocity uVel & vVel.
310    o pkg/grdchk: add gradient check for control variable xx_shifwflx
311    o pkg/shelfice/shelfice_init_fixed.F
312      fix CPP-flag combinations
313    o pkg/seaice: Merge iceage code of Pierre Rampal
314      * update/change/correct ice age calculations
315      * add age updates for pathological cases
316      Probably needs more testing...
317    
318    checkpoint62x (2011/05/13)
319    o pkg/mom_vecinv:
320       high-order vorticity scheme: use interior masks (maskInW & S)
321       to zero-out (outside OB) gradient of vorticity.
322    o verification exp.:
323       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
324       hs94.128x64x5 and seaice_obcs ; update results.
325    o pkg/obcs:
326      fix bug in OBeta for YZ sections in obcs_exf_load.F
327    o pkg/ctrl, pkg/shelfice, and optim:
328      - add new control variable xx_shifwflx (fresh water flux underneath ice
329        shelves). This is almost as tedious as obcs-ctrl, because the
330        variables needs its own mask.
331      - add a cost function term that penalizes the deviation of xx_shifwflx
332        from the first guess (zero) in analogy to other control variables
333    o pkg/shelfice:
334      - start basic adjoint
335    o pkg/ctrl:
336      - remove extra 2D field "for good measure" when initializing in
337        ctrl_set_globfld_[xy/xz/yz].F
338      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
339      - improve error messages in ctrl_set_unpack_*
340    o OBC implementation in momentum:
341       use interior masks (maskInC,W & S) in momentum S/R:
342       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
343       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
344       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
345       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
346       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
347        (and also with Leith/Smagorinsky harmonic-viscosity).
348       Update output of experiment dome and exp4 (+nlfs).
349    o exp4 test-exp:
350      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
351        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
352        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
353        time-varying OB at Western-side for wVel (NonHyd); update output.
354      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
355        and biharmonic-viscosity ; also use prescribed time varying OB.
356    o pkg/obcs:
357      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
358    o model/src:
359      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
360      - initialise startTime & nIter0 with unlikely values: allows to set one
361        from the other without ambiguity.
362    o seaice_obcs test-exp.:
363      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
364    o pkg/obcs:
365      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
366        no longer needed with maskInC,W,S in pkg/generic_advdiff.
367    o pkg/seaice:
368      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
369        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
370      - fixed bug in the initialization of sea ice salinity variable HSALT
371        in seaice_init_varia.F  (removed dependence on ICE2WATR)
372    o fizhi-cs test exp.:
373       switch reference output convention for these 2 non-standard test-exp,
374        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
375          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
376       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
377    o model/inc:
378      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
379        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
380    o pkg/seaice:
381      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
382    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
383      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
384        and initial HSALT
385    
386    checkpoint62w (2011/04/26)
387    o pkg/mom_fluxform:
388      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
389      - use parameter "sideDragFactor" in no-slip BC side-drag part.
390      - update output of exp. global_ocean.90x40x15
391    o pkg/mom_vecinv:
392      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
393    o update seaice exp.:
394      use more consistent parameter values (remove "backward compatability only":
395       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
396      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
397       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
398    o update test-exp global_ocean.90x40x15:
399      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
400      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
401      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
402      o turn on zStar & viscA4 in standard set-up (dir input/)
403        and update output files: output.txt & output.dwnslp.txt
404    o new AD-test experiment: obcs_ctrl
405      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
406    o pkg/dic:
407      fix two bugs in handling water vapour pressure in carbonate chemistry
408      and air-sea fluxes. Found by Val Bennington and Galen McKinley
409      (add DIC Option = WATERVAP_BUG to recover old results)
410      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
411    o adding allowInteriorFreezing option to check for water below freezing point
412      at depth and bring the negative heat anomaly to the surface level
413    o pkgs _fields_load:
414      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
415      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
416        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
417        rbcs to get interpolation weights and time reccord number.
418      - fix multi-threading in aim_fields_load.F
419      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
420    o external_fields_load:
421      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
422       interpolation weights) to use in a periodic time-series ; do not divide by
423       time-step to convert to integer:
424       - this fixes case where externForcingPeriod is not multiple of time-step
425          (Thanks to Christopher L. Wolfe)
426       - this fixes case where externForcingPeriod is an odd multiple of time-step
427         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
428      store index of time-record which is currently loaded:
429       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
430       - needed for the adjoint but not yet used because of extensive recomputations;
431         (to be fixed soon)
432    
433    checkpoint62v (2011/04/02)
434    o verification/1D_ocean_ice_column added to test Ian Fenty's
435      pkg/seaice_growth.F modifications for improving sea ice code differentiability
436    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
437      (new velocity statistics after changing maskInW & maskInS definition)
438    o pkg/generic_advdiff with OBCS:
439      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
440      equivalent to assumption of no tracer gradient outside the OB region.
