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revision 1.1241 by jmc, Wed Mar 24 20:54:49 2010 UTC revision 1.1501 by jmc, Tue Sep 20 22:34:03 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/kpp:
8      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
9        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
10    o optfiles:
11      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
12        into corresponding standard one, which now support different build:
13        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
14      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
15    o pkg/obcs (seaice):
16      - add missing EXCH for uIce,vIce after applying OBCS;
17      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
18        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
19        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
20      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
21      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
22        and eedata.mth for MPI and mutlti-threaded testing.
23    o pkg/flt:
24      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
25      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
26      - fix pickup and trajectories + profiles output with multi-threads;
27      - add parameter to select group of fields to write along trajectory and
28        profile (default unchanged);
29      - only call PORT_RAND* function when flt_noise <> 0;
30      - add multi-threaded test for verification exp. flt_example.
31    o eesupp/src:
32      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
33      - USE_OMP_THREADING: check that number of threads (from eedata) matches
34        actual number (from env.var. setting).
35    o pkg/ebm:
36      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
37      - add multi-threaded test for verification exp. global_ocean_ebm
38    
39    checkpoint63b (2011/08/29)
40    o pkg/ebm:
41      - fix sign of runoff;
42      - update directly forcing fields (Qnet,EmPmR) to use standard
43        external_forcing_surf.F (remove ebm_forcing_surf.F);
44      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
45      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
46        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
47      - update global_ocean_ebm parameters file data and update output (fwd+ad).
48    o verification/matrix_example:
49      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
50        MPI and mutlti-threaded testing.
51    o pkg/matrix:
52      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
53      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
54      - fix for multi-threaded (remove DATA statement);
55      - use standard DIFFERENT_MULTIPLE function;
56      - add MATRIX_OPTIONS.h
57    o verification/matrix_example:
58       To allow to split the domain in several tiles, change the domain size
59        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
60        Western side) of land points.
61    o (*_)write_pickup:
62      - fix few bugs in mypackage_read/write_pickup.F
63      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
64        array of length 1 (was caught by compiler syntax-check).
65    o pkg/diagnostics (velocity potential solver):
66      - fix initialisation of main diagonal matrix (for overlap values)
67    o tools/build_options:
68      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
69        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
70      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
71        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
72        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
73        and use "-devel" testreport option for standard testing on baudelaire.
74    o pkg/grdchk:
75      - Assume that all gradient-check position are within the same tile
76        corresponding to global indices (iGloTile,jGloTile) and that
77        positions (i,j indices or nbeg) are local to this tile;
78      - set tile local-indices and proc. number according to tile global-indices;
79      - remove grdchkwhichproc from namelist (retired param);
80      - send adjoint gradient to all procs so that all procs print it to STDOUT;
81      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
82    o adding package bbl (Bottom Boundary Layer)
83      description in MITgcm/pkg/bbl/bbl_description.tex
84      example/test experiment in MITgcm_contrib/bbl
85    o adjoint verifications
86      - changed 5 experiments to multi-tiles
87        * global_ocean.90x40x15
88        * obcs_ctrl
89        * offline_exf_seaice
90        * tutorial_dic_adjoffline
91        * tutorial_tracer_adjsens
92        changed reference output for those that crossed tile boundaries
93        (changed choices of gradient check positions)
94      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
95      - temporary bug fix in grdchk_loc.F for obcs
96    o genmake2 & testreport
97      - add target "obj" (just for OBJFILES files) to Makefile;
98      - add option to specify FEXTRAFLAGS on command line.
99    o pkg/mypackage:
100      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
101    
102    checkpoint63a (2011/08/02)
103    o pkg/diagnostics (velocity potential):
104      - fix velocity-potential calculation when using OBCS: balance net inflow
105        at each level (new S/R OBCS_DIAG_BALANCE).
106      - fix some of the problems with OBCS in stream-function calculation.
107    o pkg/exf/exf_readparms.F
108      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
109        EXF_NML_OBCS) more consistent, so that you need not have these lists
110        in data.exf when they are not used.
111    o optim/optim_readdata.F:
112      - add some output about obcs variables that might help debugging
113      - add a check about nvarlength
114    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
115    o pkg/diagnostics (velocity potential):
116      - fix mask for OBCS (still problems in stream-function with OBCS);
117      - add specific parameter (default = main code CG2D params) for solver;
118      - in case of poor convergence, use solution corresponding to lowest residual.
119    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
120      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
121      and should be avoided where possible.
122    o model/src (rStar):
123      - include r* effect on reference-state (PhiRef) in totPhiHyd
124        (so that it's really the potential anomaly at the cell center);
125        affect solution only if z* with full pressure in EOS.
126      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
127        update output (because of z* in totPhiHyd and viscA4 changes);
128      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
129        @ constant r) until interpolation at constant r is implemented.
130    o pkg/diagnostics
131      - fix RCENTER diagnostics in case cell center is not at interface middle
132    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
133      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
134      that THETA and SALT are "conservative temperature" and "absolute
135      salinity"
136    o pkg/ctrl
137      - fix computation of endrec in s/r ctrl_init_rec
138      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
139    o pkg/seaice/seaice_growth.F
140      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
141        remove then obsolete STORE directives
142      - fix STORE directives for tice and tices, so that only the
143        appropriate part of the fields are stored (and not the entire
144        field); update global_ocean.cs32x15.seaice AD output.
145      - cosmetic changes: adjust CPP flags and indentation for better
146        legibilty
147    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
148      Chris Wilson)
149    o pkg/gmredi:
150       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
151       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
152    
153    checkpoint63  (2011/07/11)
154    o pkg/exch2:
155     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
156     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
157       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
158       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
159    o pkg/diagnostics:
160     - deal with pairs of post-processed diags which are computed together; in
161       particular, re-order list of diags within 1 file to save 2nd computation.
162     - add S/R to compute velocity stream-function (called after velocity-potential
163       calculation) from divergence free transport -> new diagnostics "PsiVEL".
164     - add parameter to select grid-point location where PsiVEL == 0.
