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revision 1.1321 by dimitri, Wed Oct 27 05:48:33 2010 UTC revision 1.1499 by jmc, Thu Sep 1 15:08:45 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/flt:
8      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
9      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
10      - fix pickup and trajectories + profiles output with multi-threads;
11      - add parameter to select group of fields to write along trajectory and
12        profile (default unchanged);
13      - only call PORT_RAND* function when flt_noise <> 0;
14      - add multi-threaded test for verification exp. flt_example.
15    o eesupp/src:
16      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
17      - USE_OMP_THREADING: check that number of threads (from eedata) matches
18        actual number (from env.var. setting).
19    o pkg/ebm:
20      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
21      - add multi-threaded test for verification exp. global_ocean_ebm
22    
23    checkpoint63b (2011/08/29)
24    o pkg/ebm:
25      - fix sign of runoff;
26      - update directly forcing fields (Qnet,EmPmR) to use standard
27        external_forcing_surf.F (remove ebm_forcing_surf.F);
28      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
29      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
30        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
31      - update global_ocean_ebm parameters file data and update output (fwd+ad).
32    o verification/matrix_example:
33      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
34        MPI and mutlti-threaded testing.
35    o pkg/matrix:
36      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
37      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
38      - fix for multi-threaded (remove DATA statement);
39      - use standard DIFFERENT_MULTIPLE function;
40      - add MATRIX_OPTIONS.h
41    o verification/matrix_example:
42       To allow to split the domain in several tiles, change the domain size
43        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
44        Western side) of land points.
45    o (*_)write_pickup:
46      - fix few bugs in mypackage_read/write_pickup.F
47      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
48        array of length 1 (was caught by compiler syntax-check).
49    o pkg/diagnostics (velocity potential solver):
50      - fix initialisation of main diagonal matrix (for overlap values)
51    o tools/build_options:
52      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
53        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
54      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
55        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
56        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
57        and use "-devel" testreport option for standard testing on baudelaire.
58    o pkg/grdchk:
59      - Assume that all gradient-check position are within the same tile
60        corresponding to global indices (iGloTile,jGloTile) and that
61        positions (i,j indices or nbeg) are local to this tile;
62      - set tile local-indices and proc. number according to tile global-indices;
63      - remove grdchkwhichproc from namelist (retired param);
64      - send adjoint gradient to all procs so that all procs print it to STDOUT;
65      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
66    o adding package bbl (Bottom Boundary Layer)
67      description in MITgcm/pkg/bbl/bbl_description.tex
68      example/test experiment in MITgcm_contrib/bbl
69    o adjoint verifications
70      - changed 5 experiments to multi-tiles
71        * global_ocean.90x40x15
72        * obcs_ctrl
73        * offline_exf_seaice
74        * tutorial_dic_adjoffline
75        * tutorial_tracer_adjsens
76        changed reference output for those that crossed tile boundaries
77        (changed choices of gradient check positions)
78      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
79      - temporary bug fix in grdchk_loc.F for obcs
80    o genmake2 & testreport
81      - add target "obj" (just for OBJFILES files) to Makefile;
82      - add option to specify FEXTRAFLAGS on command line.
83    o pkg/mypackage:
84      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
85    
86    checkpoint63a (2011/08/02)
87    o pkg/diagnostics (velocity potential):
88      - fix velocity-potential calculation when using OBCS: balance net inflow
89        at each level (new S/R OBCS_DIAG_BALANCE).
90      - fix some of the problems with OBCS in stream-function calculation.
91    o pkg/exf/exf_readparms.F
92      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
93        EXF_NML_OBCS) more consistent, so that you need not have these lists
94        in data.exf when they are not used.
95    o optim/optim_readdata.F:
96      - add some output about obcs variables that might help debugging
97      - add a check about nvarlength
98    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
99    o pkg/diagnostics (velocity potential):
100      - fix mask for OBCS (still problems in stream-function with OBCS);
101      - add specific parameter (default = main code CG2D params) for solver;
102      - in case of poor convergence, use solution corresponding to lowest residual.
103    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
104      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
105      and should be avoided where possible.
106    o model/src (rStar):
107      - include r* effect on reference-state (PhiRef) in totPhiHyd
108        (so that it's really the potential anomaly at the cell center);
109        affect solution only if z* with full pressure in EOS.
110      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
111        update output (because of z* in totPhiHyd and viscA4 changes);
112      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
113        @ constant r) until interpolation at constant r is implemented.