441      This will affect the results if using obcs+biharmonic diffusion.
442      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
443    o pkg/obcs:
444      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
445      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
446      in Interior region. No impact on solution but affects Velocity monitor stats.
447    o pkg/ptracers (adjoint)
448      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
449      tape file for each tracer
450    o model/inc/src and pkg/autodiff: add parameters that allow to turn
451      of parts of the adjoint code at run time. For now, there are only
452      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
453      parameters are set in data.pkg.
454      This is the lazy coward's version of doing this, but still useful for
455      debugging. In order to do it right, everything needs to be moved to
456      pkg/autodiff.
457    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
458      the end; this fixes the adjoint balancing code for open boundaries.
459    o pkg/ctrl:
460      - change behavior of xx_${varname}period to be analogous to exf-conventions:
461        xx_${varname}period =   0.,  means time-independent control part
462        xx_${varname}period = -12., means one-year-periodic monthly control part
463      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
464        clean up ctrl_init a little, remove unused variables
465      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
466      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
467    
468    checkpoint62u (2011/03/15)
469    o model/src:
470      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
471        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
472      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
473        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
474    o pkg/ctrl/obcs/ecco:
475      - remove obsolete, unused, and partially broken code:
476        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
477        ALLOW_CTRL_OBCS_BALANCE
478      - put a stop statement into ecco/cost_obcsvol.F, but also add
479        cost_obcsvol to ecco_ad_diff.list
480    o pkg/ecco: fix counting cost function contributions for obcs (code
481      by Matt M.) and diffkr for diagnostics
482    o pkg/ecco, pkg/ctrl, pkg/grdchk:
483      add cost penalty terms for initial uvel, vvel, eta controls
484      and I/O for prior error files
485    o pkg/mdsio:
486       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
487       (new argument) to check for tiled file in mdsioLocalDir : this fix the
488       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
489    o pkg/ctrl:
490     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
491       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
492       unused and superfluous variables
493     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
494    o pkg/ecco
495     - enable adjoint of Stevens OB
496    o pkg/ctrl/ecco/grdchk:
497      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
498        Fortunately, we do not have any tests for the numerous cpp-flagged
499        option of "obcs as control parameters" so we will never know
500        if this is an improvement (but at least now things compile).
501      - remove an obsolete initialization from ecco_cost_init_barfiles.F
502      - fix some problems within never used ifdefs to make the code compile
503    o pkg/obcs:
504     - Refine Interior mask definition to work with more complex OB (e.g.
505       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
506       read in Interior mask from file. Check if Interior mask is consistent
507       with OB list of indices.
508    o pkg/seaice
509     - beginning code for a seaice tracer package,
510       but currently only used for seaice age: SEAICE_AGE
511       SEAICE_num = 4
512       iTracer = 1: area-weighted ice age
513               = 2: volume-weighted ice age
514               = 3, 4: template for one-year vs. multi-year ice
515       data.seaice has new namelist SEAICE_PARM03 for arrays related to
516       SEAICE_num
517    
518    checkpoint62t (2011/03/05)
519    o pkg/obcs:
520     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
521       then normal component. This ensures that the normal component is set
522       correctly even when it conficts with tangential setting from an other OB.
523       Affects results of test-experiment seaice_obcs: update the output.txt
524    o pkg/obcs:
525     - add code to monitor statistics of dynamical fields at OB.
526     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
527       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
528       - change default: balance the Net inflow through all OB (instead of balancing
529         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
530     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
531       to match Nortern OB inflow (OBCS_balanceFacN=0).
532    o pkg/seaice:
533     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
534    o pkg/seaice (seaice_growth v 1.113):
535     - reverting seaice_growth to v 1.111 in order to have code with exact bit
536       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
537       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
538       runtime flag SEAICEareaFormula is kept but is inactive
539    o model/src:
540     - add new param to scale curvilinear grid distance and area when using
541       a different sphere radius from the grid-files.