165    o eesupp/src:
166       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
167       (specific S/R needed with exch2 topology - for now, just print an error msg)
168    o pkg/shelfice
169     - Implement friction velocity-dependent transfer coefficients following
170       Holland and Jenkins, JPO, 1999
171       Original code by M. Losch with small modifs.
172       Enable with CPP option SHI_ALLOW_GAMMAFRICT
173       and runtime flag SHELFICEuseGammaFrict
174    o verification lab_sea & global_ocean.cs32x15:
175     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
176       does not miss some dependencies (but is slower) and also works with many files
177       (default makedepend limitation for AD built).
178     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
179    o pkg/diagnostics:
180     - add run-time parameter "useMissingValue" (def=False) to fill land-point
181        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
182       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
183     - Extend the use of "missing_value" setting from data.diagnostics for the case
184       of counter-diagnostics (where fraction-weight is zero). This applies both to
185       MNC and MDS output files.
186    o pkg/seaice/seaice_growth.F:
187      - add 'a priori' cap of latent heat flux based on actual mass considerations
188        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
189        non-legacy seaice_solve4temp.
190      - add diagnostic of the residual sublimation freshwater flux (the freshwater
191        flux taken from the ocean if the total actual latent heat fluxes exceed
192        the maximum)
193      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
194       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
195      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
196       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
197      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
198      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
199    o verification 1D_ocean_ice_column:
200       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
201       update results
202    o pkg/diagnostics:
203     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
204       which are not filled-up but computed from other diags ; In this case, the mate
205       diag points to the primary (filled-up) diag to used for post processing.
206     - Update Velocity-potential computation using post-processed diag framework.
207     ==> Change the ordering of fields and time-periods in MDS output file
208       when using periodic averaging: now writes one time record with the full set
209       of fields for this time period, then the next time reccord (it used to be
210       one field with the full set of time records then the next field).
211         Note: this is now similar to NetCDF (MNC) output file. <==
212    
213    checkpoint62z (2011/06/21)
214    o adjoint monitor:
215     - Add adjoint monitor output for packages exf, seaice
216       and update relevant testreport output
217    o pkg/seaice:
218     - re-order diags inits so that they appear in order in available_diagnostics.log
219     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
220       area/heff/hsnow preceeding thermodynamic growth/melt.
221     - modified diag: SIdA; output actual effect, as the description states.
222     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
223     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
224       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
225        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
226     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
227     - added diagnostics for seaice generic tracers (SItr*).
228     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
229     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
230     I. Fenty: 18-Jun-2011:
231     Minor changes to seaice package:
232     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
233        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
234       - Differentiated "regularization variables" from "floor variables"
235        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
236        * hiceMin became SEAICE_hice_reg (old hiceMin)
237          (with _reg meaning regularization variable)
238       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
239        so as to ensure energy conservation when going between phases
240      - A22 was not used anywhere
241     2) Changed regularization procedure for heffActual and hsnowActual to ensure
242        well-boundedness and smooth adjoint in seaice_growth.F
243     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
244        because the old regularization always set heffActual >= 0.05 cm
245     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
246        on AREA when HEFF > 0.
247      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
248        requiring that DISABLE_AREA_FLOOR *not* be defined
249     Affected verifications:
250      - 1D_ocean_ice_column (output.txt output_adm.txt)
251      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
252    o pkg/diagnostics:
253      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
254      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
255        (was _RL, now integer) with option = 0 to retrieve all levels.
256      - add pieces of code to compute velocity potential at each level (new diagnostics
257        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
258        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
259      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
260        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
261        and in diagnostics_fract_fill.F (do not need a valid pointer for the
262        diagnostics counter-mate); check that definition of counter-diagnostic
263        includes a valid counter-mate (in diagnostics_set_levels.F).
264    o model/src (rStar):
265      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
266        affect solution only if z* with full pressure in EOS;
267        update output of test-exp global_ocean.90x40x15.
268    o pkg/seaice:
269      - introduce siEps=1e-5 parameter
270      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
271      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
272      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
273        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
274        as well as ice cover age and ridging index (attached to AREA).
275        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
276        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
277        Up to SItrMaxNum=3 tracers can be used simultaneously.
278    o pkg/salt_plume:
279      -introduce SPsalFRAC run time parameter that sets the fraction of the
280       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
281       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
282    o model debug options:
283      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
284        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
285      - Refine debug-msg printing selection (3 new levels):
286        debugMode  : controls printing of debug messages (sequence of S/R calls).
287        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
288         debLevZero =  0 ; /* level of disabled aux. msg printing */
289         debLevA =  1 ; /* level of minimum  aux. msg printing */
290         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
291         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
292         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
293         debLevE =  5 ; /* level of extensive debug printing */
294        New debugLevel default: with default debugMode value (=F),
295          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
296          and if debugMode=T, default debugLevel = 4 (debLevD).
297        Relation with previous settings:
298         debLevB (=2) corresponds to former debLevA (=1)
299         debLevD (=4) corresponds to former debLevB (=2)
300        Note:
301         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
302         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
303            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
304      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
305        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
306    o pkg/obcs:
307      - change OBCSfixTopo default from True to False (should not change the results);
308        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
309    o pkg/thsice:
310      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
311        2nd layer seaice sublimation (unlikely to happen)
312      - use Interior mask for OBCS in thsice_advection.F (similar to what is
313        done in gad_advection & seaice_advection).
314    o adjoint:
315      bug fix spotted by Gael Forget:
316      seaice_advection and thsice_advection still had
317      legacy CPP options to avoid CS corner updates for adjoint
318    o pkg/seaice:
319      => Change some of the defaults (2011/05/29):
320         - change SEAICEuseFluxForm default (from False to True)
321         - change DIFF1 default (from 0.004 m/s to 0. m/s)
322         And print warnings if DIFF1 is not set in data.seaice and centered
323          avection scheme is used without any diffusion.
324      also:
325      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
326      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
327      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
328        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
329        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
330      update results of test exp.:
331         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
332             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
333             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
334         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
335         seaice_obcs: output (SEAICEuseFluxForm=T)
336      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
337          for standard fwd & AD lab_sea tests (to keep the same output).
338    o pkg/seaice/seaice_growth.F:
339      - use Ian Fenty's capping formulas for actual ice
340      thickness thoughout EVOLUTION branch.