114    o pkg/diagnostics
115      - fix RCENTER diagnostics in case cell center is not at interface middle
116    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
117      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
118      that THETA and SALT are "conservative temperature" and "absolute
119      salinity"
120    o pkg/ctrl
121      - fix computation of endrec in s/r ctrl_init_rec
122      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
123    o pkg/seaice/seaice_growth.F
124      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
125        remove then obsolete STORE directives
126      - fix STORE directives for tice and tices, so that only the
127        appropriate part of the fields are stored (and not the entire
128        field); update global_ocean.cs32x15.seaice AD output.
129      - cosmetic changes: adjust CPP flags and indentation for better
130        legibilty
131    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
132      Chris Wilson)
133    o pkg/gmredi:
134       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
135       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
136    
137    checkpoint63  (2011/07/11)
138    o pkg/exch2:
139     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
140     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
141       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
142       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
143    o pkg/diagnostics:
144     - deal with pairs of post-processed diags which are computed together; in
145       particular, re-order list of diags within 1 file to save 2nd computation.
146     - add S/R to compute velocity stream-function (called after velocity-potential
147       calculation) from divergence free transport -> new diagnostics "PsiVEL".
148     - add parameter to select grid-point location where PsiVEL == 0.
149    o eesupp/src:
150       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
151       (specific S/R needed with exch2 topology - for now, just print an error msg)
152    o pkg/shelfice
153     - Implement friction velocity-dependent transfer coefficients following
154       Holland and Jenkins, JPO, 1999
155       Original code by M. Losch with small modifs.
156       Enable with CPP option SHI_ALLOW_GAMMAFRICT
157       and runtime flag SHELFICEuseGammaFrict
158    o verification lab_sea & global_ocean.cs32x15:
159     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
160       does not miss some dependencies (but is slower) and also works with many files
161       (default makedepend limitation for AD built).
162     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
163    o pkg/diagnostics:
164     - add run-time parameter "useMissingValue" (def=False) to fill land-point
165        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
166       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
167     - Extend the use of "missing_value" setting from data.diagnostics for the case
168       of counter-diagnostics (where fraction-weight is zero). This applies both to
169       MNC and MDS output files.
170    o pkg/seaice/seaice_growth.F:
171      - add 'a priori' cap of latent heat flux based on actual mass considerations
172        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
173        non-legacy seaice_solve4temp.
174      - add diagnostic of the residual sublimation freshwater flux (the freshwater
175        flux taken from the ocean if the total actual latent heat fluxes exceed
176        the maximum)
177      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
178       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
179      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
180       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
181      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
182      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
183    o verification 1D_ocean_ice_column:
184       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
185       update results
186    o pkg/diagnostics:
187     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
188       which are not filled-up but computed from other diags ; In this case, the mate
189       diag points to the primary (filled-up) diag to used for post processing.
190     - Update Velocity-potential computation using post-processed diag framework.
191     ==> Change the ordering of fields and time-periods in MDS output file
192       when using periodic averaging: now writes one time record with the full set
193       of fields for this time period, then the next time reccord (it used to be
194       one field with the full set of time records then the next field).
195         Note: this is now similar to NetCDF (MNC) output file. <==
196    
197    checkpoint62z (2011/06/21)
198    o adjoint monitor:
199     - Add adjoint monitor output for packages exf, seaice
200       and update relevant testreport output
201    o pkg/seaice:
202     - re-order diags inits so that they appear in order in available_diagnostics.log
203     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
204       area/heff/hsnow preceeding thermodynamic growth/melt.
205     - modified diag: SIdA; output actual effect, as the description states.
206     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
207     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
208       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
209        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
210     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
211     - added diagnostics for seaice generic tracers (SItr*).
212     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
213     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
214     I. Fenty: 18-Jun-2011:
215     Minor changes to seaice package:
216     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
217        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
218       - Differentiated "regularization variables" from "floor variables"
219        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
220        * hiceMin became SEAICE_hice_reg (old hiceMin)
221          (with _reg meaning regularization variable)
222       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
223        so as to ensure energy conservation when going between phases
224      - A22 was not used anywhere
225     2) Changed regularization procedure for heffActual and hsnowActual to ensure
226        well-boundedness and smooth adjoint in seaice_growth.F
227     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
228        because the old regularization always set heffActual >= 0.05 cm
229     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
230        on AREA when HEFF > 0.
231      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
232        requiring that DISABLE_AREA_FLOOR *not* be defined
233     Affected verifications:
234      - 1D_ocean_ice_column (output.txt output_adm.txt)
235      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
236    o pkg/diagnostics:
237      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
238      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
239        (was _RL, now integer) with option = 0 to retrieve all levels.
240      - add pieces of code to compute velocity potential at each level (new diagnostics
241        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
242        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
243      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
244        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
245        and in diagnostics_fract_fill.F (do not need a valid pointer for the
246        diagnostics counter-mate); check that definition of counter-diagnostic
247        includes a valid counter-mate (in diagnostics_set_levels.F).