542     - test/check multi-threads EXCH applied to local variable (cg2d_x)
543    o adjoint:
544     - enable adjoint of Stevens OB
545     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
546       (a bit delicate because of potentially modified adj. common block structure;
547       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
548    
549    checkpoint62s (2011/02/15)
550    o pkg/seaice (seaice_growth v 1.112):
551     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
552       computing the ice cover tendency from effective thickness tendencies. Include
553       Ian Fenty's formula.
554     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
555       SEAICEareaFormula.
556     - simplify notations for the various d_HEFF/d_AREA terms.
557    o pkg/gmredi:
558     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
559       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
560       add a verification test-run (front_relax.bvp) to test GM_useBVP.
561    o pkg/seaice (seaice_growth v 1.111):
562     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
563     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
564       also melt ice.
565    o pkg/seaice:
566     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
567     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
568    o pkg/cheapaml:
569     - from Nico Wienders: New version of this package.
570    o pkg/flt:
571     - add CPP options to prevent floats to re-enter the opposite side of
572       a periodic domain (default: keep periodicity)
573    o pkg/gmredi:
574     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
575       (needed for multi-dim advection).
576     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
577    o model/src:
578     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
579    o tutorial_tracer_adjsens
580     - extend to NLFS and replace maskC by hFacC
581       (change reference output accordingly)
582    
583    checkpoint62r (2011/01/24)
584    o testreport:
585     - add option -deloutp (-do) to remove output file after successful run
586     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
587       extract exact list of procs from this file ; adjust COMMAND by
588       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
589    o pkg/ecco: replace old ineffective way of penalizing deviations from
590      first guess (of obcs) with code by Matt Mazloff
591    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
592      exf/cal
593      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
594        and handle case of obcs?period == 0
595        Not affected by these changes: There is still an inconsistency in
596        the computation of start/endrec for the obcs variables for ALLOW_CAL
597        defined (see comment by Menemenlis, 7-Mar-2003)
598      - make S/R ctrl_get_gen_rec return something meaningful even if
599        ALLOW_CAL is not defined
600      - ctrl_getobcs?: simplify code so that it does not need to use
601                       S/R exf_swapfields
602    o testreport:
603       allow to test MPI with different number of processors for each experiment:
604       create file "SIZE.h.mpi" in each build dir.
605       Note: update of "-command" argument not yet implemented.
606    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
607      alleviate the need for additional 3D tapes when using
608      the non-inear free surface in the adjoint. This is done
609      by adding an 'update' of hfacc etc. to their current
610      value at the beginning of forward_step.F.
611    o pkg/seaice
612      seaice_lsr: move stress-divergence computations out of outer pseudo-
613      timestepping loop
614    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
615      up, so that the calls of the ctrl_* subroutines are really at the end
616      of the routine.
617    o pkg/gmredi:
618      allow to specify a 2-D horizontal map and a 1-D vertical profil
619      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
620    o pkg/seaice:
621      move lsr iterations from seaice_dynsolver to seaice_lsr.
622    o pkg/seaice:
623      reduce memory footprint of seaice mutldim advection tapes,
624      by using a 2D tape independent of the generic_advdiff ones,
625      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
626    
627    checkpoint62q (2010/12/29)
628    o model/src:
629      - check horizontal grid-spacing for unset or zero/negative values.
630      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
631    o pkg/flt:
632      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
633      - precision of input and output files set according to readBinaryPrec
634        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
635      - initial float position from tiled file was not converted to index space
636        (looks like a bug): fixed to make it similar to initial pos. global file.
637    o global_ocean.cs32x15:
638       change SIZE.h of AD set-up to get same tiling as with MPI.
639       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
640    o model/src:
641       add flag to control printing of domain fields (bathymetry, hFac ...) in
642       ini_mask_etc (call to plot_fieds_xy*).
643    o pkg/thsice:
644       if useEXF, some forcing fields are not valid in overlap: fixed by computing
645       over the interior only + apply EXCH at the end (like with SEAICE advection).
646    o pkg/mdsio:
647      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
648        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
649      - change barrier call for safe multi-threads access to 3-D shared buffer.
650      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
651      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
652        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
653    o pkg/flt:
654      - add fourth-order Runge-Kutta integration
655      - add basic exch2 support (only 1 facet supported so far!)
656    o pkg/mdsio+rw:
657      new S/R to read local (or tile independent) vector (read counterpart of
658       mds_writevec_loc, and front-end write_glvec_rl/rs).