341      - put treatment pathological case #2) in CPP brackets
342      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
343      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
344    o pkg/seaice:
345      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
346      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
347      also pass fac as a param, which can be 1. (to update the tendency
348      field) or the time step (to update the field itself).
349      - seaice_advdiff.F: for multidim, call seaice_diffusion with
350      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
351      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
352      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
353      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
354    o pkg/seaice:
355      diffusion with centered advection scheme (diffus.F & advect.F):
356      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
357        to just compute the laplacian of input-field.
358      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
359      - fix flux-form version in diffus.F to conserve tracer.
360      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
361       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
362    
363    checkpoint62y (2011/05/26)
364    o pkg/seaice:
365     - seaice_growth.F : in EVOLUTION branch, always include
366       a_QSWbyATM_cover in qnet (as it should be).
367     - verification/global_ocean.cs32x15 : update results accordingly
368       (output.seaice.txt output_adm.seaice.txt).
369    o pkg/seaice + obcs:
370     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
371       equivalent of assuming no tracer gradient outside the OB region.
372       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
373     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
374       after changes above);
375     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
376       only at OB location (instead of over a band of OLx width).
377    o pkg/seaice:
378     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
379       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
380    o pkg/obcs:
381      - split header file "OBCS.h" into 4 separated files:
382        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
383       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
384         (contain no conditional statement which depends on OBCS options).
385      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
386        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
387    o ctrl, cost, grdchk & autodiff pkgs:
388      - make options file more standard (like other {PKG}_OPTIONS.h file but
389        with AD_CONFIG.h); clean-up some of the included header files.
390    o pkg/obcs:
391      - do not mask tracer when applying OB (tracer == 0 could generate problems)
392      - apply tracer OB values to tracer field only at OB location (instead of
393        over a band of OLx width)
394      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
395      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
396        obcs_apply_tloc.F & obcs_apply_sloc.F
397    o obcs in model/src:
398      - call OBCS_APPLY_W only if NonHydrostatic.
399      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
400      - reset dEtaHdt and wVel to zero outside OB interior region ;
401      - leave tracer unchanged outside OB interior region: This has no effect
402        on the solution but just to prevent unrealistic tracer value outside OB.
403      - zero out velocity outside OB interior region: This has no effect on
404        the solution but just to prevent unrealistic velocity outside OB.
405    o obcs and non-lin free-surf:
406       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
407       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
408       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
409       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
410       update results of test-exp. exp4(nlfs).
411    o exp4 (nlfs) test-exp:
412       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
413       with NonLin-FreeSurf); update output.nlfs.txt
414    o obcs and 2d/3d solver norm:
415       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
416       and outside OB interior region (will allow to place OB further inside the
417       domain). Depending on the domain, can affects cg2d-Norm (previous
418       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
419       and cg3d-Norm (previous Norm was computed before canceling OB terms),
420       e.g. in tutorial_plume_on_slope.
421      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
422    o pkg rbcs:
423      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
424      - add capability to apply relaxation to horizontal velocity uVel & vVel.
425    o pkg/grdchk: add gradient check for control variable xx_shifwflx
426    o pkg/shelfice/shelfice_init_fixed.F
427      fix CPP-flag combinations
428    o pkg/seaice: Merge iceage code of Pierre Rampal
429      * update/change/correct ice age calculations
430      * add age updates for pathological cases
431      Probably needs more testing...
432    
433    checkpoint62x (2011/05/13)
434    o pkg/mom_vecinv:
435       high-order vorticity scheme: use interior masks (maskInW & S)
436       to zero-out (outside OB) gradient of vorticity.
437    o verification exp.:
438       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
439       hs94.128x64x5 and seaice_obcs ; update results.
440    o pkg/obcs:
441      fix bug in OBeta for YZ sections in obcs_exf_load.F
442    o pkg/ctrl, pkg/shelfice, and optim:
443      - add new control variable xx_shifwflx (fresh water flux underneath ice
444        shelves). This is almost as tedious as obcs-ctrl, because the
445        variables needs its own mask.
446      - add a cost function term that penalizes the deviation of xx_shifwflx
447        from the first guess (zero) in analogy to other control variables
448    o pkg/shelfice:
449      - start basic adjoint
450    o pkg/ctrl:
451      - remove extra 2D field "for good measure" when initializing in
452        ctrl_set_globfld_[xy/xz/yz].F
453      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
454      - improve error messages in ctrl_set_unpack_*
455    o OBC implementation in momentum:
456       use interior masks (maskInC,W & S) in momentum S/R:
457       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
458       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
459       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
460       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
461       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
462        (and also with Leith/Smagorinsky harmonic-viscosity).
463       Update output of experiment dome and exp4 (+nlfs).
464    o exp4 test-exp:
465      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
466        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
467        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
468        time-varying OB at Western-side for wVel (NonHyd); update output.
469      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
470        and biharmonic-viscosity ; also use prescribed time varying OB.
471    o pkg/obcs:
472      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
473    o model/src:
474      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
475      - initialise startTime & nIter0 with unlikely values: allows to set one
476        from the other without ambiguity.
477    o seaice_obcs test-exp.:
478      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
479    o pkg/obcs:
480      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
481        no longer needed with maskInC,W,S in pkg/generic_advdiff.
482    o pkg/seaice:
483      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
484        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
485      - fixed bug in the initialization of sea ice salinity variable HSALT
486        in seaice_init_varia.F  (removed dependence on ICE2WATR)
487    o fizhi-cs test exp.:
488       switch reference output convention for these 2 non-standard test-exp,
489        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
490          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
491       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
492    o model/inc:
493      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
494        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
495    o pkg/seaice:
496      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
497    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
498      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
499        and initial HSALT
500    
501    checkpoint62w (2011/04/26)
502    o pkg/mom_fluxform:
503      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
504      - use parameter "sideDragFactor" in no-slip BC side-drag part.