659    o global_ocean.cs32x15: additional input_ad.seaice experiment
660        that uses pkg/seaice rather than pkg/thsice.
661        (using multidim advection for seaice)
662    o towards more F95 syntax for array specification in namelist:
663      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
664        of all verification experiments.
665           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
666          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
667      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
668    o global_ocean.cs32x15: additional input.seaice experiment
669        that uses pkg/seaice rather than pkg/thsice.
670    
671    checkpoint62p (2010/12/17)
672    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
673        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
674    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
675        allow for use of multim. advection in seaice adjoint.
676    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
677      - first attempt to close budgets by taking into account the freshwater
678        flux implied by the sublimation of snow and ice. So far only the
679        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
680        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
681    o eesupp/src:
682      new S/R with new option (NML_EXTENDED_F77) to change array specification
683      from F95 standard to commonly accepted extended F77 form.
684      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
685      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
686      for less tolerant f77 compiler (e.g., pgf77, g77).
687    o globalFiles:
688      commented out in parameter file "data" since it's not safe with MPI
689      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
690      in this case); no longer commented out in restart test (tst_2+2).
691    o add adTapeDir to specify a special directory where adjoint tapes are
692      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
693      and cannot be used together with mdsioLocalDir.
694    o nesting pkgs:
695      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
696      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
697      - add parameter files + utils dir + output from short run on beagle.
698    o pkg/seaice:
699        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
700    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
701      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
702    
703    checkpoint62o (2010/11/25)
704    o pkg/exf:
705      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
706    o pkg/seaice:
707      - seaice_ocean_stress: split a loop for better vectorization of the
708        adjoint code
709      - seaice_growth.F: fix bug in conservation of freshwater connected to
710        capping of heff, put contribution into d_HEFFbyNEG
711      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
712        by something more sensible (parameters that are what their name implies)
713      - change some defaults, so that by default exf-parameters are used for
714        things like rhoAir, cpAir,latent/sensible heat parameters, in order
715        to reproduce the old results, many data.seaice now contain funny values
716        for cpAir and latent heat of sublimation
717    o packages_readparms.F: move exf_readparms up in line so that
718        exf-parameters are visible for other packages (e.g. seaice)
719    o debugMode & debugLevel=2:
720      - differentiate between debugMode & debugLevel=2:
721        debugMode: controls printing of debug messages (sequence of S/R calls).
722        debugLevel: controls printing of algorithm intermediate results and stats.
723      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
724        => allows to print debug-stats without all sequence of call messages.
725      - switch control of debug print from debugLevel to debugMode in many S/R.
726    o pkg/obcs (obcs-sponge):
727        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
728        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
729    o pkg/generic_advdiff:
730      - record overlap minimum size for each advection scheme;
731      - refine criteria on overlap minimum size;
732      - check and stop (in gad_check) if overlap size is too small.
733    o pkg/obcs:
734      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
735        once, in ptracers_implicit.F)
736      - with seaice: remove test on empty file name in obcs_apply_seaice (always
737        apply OB values when tile has OB)
738    o model/src, coriolis setting:
739      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
740        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
741        files (selectCoriMap=3) with any grid.
742      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
743    o pkg/seaice/seaice_growth.F:
744        a few cosmetic changes that reduce the number of lines of code
745    o pkg/obcs: add boundary conditions following Stevens (1990)
746      - the code follows old MOM/NAOSIM code
747      - so far it is only implemented for the eastern and western boundaries
748        and NOT for pTracers
749    o pkg/rbcs:
750      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
751        beginning of the first rbcs forcing period.
752      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
753        offline package, i.e., one file per time, labeled by iteration number;
754        deltaTrbcs sets the timestep with which the data was generated;
755        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
756      - rbcsForcingCycle=0 makes forcing non-cyclic.
757      - make arithmetic safe for negative times and odd forcing periods.
758    
759    checkpoint62n (2010/11/09)
760    o pkg/seaice:
761        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
762    o pkg/obcs:
763       New S/R to copy tracer value from the OB location to narrow band region
764        (width = same as overlap) beyond the OB: preserve OB value (needed for
765        high-order scheme) which were overwritten by EXCH call if in overlap
766        region. Applied to theta, salt, ptracer and advected seaice variables.
767       With seaice: use maskInC in similar way as in gad_advection.F,
768        in seaice_advection.F and advect.F.