505      - update output of exp. global_ocean.90x40x15
506    o pkg/mom_vecinv:
507      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
508    o update seaice exp.:
509      use more consistent parameter values (remove "backward compatability only":
510       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
511      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
512       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
513    o update test-exp global_ocean.90x40x15:
514      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
515      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
516      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
517      o turn on zStar & viscA4 in standard set-up (dir input/)
518        and update output files: output.txt & output.dwnslp.txt
519    o new AD-test experiment: obcs_ctrl
520      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
521    o pkg/dic:
522      fix two bugs in handling water vapour pressure in carbonate chemistry
523      and air-sea fluxes. Found by Val Bennington and Galen McKinley
524      (add DIC Option = WATERVAP_BUG to recover old results)
525      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
526    o adding allowInteriorFreezing option to check for water below freezing point
527      at depth and bring the negative heat anomaly to the surface level
528    o pkgs _fields_load:
529      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
530      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
531        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
532        rbcs to get interpolation weights and time reccord number.
533      - fix multi-threading in aim_fields_load.F
534      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
535    o external_fields_load:
536      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
537       interpolation weights) to use in a periodic time-series ; do not divide by
538       time-step to convert to integer:
539       - this fixes case where externForcingPeriod is not multiple of time-step
540          (Thanks to Christopher L. Wolfe)
541       - this fixes case where externForcingPeriod is an odd multiple of time-step
542         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
543      store index of time-record which is currently loaded:
544       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
545       - needed for the adjoint but not yet used because of extensive recomputations;
546         (to be fixed soon)
547    
548    checkpoint62v (2011/04/02)
549    o verification/1D_ocean_ice_column added to test Ian Fenty's
550      pkg/seaice_growth.F modifications for improving sea ice code differentiability
551    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
552      (new velocity statistics after changing maskInW & maskInS definition)
553    o pkg/generic_advdiff with OBCS:
554      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
555      equivalent to assumption of no tracer gradient outside the OB region.
556      This will affect the results if using obcs+biharmonic diffusion.
557      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
558    o pkg/obcs:
559      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
560      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
561      in Interior region. No impact on solution but affects Velocity monitor stats.
562    o pkg/ptracers (adjoint)
563      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
564      tape file for each tracer
565    o model/inc/src and pkg/autodiff: add parameters that allow to turn
566      of parts of the adjoint code at run time. For now, there are only
567      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
568      parameters are set in data.pkg.
569      This is the lazy coward's version of doing this, but still useful for
570      debugging. In order to do it right, everything needs to be moved to
571      pkg/autodiff.
572    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
573      the end; this fixes the adjoint balancing code for open boundaries.
574    o pkg/ctrl:
575      - change behavior of xx_${varname}period to be analogous to exf-conventions:
576        xx_${varname}period =   0.,  means time-independent control part
577        xx_${varname}period = -12., means one-year-periodic monthly control part
578      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
579        clean up ctrl_init a little, remove unused variables
580      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
581      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
582    
583    checkpoint62u (2011/03/15)
584    o model/src:
585      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
586        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
587      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
588        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
589    o pkg/ctrl/obcs/ecco:
590      - remove obsolete, unused, and partially broken code:
591        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
592        ALLOW_CTRL_OBCS_BALANCE
593      - put a stop statement into ecco/cost_obcsvol.F, but also add
594        cost_obcsvol to ecco_ad_diff.list
595    o pkg/ecco: fix counting cost function contributions for obcs (code
596      by Matt M.) and diffkr for diagnostics
597    o pkg/ecco, pkg/ctrl, pkg/grdchk:
598      add cost penalty terms for initial uvel, vvel, eta controls
599      and I/O for prior error files
600    o pkg/mdsio:
601       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
602       (new argument) to check for tiled file in mdsioLocalDir : this fix the
603       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
604    o pkg/ctrl:
605     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
606       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
607       unused and superfluous variables
608     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
609    o pkg/ecco
610     - enable adjoint of Stevens OB
611    o pkg/ctrl/ecco/grdchk:
612      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
613        Fortunately, we do not have any tests for the numerous cpp-flagged
614        option of "obcs as control parameters" so we will never know
615        if this is an improvement (but at least now things compile).
616      - remove an obsolete initialization from ecco_cost_init_barfiles.F
617      - fix some problems within never used ifdefs to make the code compile
618    o pkg/obcs:
619     - Refine Interior mask definition to work with more complex OB (e.g.
620       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
621       read in Interior mask from file. Check if Interior mask is consistent
622       with OB list of indices.
623    o pkg/seaice
624     - beginning code for a seaice tracer package,
625       but currently only used for seaice age: SEAICE_AGE
626       SEAICE_num = 4
627       iTracer = 1: area-weighted ice age
628               = 2: volume-weighted ice age
629               = 3, 4: template for one-year vs. multi-year ice
630       data.seaice has new namelist SEAICE_PARM03 for arrays related to
631       SEAICE_num
632    
633    checkpoint62t (2011/03/05)
634    o pkg/obcs:
635     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
636       then normal component. This ensures that the normal component is set
637       correctly even when it conficts with tangential setting from an other OB.
638       Affects results of test-experiment seaice_obcs: update the output.txt
639    o pkg/obcs:
640     - add code to monitor statistics of dynamical fields at OB.
641     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
642       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
643       - change default: balance the Net inflow through all OB (instead of balancing
644         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
645     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
646       to match Nortern OB inflow (OBCS_balanceFacN=0).
647    o pkg/seaice:
648     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
649    o pkg/seaice (seaice_growth v 1.113):
650     - reverting seaice_growth to v 1.111 in order to have code with exact bit
651       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
652       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
653       runtime flag SEAICEareaFormula is kept but is inactive
654    o model/src:
655     - add new param to scale curvilinear grid distance and area when using
656       a different sphere radius from the grid-files.
657     - test/check multi-threads EXCH applied to local variable (cg2d_x)
658    o adjoint:
659     - enable adjoint of Stevens OB
660     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
661       (a bit delicate because of potentially modified adj. common block structure;
662       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
663    
664    checkpoint62s (2011/02/15)
665    o pkg/seaice (seaice_growth v 1.112):
666     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
667       computing the ice cover tendency from effective thickness tendencies. Include
668       Ian Fenty's formula.
669     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
670       SEAICEareaFormula.
671     - simplify notations for the various d_HEFF/d_AREA terms.