769       Update output of experiment seaice_obcs and change exp4 to test OBCS with
770        4th order Adv.Scheme. for pasive salt and ptracer.
771    o tools/genmake2:
772      - when looking for an optfile (not specified), only search for Fortran compiler
773        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
774      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
775        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
776      - set default for CPP to "cpp -traditional -P" (was the case without specifying
777        an optfile, but otherwise default was just "cpp".
778      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
779      - when "CC" is not set in the optfile, look for possible C compiler
780        (instead of just setting CC=cc)
781      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
782        => add a ".F" to ".o" rule for source files with no "#include" (such as
783           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
784      - move gfortran before g77 in list of possible Fortran compiler (consistent
785        with reference compiler switch from g77 to gfortran)
786    o pkg/seaice:
787      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
788        seaice_check that stops the model, when the CPP flag is used.
789      o seaice_growth.F: make capping of ice volume conserving by returning the
790        capped ice as freshwater to EmPmR. This does not change the verification
791        experiments but will change runs where the capping is acutally active
792    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
793      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
794         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
795         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
796    o tools/genmake2:
797      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
798      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
799      - clean previous genmake log files before anything else.
800      - change Makefile to remove testreport log files (*.tr_log) and genmake log
801        files only with "CLEAN" target (instead of "Clean");
802    o pkg/generic_advdiff:
803      Change OBCS in multiDim advection (gad_advection.F):
804       Use maskInC to prevent intermediate update of tracer-field in OB regions,
805       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
806       which were applying future time-step OB values.
807      This way, all explicit calculations use current-time-step OB values
808       (simpler and more consistent).
809      Affects results when set-up uses time-varying OBC and multi-dim advection;
810       update output of experiment seaice_obcs.
811    o pkg/seaice:
812      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
813       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
814         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
815      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
816       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
817       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
818    o pkg aim (2010/10/26):
819      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
820        formulation with obliquity, eccentricity, ... as run-time parameters,
821      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
822        upward shortwave radition at the surface (all-sky and clear-sky).
823    o pkg/obcs:
824      - writing sections with globalFiles=T does not work: switch to tiled-files
825        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
826      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
827      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
828    
829    checkpoint62m (2010/10/21)
830    o pkg/seaice: vectorize seaice_solve4temp.F
831      - move iterations loops outside of i/j-loops
832      - requires 2D arrays for TB and effConduct
833      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
834        modified in this routine
835      - a little bit of clean up, adjusting indentation, etc.
836      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
837        performance and '**TWO' by '**2' (because TWO is a float),
838        replaced ONE, ZERO
839    o eesupp/src:
840       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
841    o pkg/seaice/seaice_growth.F
842      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
843      merging process. The merged routine has two branches, and one activates the 'evolution'
844      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
845      In summary, here is what the '10/10 revision' did consist of
846        part 1: seaice_growth.F revisions 1.71 to 1.75
847          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
848            The emphasis here was on improving readability (e.g. by trying to use meaningful
849            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
850        part 1.5:
851          - revising the lab_sea experiment to make it a more useful (i.e. stable
852            and representative of an actual model run). This was done by generating a
853            (winter) pickup to start from, switching back the main experiment dynamic
854            solver from evp to lsr, having one of the experiments use the free drift solution.
855        part 2: seaice_growth.F revisions 1.76 to 1.85
856          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
857          - Sorting out the various fields units and sign (set early on and reset at the end)
858            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
859            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
860          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
861            and simplifying logical expressions to further improve readibility.
862        part 3: seaice_growth.F revisions 1.86 to 1.89
863          - Re-organize the blocks of code more logically.
864          - Merging the '_if.F' pieces that add something new.
865    o pkg/thsice:
866      - vectorize thsice_solve4temp and thsice_get_exf.
867        Problem: thsice_solve4temp has an unvectorizable statement that
868        might also be problematic for TAF
869      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
870        does not change the verifcation experiment, but will change all
871        experiments that have this flag undefined (not tested in verification);
872        a little reorganization to save a few 2D fields and recomputations
873      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
874      - 2nd step:  fix some store dirs
875        o seems to work somewhat, i.e. using ifort but not g77
876        o likely cause are incomplete init. or recomputation
877        o start verification/global_ocean.cs32x15/input_ad.thsice
878    o pkg/obcs: add support for exch2
879      - the position of the boundary and prescribed values are specified using
880        a global domain with exch2 facets stacked
881        - in x for N,S boundaries (like W2_mapIO=-1)
882        - in y for E,W boundaries (so E,W boundaries do not overlap)
883    o pkg/mdsio: add support for writing global sections with exch2
884        file layout is as for obcs described above:
885        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
886        - for y-z sections, facets are stacked in y
887    o pkg/thsice:
888       - change a few routines for better vectorization: thsice_albedo.F,
889         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
890         not affected, but in particular the latter routine has changed
891         dramatically (not necessarily easier to read now).