672    o pkg/gmredi:
673     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
674       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
675       add a verification test-run (front_relax.bvp) to test GM_useBVP.
676    o pkg/seaice (seaice_growth v 1.111):
677     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
678     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
679       also melt ice.
680    o pkg/seaice:
681     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
682     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
683    o pkg/cheapaml:
684     - from Nico Wienders: New version of this package.
685    o pkg/flt:
686     - add CPP options to prevent floats to re-enter the opposite side of
687       a periodic domain (default: keep periodicity)
688    o pkg/gmredi:
689     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
690       (needed for multi-dim advection).
691     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
692    o model/src:
693     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
694    o tutorial_tracer_adjsens
695     - extend to NLFS and replace maskC by hFacC
696       (change reference output accordingly)
697    
698    checkpoint62r (2011/01/24)
699    o testreport:
700     - add option -deloutp (-do) to remove output file after successful run
701     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
702       extract exact list of procs from this file ; adjust COMMAND by
703       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
704    o pkg/ecco: replace old ineffective way of penalizing deviations from
705      first guess (of obcs) with code by Matt Mazloff
706    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
707      exf/cal
708      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
709        and handle case of obcs?period == 0
710        Not affected by these changes: There is still an inconsistency in
711        the computation of start/endrec for the obcs variables for ALLOW_CAL
712        defined (see comment by Menemenlis, 7-Mar-2003)
713      - make S/R ctrl_get_gen_rec return something meaningful even if
714        ALLOW_CAL is not defined
715      - ctrl_getobcs?: simplify code so that it does not need to use
716                       S/R exf_swapfields
717    o testreport:
718       allow to test MPI with different number of processors for each experiment:
719       create file "SIZE.h.mpi" in each build dir.
720       Note: update of "-command" argument not yet implemented.
721    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
722      alleviate the need for additional 3D tapes when using
723      the non-inear free surface in the adjoint. This is done
724      by adding an 'update' of hfacc etc. to their current
725      value at the beginning of forward_step.F.
726    o pkg/seaice
727      seaice_lsr: move stress-divergence computations out of outer pseudo-
728      timestepping loop
729    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
730      up, so that the calls of the ctrl_* subroutines are really at the end
731      of the routine.
732    o pkg/gmredi:
733      allow to specify a 2-D horizontal map and a 1-D vertical profil
734      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
735    o pkg/seaice:
736      move lsr iterations from seaice_dynsolver to seaice_lsr.
737    o pkg/seaice:
738      reduce memory footprint of seaice mutldim advection tapes,
739      by using a 2D tape independent of the generic_advdiff ones,
740      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
741    
742    checkpoint62q (2010/12/29)
743    o model/src:
744      - check horizontal grid-spacing for unset or zero/negative values.
745      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
746    o pkg/flt:
747      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
748      - precision of input and output files set according to readBinaryPrec
749        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
750      - initial float position from tiled file was not converted to index space
751        (looks like a bug): fixed to make it similar to initial pos. global file.
752    o global_ocean.cs32x15:
753       change SIZE.h of AD set-up to get same tiling as with MPI.
754       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
755    o model/src:
756       add flag to control printing of domain fields (bathymetry, hFac ...) in
757       ini_mask_etc (call to plot_fieds_xy*).
758    o pkg/thsice:
759       if useEXF, some forcing fields are not valid in overlap: fixed by computing
760       over the interior only + apply EXCH at the end (like with SEAICE advection).
761    o pkg/mdsio:
762      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
763        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
764      - change barrier call for safe multi-threads access to 3-D shared buffer.
765      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
766      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
767        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
768    o pkg/flt:
769      - add fourth-order Runge-Kutta integration
770      - add basic exch2 support (only 1 facet supported so far!)
771    o pkg/mdsio+rw:
772      new S/R to read local (or tile independent) vector (read counterpart of
773       mds_writevec_loc, and front-end write_glvec_rl/rs).
774    o global_ocean.cs32x15: additional input_ad.seaice experiment
775        that uses pkg/seaice rather than pkg/thsice.
776        (using multidim advection for seaice)
777    o towards more F95 syntax for array specification in namelist:
778      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
779        of all verification experiments.
780           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
781          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
782      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
783    o global_ocean.cs32x15: additional input.seaice experiment
784        that uses pkg/seaice rather than pkg/thsice.
785    
786    checkpoint62p (2010/12/17)
787    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
788        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
789    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
790        allow for use of multim. advection in seaice adjoint.
791    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
792      - first attempt to close budgets by taking into account the freshwater
793        flux implied by the sublimation of snow and ice. So far only the
794        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
795        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
796    o eesupp/src:
797      new S/R with new option (NML_EXTENDED_F77) to change array specification
798      from F95 standard to commonly accepted extended F77 form.
799      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
800      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
801      for less tolerant f77 compiler (e.g., pgf77, g77).
802    o globalFiles:
803      commented out in parameter file "data" since it's not safe with MPI
804      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
805      in this case); no longer commented out in restart test (tst_2+2).
806    o add adTapeDir to specify a special directory where adjoint tapes are
807      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
808      and cannot be used together with mdsioLocalDir.
809    o nesting pkgs:
810      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
811      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
812      - add parameter files + utils dir + output from short run on beagle.
813    o pkg/seaice:
814        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
815    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
816      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
817    
818    checkpoint62o (2010/11/25)
819    o pkg/exf:
820      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
821    o pkg/seaice:
822      - seaice_ocean_stress: split a loop for better vectorization of the
823        adjoint code
824      - seaice_growth.F: fix bug in conservation of freshwater connected to
825        capping of heff, put contribution into d_HEFFbyNEG
826      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
827        by something more sensible (parameters that are what their name implies)
828      - change some defaults, so that by default exf-parameters are used for
829        things like rhoAir, cpAir,latent/sensible heat parameters, in order
830        to reproduce the old results, many data.seaice now contain funny values
831        for cpAir and latent heat of sublimation
832    o packages_readparms.F: move exf_readparms up in line so that
833        exf-parameters are visible for other packages (e.g. seaice)
834    o debugMode & debugLevel=2:
835      - differentiate between debugMode & debugLevel=2:
836        debugMode: controls printing of debug messages (sequence of S/R calls).