892       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
893       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
894    o verification/lab_sea:
895      - overhaul of the forward model experiments. The main motivation
896        for this revision is that lab_sea has proven quite fragile (when
897        changing the sea-ice code, and switching platforms) to a point
898        when failures were very hard to attribute to specific code problems.
899      - the suspected reason for this fragility is noise amplification by evp so,
900        to start with, we decided to replace evp with lsr in the main experiment.
901      - the input.lsr experiment thus became obsolete and was removed.
902      - it was replaced with the input.fd experiment that uses an
903        analytical "free drift" solution as the ice velocity field.
904      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
905        will hopefully allow us to discriminate problems due to dynamic solvers
906        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
907        us to test additional options, along with the salt plume package.
908      - Finally a pickup was generated (at the end of a one year run) to
909        make the tests more representative of an actual model run. Previously
910        the tests starting point was a 1m thickness of ice everywhere.
911    o pkg/seaice:
912      - introducing S\R seaice_freedrift.F that compute the
913        analytical solution to an approximate ice momentum
914        equation (i.e. the simple stress/coriolis balance).
915      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
916        of the free drift velocity field, and enable its use.
917        To actually use the free drift solution as the model ice
918        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
919    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
920    
921    checkpoint62l (2010/10/04)
922    o pkg/seaice:
923      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
924      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
925       version (with USE_ORIGINAL_SBI undef);
926    o add hooks for new packages OASIS, the package will follow
927      (hooks exclude the seaice pkg for now)
928    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
929      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
930      rather than mdsio_readvector.F/mdsio_writevector.F, within
931      adread_adwrite.F to read/write adjoint-related tapes to disk.
932    o eesupp and pkg/mdsio: ALLOW_WHIO
933      Option to write/read 2D fields to files including tiles halos.
934      The main purpose is for adjoint related "tape I/O".
935      The secondary purpose is for debugging phases.
936      A word on those rather specifically intended purposes.
937      The code was meant to be stripped down to the bare minimum.
938      Typically, there is a unique and basic mapping to the global
939      buffer (tile by tile, then proc by proc, then level by level), and
940      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
941      meant to generate user friendly outputs of various shapes and forms.
942      Rather it is intended, for the knowledgeabale developers,
943      to be largely independent of the many mdsio options, to allow
944      outputs of tiles+halos in debugging phases and in adjoint runs,
945      and to allow some flexibility in tuning (adoint) I/O depending on each
946      file system behavior. With regard to tuning, most of the potential knobs
947      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
948      to specify directories, to specify the typical size of I/O calls, etc.)
949      are not yet included, and will be added if they prove useful.
950    o pkg/seaice:
951       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
952    o pkg/seaice:
953       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
954       code (seaice_budget_ice_if.F) which enable to recover old standard
955       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
956       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
957    o model/src (rStar):
958       use simple average (not area weighted) of rStarFac at U,V point when using
959       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
960       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
961    
962    checkpoint62k (2010/09/17)
963    o adjoint
964       * changed verification/global_ocean.cs32x15 ; adjoint now tests
965         Adams-Bashforth 3 + NLFS + RSTAR
966       * some more modifs required for ECCO-GODAE v4
967    o pkg/seaice
968       add SEAICE_AGE_VOL option to use volume instead of area for
969       integrating SEAICE_AGE
970    o model/src:
971       first check-in of sigma & hybrid-sigma coordinate code ; also includes
972       non-linear free-surface parts ; but pressure-gradient not yet coded.
973    o pkg/ptracers:
974       option for ptracer to convert Salt Relax into additional EmP.