837        debugLevel: controls printing of algorithm intermediate results and stats.
838      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
839        => allows to print debug-stats without all sequence of call messages.
840      - switch control of debug print from debugLevel to debugMode in many S/R.
841    o pkg/obcs (obcs-sponge):
842        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
843        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
844    o pkg/generic_advdiff:
845      - record overlap minimum size for each advection scheme;
846      - refine criteria on overlap minimum size;
847      - check and stop (in gad_check) if overlap size is too small.
848    o pkg/obcs:
849      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
850        once, in ptracers_implicit.F)
851      - with seaice: remove test on empty file name in obcs_apply_seaice (always
852        apply OB values when tile has OB)
853    o model/src, coriolis setting:
854      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
855        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
856        files (selectCoriMap=3) with any grid.
857      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
858    o pkg/seaice/seaice_growth.F:
859        a few cosmetic changes that reduce the number of lines of code
860    o pkg/obcs: add boundary conditions following Stevens (1990)
861      - the code follows old MOM/NAOSIM code
862      - so far it is only implemented for the eastern and western boundaries
863        and NOT for pTracers
864    o pkg/rbcs:
865      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
866        beginning of the first rbcs forcing period.
867      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
868        offline package, i.e., one file per time, labeled by iteration number;
869        deltaTrbcs sets the timestep with which the data was generated;
870        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
871      - rbcsForcingCycle=0 makes forcing non-cyclic.
872      - make arithmetic safe for negative times and odd forcing periods.
873    
874    checkpoint62n (2010/11/09)
875    o pkg/seaice:
876        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
877    o pkg/obcs:
878       New S/R to copy tracer value from the OB location to narrow band region
879        (width = same as overlap) beyond the OB: preserve OB value (needed for
880        high-order scheme) which were overwritten by EXCH call if in overlap
881        region. Applied to theta, salt, ptracer and advected seaice variables.
882       With seaice: use maskInC in similar way as in gad_advection.F,
883        in seaice_advection.F and advect.F.
884       Update output of experiment seaice_obcs and change exp4 to test OBCS with
885        4th order Adv.Scheme. for pasive salt and ptracer.
886    o tools/genmake2:
887      - when looking for an optfile (not specified), only search for Fortran compiler
888        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
889      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
890        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
891      - set default for CPP to "cpp -traditional -P" (was the case without specifying
892        an optfile, but otherwise default was just "cpp".
893      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
894      - when "CC" is not set in the optfile, look for possible C compiler
895        (instead of just setting CC=cc)
896      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
897        => add a ".F" to ".o" rule for source files with no "#include" (such as
898           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
899      - move gfortran before g77 in list of possible Fortran compiler (consistent
900        with reference compiler switch from g77 to gfortran)
901    o pkg/seaice:
902      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
903        seaice_check that stops the model, when the CPP flag is used.
904      o seaice_growth.F: make capping of ice volume conserving by returning the
905        capped ice as freshwater to EmPmR. This does not change the verification
906        experiments but will change runs where the capping is acutally active
907    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
908      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
909         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
910         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
911    o tools/genmake2:
912      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
913      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
914      - clean previous genmake log files before anything else.
915      - change Makefile to remove testreport log files (*.tr_log) and genmake log
916        files only with "CLEAN" target (instead of "Clean");
917    o pkg/generic_advdiff:
918      Change OBCS in multiDim advection (gad_advection.F):
919       Use maskInC to prevent intermediate update of tracer-field in OB regions,
920       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
921       which were applying future time-step OB values.
922      This way, all explicit calculations use current-time-step OB values
923       (simpler and more consistent).
924      Affects results when set-up uses time-varying OBC and multi-dim advection;
925       update output of experiment seaice_obcs.
926    o pkg/seaice:
927      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
928       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
929         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
930      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
931       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
932       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
933    o pkg aim (2010/10/26):
934      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
935        formulation with obliquity, eccentricity, ... as run-time parameters,
936      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
937        upward shortwave radition at the surface (all-sky and clear-sky).
938    o pkg/obcs:
939      - writing sections with globalFiles=T does not work: switch to tiled-files
940        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
941      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
942      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
943    
944    checkpoint62m (2010/10/21)
945    o pkg/seaice: vectorize seaice_solve4temp.F
946      - move iterations loops outside of i/j-loops
947      - requires 2D arrays for TB and effConduct
948      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
949        modified in this routine
950      - a little bit of clean up, adjusting indentation, etc.
951      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
952        performance and '**TWO' by '**2' (because TWO is a float),
953        replaced ONE, ZERO
954    o eesupp/src:
955       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
956    o pkg/seaice/seaice_growth.F
957      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
958      merging process. The merged routine has two branches, and one activates the 'evolution'
959      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
960      In summary, here is what the '10/10 revision' did consist of
961        part 1: seaice_growth.F revisions 1.71 to 1.75
962          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
963            The emphasis here was on improving readability (e.g. by trying to use meaningful
964            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
965        part 1.5:
966          - revising the lab_sea experiment to make it a more useful (i.e. stable
967            and representative of an actual model run). This was done by generating a
968            (winter) pickup to start from, switching back the main experiment dynamic
969            solver from evp to lsr, having one of the experiments use the free drift solution.
970        part 2: seaice_growth.F revisions 1.76 to 1.85
971          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
972          - Sorting out the various fields units and sign (set early on and reset at the end)
973            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
974            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
975          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
976            and simplifying logical expressions to further improve readibility.
977        part 3: seaice_growth.F revisions 1.86 to 1.89
978          - Re-organize the blocks of code more logically.
979          - Merging the '_if.F' pieces that add something new.
980    o pkg/thsice:
981      - vectorize thsice_solve4temp and thsice_get_exf.