975        tested in exp. global_ocean.90x40x15.dwnslp (update output)
976    
977    checkpoint62j (2010/08/25)
978    o pkg/ggl90:
979       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
980    o pkg/dic: car_flux.F, phos_flux.F
981      - reduce number of exp-calls in order to improve performance
982      - clean up a little (replace fields by their macros, etc., fix
983        typo in CPP-flag)
984    o pkg/ggl90: minor changes
985      - GGL90diffKrS was removed --> always use GGL90diffKr
986      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
987      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
988        (commented out for now)
989      - change in max/min operations to ensure that smoothing is ok
990      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
991      - always use diffKrNrT as background profile (i.e. never use diffKr field)
992    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
993    o pkg/dic:
994      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
995        vectorization
996      - small bug fix in insol for the unlikely case of a cartesian grid
997      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
998        + now vectorize, which also removes adjoint recomputations;
999        + replace integer maksp1 by _RL maskp1
1000        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1001    
1002    checkpoint62i (2010/07/21)
1003    o pkg/flt:
1004      - with OBCS: stop floats which enter the OB region
1005    o model/src:
1006      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1007        for implicit vertical advection.
1008    o pkg/seaice:
1009     - account for melting in seaice age evolution.
1010     - remove double counting of seaice ridging effect on seaice age.
1011    
1012    checkpoint62h (2010/06/18)
1013    o pkg/exch2:
1014     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1015    o tools/genmake2
1016      - remove "-pdefault" option: redundant with the use of "packages.conf";
1017      - remove file pkg/pkg_default : set the default as a pkg group
1018        ("default_pkg_list") defined in pkg/pkg_groups;
1019      - fix for case pkg/pkg_depend is missing (was hanging before);
1020      - add option "-pgroups" to specify a different pkg_groups than the default.
1021    o verification/adjustment.cs-32x32x1:
1022       add a "minimal" set-up test (code_min & input_min) which only compiles
1023       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1024    o tools/genmake2
1025      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1026      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1027    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1028      files are nearly the same anyway.
1029      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1030       - redefinition of tau(i,i) (by a factor of ustar)
1031       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1032       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1033       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1034       - replace
1035         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1036         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1037         by
1038         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1039         (changes results)
1040       -> exf_bulkformulae v1.22,
1041          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1042          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1043                    output.txt 1.63
1044           offline_exf_seaice: output.seaicetd.txt 1.7
1045           seaice_obcs: output.txt 1.10)
1046      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1047       -> exf_bulkformulae v1.23,
1048          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1049          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1050      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1051    o adjoint of exch-1:
1052     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1053       (note: was already like this when using EXCH-2) and remove flow dir
1054       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1055     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1056     - update pkg/exch2 diff list.
1057    
1058    checkpoint62g (2010/05/19)
1059    o eesupp/src (exch-1):
1060     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1061       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1062       (renamed to exch1_*rx_cube.F).
1063     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1064       to call new exch1 S/R ; update Makefile and .cvsignore.
1065     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1066       exch2_xy_rx later)
1067      Note: after updating your code, need to run "make clean" in eesupp/src
1068    o test experiment bottom_ctrl_5x5:
1069       new output_adm.txt with fewer grdchk & less monitor output.
1070    o model/src:
1071      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1072       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1073       beeing treated in the same way (ini_grid is not called a 2nd time).
1074    o pkg/exf:
1075      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1076      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1077      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1078      - cosmetic changes to exf_bulkformulae.F to make it look more like
1079        exf_bulk_largeyeager04.F
1080    o eesupp/src (exch-1):
1081      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1082      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1083        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1084        (even without using MPI).
1085      - Message mode: move RecvAck setting (indicator of buffer being ready)
1086        from send_put to recv_get S/R (was useless before, but not sure if
1087        it's much more useful now);
1088      - Switch the order of sync: MPI-proc 1rst and then threads;
1089      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1090      - fix AD code for communication mode ='get' (but not used).
1091    o model/src:
1092      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1093      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1094    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1095    o pkg/ctrl: require a specific set of control variables and exf-flags for
1096      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1097    o model/src:
1098     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1099       1rst forward sweep, to avoid over-writing output files during recomputations
1100       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1101     b) 2nd version:
1102      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1103      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1104         writePickupAtEnd) + seaice & ptracers output;
1105      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1106    o model/src:
1107      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1108    o pkg/exch2:
1109      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1110      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1111    o pkg/autodiff & exch2:
1112      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1113      (for now, only if ALLOW_EXCH2 is defined).
1114    o pkg/autodiff:
1115      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1116        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1117       + clean-up comments (_RS is not always real*4)
1118      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1119      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1120        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1121    o testreport (AD-tests):
1122      no longer link files from dir "../input" (1rst link files from
1123      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1124    
1125    checkpoint62f (2010/04/29)
1126    o model/src/the_main_loop.F:
1127      adjust store directives for seaice evp and multicategory according to
1128      pkg/ecco/the_main_loop.F
1129    o adjoint:
1130      global_sum_ad was incomplete (noted many times by many people ;)
1131      nice description by Jean U. as follows:
1132      * allreduce(var) in global_sum.F can be interpreted as
1133        reduce(sum) followed by broadcast of sum.
1134      * The adjoint of that is
1135        sum(adjoint) followed by broadcast(summed adjoint value)
1136        or in other words, allreduce(sum, adjoint vars)
1137      We were missing the sum(adjoint)!
1138      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1139      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1140      The fix should produce 16-digit accuracy between
1141      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1142      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1143      We'll probably change this yet again shortly
1144    o eesupp/src:
1145      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1146    o pkg/icefront
1147      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1148        specification of addmass array based on a 2D field, which is added
1149        at bottommost wet level at each horizontal location.
1150    o model/src:
1151     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1152     layout; (not always compatible with delX,delY setting; commented out for now).
1153    o pkg/exch2:
1154     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1155     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1156    
1157    checkpoint62e (2010/04/15)
1158    o pkg/obcs:
1159      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1160    o pkg/dic:
1161      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1162        (note: not presently tested in any forward verification exp.)
1163       update tutorial_global_oce_biogeo AD output file.
1164    o pkg/exf:
1165      - account for the variation of albedo as a function of zenith angle
1166        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1167    o build_options:
1168     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1169    o pkg/dic:
1170      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1171      - use binary pickup file for restart;
1172      - initialise atmos-CO2 box from dic_pCO2 parameter;
1173      - fix multi-threaded.
1174    o pkg/rbcs:
1175     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1176       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1177     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1178       and update output.txt
1179    o pkg/kpp:
1180     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1181     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1182       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1183       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1184     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1185       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1186    o pkg/offline:
1187      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1188      (bug was added in version 1.10 on 2007-08-23).
1189    o pkg/offline:
1190      - no need to specify periodicExternalForcing, etc ... to use offline pack
1191      - offline input files no longer just single prec --> parameter offlineLoadPrec
1192    o verification/lab_sea:
1193      change AD test to multi-tile setup and update all 4 AD output.
1194      NOTE: while cost function values remain very similar,
1195      gradients are very different, although gradient checks are self-consistent
1196      Should try to get to the bottom of this (cost function summation order?)
1197    o pkg/dic:
1198      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1199      a weakness of TAF that drops part of double precision in log10 derivative.
1200      <= changes removed since problem has been fixed in current TAF version 1.9.71
1201      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1202    o pkg/ecco:
1203      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1204      update all 4 lab_sea AD output.
1205    
1206    checkpoint62d (2010/03/22)
1207    o build_options:
1208      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1209    o remove unbalanced quote (single or double) in commented line of source code
1210      (may cause some warning with some preprocessor/makedepend versions).
1211    o pkg/seaice:
1212      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1213       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1214    o testreport:
1215      add option '-runonly' (short: '-ro') to just do the run part (without make).
1216    o eesupp: remove JAM communication code (obsolete).
1217    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1218      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1219      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1220      (update also the output).
1221    
1222    checkpoint62c (2010/03/02)
1223    o tools/build_options :
1224       move (some) old optfiles from build_options/ to build_options/unsupported/
1225    o model/src and pkg/exf
1226       surface relaxation -- separating data and data.exf options
1227       The point is to ensure that we specify the surface relaxation
1228       either in data or in data.exf (but not half and half) and to
1229       avoid an accidental relaxation to 0 (which happened if a time
1230       scale was specified but the file name was left empty)
1231    o model/src model/inc and pkg/mom_common
1232       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1233       => addition to the viscosity field as computed by others schemes
1234    o tools/build_options:
1235      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1236        but keep the former optfile for few weeks for smooth transition
1237    o pkg/ecco
1238      - allow user defined cost function contributions
1239         CPP: ALLOW_USERCOST_CONTRIBUTION
1240         USAGE: compute contributions in cost_usercost_all.F
1241      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1242          the two options are complementary.
1243    o pkg/smooth
1244      - migration from contrib to the main repository
1245    
1246  checkpoint62b (2010/01/26)  checkpoint62b (2010/01/26)
1247  o pkg/monitor:  o pkg/monitor:
1248    - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop    - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
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