982        Problem: thsice_solve4temp has an unvectorizable statement that
983        might also be problematic for TAF
984      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
985        does not change the verifcation experiment, but will change all
986        experiments that have this flag undefined (not tested in verification);
987        a little reorganization to save a few 2D fields and recomputations
988      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
989      - 2nd step:  fix some store dirs
990        o seems to work somewhat, i.e. using ifort but not g77
991        o likely cause are incomplete init. or recomputation
992        o start verification/global_ocean.cs32x15/input_ad.thsice
993    o pkg/obcs: add support for exch2
994      - the position of the boundary and prescribed values are specified using
995        a global domain with exch2 facets stacked
996        - in x for N,S boundaries (like W2_mapIO=-1)
997        - in y for E,W boundaries (so E,W boundaries do not overlap)
998    o pkg/mdsio: add support for writing global sections with exch2
999        file layout is as for obcs described above:
1000        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1001        - for y-z sections, facets are stacked in y
1002    o pkg/thsice:
1003       - change a few routines for better vectorization: thsice_albedo.F,
1004         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1005         not affected, but in particular the latter routine has changed
1006         dramatically (not necessarily easier to read now).
1007       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1008       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1009    o verification/lab_sea:
1010      - overhaul of the forward model experiments. The main motivation
1011        for this revision is that lab_sea has proven quite fragile (when
1012        changing the sea-ice code, and switching platforms) to a point
1013        when failures were very hard to attribute to specific code problems.
1014      - the suspected reason for this fragility is noise amplification by evp so,
1015        to start with, we decided to replace evp with lsr in the main experiment.
1016      - the input.lsr experiment thus became obsolete and was removed.
1017      - it was replaced with the input.fd experiment that uses an
1018        analytical "free drift" solution as the ice velocity field.
1019      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1020        will hopefully allow us to discriminate problems due to dynamic solvers
1021        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1022        us to test additional options, along with the salt plume package.
1023      - Finally a pickup was generated (at the end of a one year run) to
1024        make the tests more representative of an actual model run. Previously
1025        the tests starting point was a 1m thickness of ice everywhere.
1026    o pkg/seaice:
1027      - introducing S\R seaice_freedrift.F that compute the
1028        analytical solution to an approximate ice momentum
1029        equation (i.e. the simple stress/coriolis balance).
1030      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1031        of the free drift velocity field, and enable its use.
1032        To actually use the free drift solution as the model ice
1033        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1034    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1035    
1036    checkpoint62l (2010/10/04)
1037    o pkg/seaice:
1038      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1039      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1040       version (with USE_ORIGINAL_SBI undef);
1041    o add hooks for new packages OASIS, the package will follow
1042      (hooks exclude the seaice pkg for now)
1043    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1044      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1045      rather than mdsio_readvector.F/mdsio_writevector.F, within
1046      adread_adwrite.F to read/write adjoint-related tapes to disk.
1047    o eesupp and pkg/mdsio: ALLOW_WHIO
1048      Option to write/read 2D fields to files including tiles halos.
1049      The main purpose is for adjoint related "tape I/O".
1050      The secondary purpose is for debugging phases.
1051      A word on those rather specifically intended purposes.
1052      The code was meant to be stripped down to the bare minimum.
1053      Typically, there is a unique and basic mapping to the global
1054      buffer (tile by tile, then proc by proc, then level by level), and
1055      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1056      meant to generate user friendly outputs of various shapes and forms.
1057      Rather it is intended, for the knowledgeabale developers,
1058      to be largely independent of the many mdsio options, to allow
1059      outputs of tiles+halos in debugging phases and in adjoint runs,
1060      and to allow some flexibility in tuning (adoint) I/O depending on each
1061      file system behavior. With regard to tuning, most of the potential knobs
1062      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1063      to specify directories, to specify the typical size of I/O calls, etc.)
1064      are not yet included, and will be added if they prove useful.
1065    o pkg/seaice:
1066       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1067    o pkg/seaice:
1068       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1069       code (seaice_budget_ice_if.F) which enable to recover old standard
1070       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1071       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1072    o model/src (rStar):
1073       use simple average (not area weighted) of rStarFac at U,V point when using
1074       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1075       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1076    
1077    checkpoint62k (2010/09/17)
1078    o adjoint
1079       * changed verification/global_ocean.cs32x15 ; adjoint now tests
1080         Adams-Bashforth 3 + NLFS + RSTAR
1081       * some more modifs required for ECCO-GODAE v4
1082    o pkg/seaice
1083       add SEAICE_AGE_VOL option to use volume instead of area for
1084       integrating SEAICE_AGE
1085    o model/src:
1086       first check-in of sigma & hybrid-sigma coordinate code ; also includes
1087       non-linear free-surface parts ; but pressure-gradient not yet coded.
1088    o pkg/ptracers:
1089       option for ptracer to convert Salt Relax into additional EmP.
1090        tested in exp. global_ocean.90x40x15.dwnslp (update output)
1091    
1092    checkpoint62j (2010/08/25)
1093    o pkg/ggl90:
1094       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1095    o pkg/dic: car_flux.F, phos_flux.F
1096      - reduce number of exp-calls in order to improve performance
1097      - clean up a little (replace fields by their macros, etc., fix
1098        typo in CPP-flag)
1099    o pkg/ggl90: minor changes
1100      - GGL90diffKrS was removed --> always use GGL90diffKr
1101      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1102      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1103        (commented out for now)
1104      - change in max/min operations to ensure that smoothing is ok
1105      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1106      - always use diffKrNrT as background profile (i.e. never use diffKr field)
1107    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1108    o pkg/dic:
1109      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1110        vectorization
1111      - small bug fix in insol for the unlikely case of a cartesian grid
1112      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1113        + now vectorize, which also removes adjoint recomputations;
1114        + replace integer maksp1 by _RL maskp1
1115        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1116    
1117    checkpoint62i (2010/07/21)
1118    o pkg/flt:
1119      - with OBCS: stop floats which enter the OB region
1120    o model/src:
1121      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1122        for implicit vertical advection.
1123    o pkg/seaice:
1124     - account for melting in seaice age evolution.
1125     - remove double counting of seaice ridging effect on seaice age.
1126    
1127    checkpoint62h (2010/06/18)
1128    o pkg/exch2:
1129     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1130    o tools/genmake2
1131      - remove "-pdefault" option: redundant with the use of "packages.conf";
1132      - remove file pkg/pkg_default : set the default as a pkg group
1133        ("default_pkg_list") defined in pkg/pkg_groups;
1134      - fix for case pkg/pkg_depend is missing (was hanging before);
1135      - add option "-pgroups" to specify a different pkg_groups than the default.
1136    o verification/adjustment.cs-32x32x1:
1137       add a "minimal" set-up test (code_min & input_min) which only compiles
1138       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1139    o tools/genmake2
1140      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1141      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1142    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1143      files are nearly the same anyway.
1144      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1145       - redefinition of tau(i,i) (by a factor of ustar)
1146       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1147       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1148       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1149       - replace
1150         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1151         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1152         by
1153         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1154         (changes results)
1155       -> exf_bulkformulae v1.22,
1156          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1157          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1158                    output.txt 1.63
1159           offline_exf_seaice: output.seaicetd.txt 1.7
1160           seaice_obcs: output.txt 1.10)
1161      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1162       -> exf_bulkformulae v1.23,
1163          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1164          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1165      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1166    o adjoint of exch-1:
1167     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1168       (note: was already like this when using EXCH-2) and remove flow dir
1169       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1170     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1171     - update pkg/exch2 diff list.
1172    
1173    checkpoint62g (2010/05/19)
1174    o eesupp/src (exch-1):
1175     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1176       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1177       (renamed to exch1_*rx_cube.F).
1178     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1179       to call new exch1 S/R ; update Makefile and .cvsignore.
1180     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1181       exch2_xy_rx later)
1182      Note: after updating your code, need to run "make clean" in eesupp/src
1183    o test experiment bottom_ctrl_5x5:
1184       new output_adm.txt with fewer grdchk & less monitor output.
1185    o model/src:
1186      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1187       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1188       beeing treated in the same way (ini_grid is not called a 2nd time).
1189    o pkg/exf:
1190      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1191      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1192      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1193      - cosmetic changes to exf_bulkformulae.F to make it look more like
1194        exf_bulk_largeyeager04.F
1195    o eesupp/src (exch-1):
1196      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1197      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1198        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1199        (even without using MPI).
1200      - Message mode: move RecvAck setting (indicator of buffer being ready)
1201        from send_put to recv_get S/R (was useless before, but not sure if
1202        it's much more useful now);
1203      - Switch the order of sync: MPI-proc 1rst and then threads;
1204      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1205      - fix AD code for communication mode ='get' (but not used).
1206    o model/src:
1207      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1208      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1209    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1210    o pkg/ctrl: require a specific set of control variables and exf-flags for
1211      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1212    o model/src:
1213     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1214       1rst forward sweep, to avoid over-writing output files during recomputations
1215       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1216     b) 2nd version:
1217      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1218      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1219         writePickupAtEnd) + seaice & ptracers output;
1220      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1221    o model/src:
1222      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1223    o pkg/exch2:
1224      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1225      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1226    o pkg/autodiff & exch2:
1227      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1228      (for now, only if ALLOW_EXCH2 is defined).
1229    o pkg/autodiff:
1230      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1231        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1232       + clean-up comments (_RS is not always real*4)
1233      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1234      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1235        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1236    o testreport (AD-tests):
1237      no longer link files from dir "../input" (1rst link files from
1238      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1239    
1240    checkpoint62f (2010/04/29)
1241    o model/src/the_main_loop.F:
1242      adjust store directives for seaice evp and multicategory according to
1243      pkg/ecco/the_main_loop.F
1244    o adjoint:
1245      global_sum_ad was incomplete (noted many times by many people ;)
1246      nice description by Jean U. as follows:
1247      * allreduce(var) in global_sum.F can be interpreted as
1248        reduce(sum) followed by broadcast of sum.
1249      * The adjoint of that is
1250        sum(adjoint) followed by broadcast(summed adjoint value)
1251        or in other words, allreduce(sum, adjoint vars)
1252      We were missing the sum(adjoint)!
1253      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1254      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1255      The fix should produce 16-digit accuracy between
1256      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1257      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1258      We'll probably change this yet again shortly
1259    o eesupp/src:
1260      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1261    o pkg/icefront
1262      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1263        specification of addmass array based on a 2D field, which is added
1264        at bottommost wet level at each horizontal location.
1265    o model/src:
1266     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1267     layout; (not always compatible with delX,delY setting; commented out for now).
1268    o pkg/exch2:
1269     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1270     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1271    
1272    checkpoint62e (2010/04/15)
1273    o pkg/obcs:
1274      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1275    o pkg/dic:
1276      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1277        (note: not presently tested in any forward verification exp.)
1278       update tutorial_global_oce_biogeo AD output file.
1279    o pkg/exf:
1280      - account for the variation of albedo as a function of zenith angle
1281        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1282    o build_options:
1283     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1284    o pkg/dic:
1285      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1286      - use binary pickup file for restart;
1287      - initialise atmos-CO2 box from dic_pCO2 parameter;
1288      - fix multi-threaded.
1289    o pkg/rbcs:
1290     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1291       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1292     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1293       and update output.txt
1294    o pkg/kpp:
1295     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1296     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1297       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1298       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1299     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1300       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1301    o pkg/offline:
1302      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1303      (bug was added in version 1.10 on 2007-08-23).
1304    o pkg/offline:
1305      - no need to specify periodicExternalForcing, etc ... to use offline pack
1306      - offline input files no longer just single prec --> parameter offlineLoadPrec
1307    o verification/lab_sea:
1308      change AD test to multi-tile setup and update all 4 AD output.
1309      NOTE: while cost function values remain very similar,
1310      gradients are very different, although gradient checks are self-consistent
1311      Should try to get to the bottom of this (cost function summation order?)
1312  o pkg/dic:  o pkg/dic:
1313    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1314    a weakness of TAF that drops part of double precision in log10 derivative.    a weakness of TAF that drops part of double precision in log10 derivative.
1315      <= changes removed since problem has been fixed in current TAF version 1.9.71
1316    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1317  o pkg/ecco:  o pkg/ecco:
1318    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
# Line 45  o tools/build_options: Line 1351  o tools/build_options:
1351      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1352  o pkg/ecco  o pkg/ecco
1353    - allow user defined cost function contributions    - allow user defined cost function contributions
1354          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1355          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1356    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1357        the two options are complementary.        the two options are complementary.
1358  o pkg/smooth  o pkg/smooth
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