248    o model/src (rStar):
249      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
250        affect solution only if z* with full pressure in EOS;
251        update output of test-exp global_ocean.90x40x15.
252    o pkg/seaice:
253      - introduce siEps=1e-5 parameter
254      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
255      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
256      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
257        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
258        as well as ice cover age and ridging index (attached to AREA).
259        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
260        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
261        Up to SItrMaxNum=3 tracers can be used simultaneously.
262    o pkg/salt_plume:
263      -introduce SPsalFRAC run time parameter that sets the fraction of the
264       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
265       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
266    o model debug options:
267      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
268        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
269      - Refine debug-msg printing selection (3 new levels):
270        debugMode  : controls printing of debug messages (sequence of S/R calls).
271        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
272         debLevZero =  0 ; /* level of disabled aux. msg printing */
273         debLevA =  1 ; /* level of minimum  aux. msg printing */
274         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
275         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
276         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
277         debLevE =  5 ; /* level of extensive debug printing */
278        New debugLevel default: with default debugMode value (=F),
279          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
280          and if debugMode=T, default debugLevel = 4 (debLevD).
281        Relation with previous settings:
282         debLevB (=2) corresponds to former debLevA (=1)
283         debLevD (=4) corresponds to former debLevB (=2)
284        Note:
285         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
286         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
287            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
288      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
289        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
290    o pkg/obcs:
291      - change OBCSfixTopo default from True to False (should not change the results);
292        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
293    o pkg/thsice:
294      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
295        2nd layer seaice sublimation (unlikely to happen)
296      - use Interior mask for OBCS in thsice_advection.F (similar to what is
297        done in gad_advection & seaice_advection).
298    o adjoint:
299      bug fix spotted by Gael Forget:
300      seaice_advection and thsice_advection still had
301      legacy CPP options to avoid CS corner updates for adjoint
302    o pkg/seaice:
303      => Change some of the defaults (2011/05/29):
304         - change SEAICEuseFluxForm default (from False to True)
305         - change DIFF1 default (from 0.004 m/s to 0. m/s)
306         And print warnings if DIFF1 is not set in data.seaice and centered
307          avection scheme is used without any diffusion.
308      also:
309      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
310      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
311      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
312        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
313        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
314      update results of test exp.:
315         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
316             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
317             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
318         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
319         seaice_obcs: output (SEAICEuseFluxForm=T)
320      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
321          for standard fwd & AD lab_sea tests (to keep the same output).
322    o pkg/seaice/seaice_growth.F:
323      - use Ian Fenty's capping formulas for actual ice
324      thickness thoughout EVOLUTION branch.
325      - put treatment pathological case #2) in CPP brackets
326      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
327      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
328    o pkg/seaice:
329      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
330      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
331      also pass fac as a param, which can be 1. (to update the tendency
332      field) or the time step (to update the field itself).
333      - seaice_advdiff.F: for multidim, call seaice_diffusion with
334      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
335      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
336      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
337      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
338    o pkg/seaice:
339      diffusion with centered advection scheme (diffus.F & advect.F):
340      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
341        to just compute the laplacian of input-field.
342      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
343      - fix flux-form version in diffus.F to conserve tracer.
344      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
345       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
346    
347    checkpoint62y (2011/05/26)
348    o pkg/seaice:
349     - seaice_growth.F : in EVOLUTION branch, always include
350       a_QSWbyATM_cover in qnet (as it should be).
351     - verification/global_ocean.cs32x15 : update results accordingly
352       (output.seaice.txt output_adm.seaice.txt).
353    o pkg/seaice + obcs:
354     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
355       equivalent of assuming no tracer gradient outside the OB region.
356       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
357     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
358       after changes above);
359     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
360       only at OB location (instead of over a band of OLx width).
361    o pkg/seaice:
362     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
363       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
364    o pkg/obcs:
365      - split header file "OBCS.h" into 4 separated files:
366        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
367       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
368         (contain no conditional statement which depends on OBCS options).
369      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
370        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
371    o ctrl, cost, grdchk & autodiff pkgs:
372      - make options file more standard (like other {PKG}_OPTIONS.h file but
373        with AD_CONFIG.h); clean-up some of the included header files.
374    o pkg/obcs:
375      - do not mask tracer when applying OB (tracer == 0 could generate problems)
376      - apply tracer OB values to tracer field only at OB location (instead of
377        over a band of OLx width)
378      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
379      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
380        obcs_apply_tloc.F & obcs_apply_sloc.F
381    o obcs in model/src:
382      - call OBCS_APPLY_W only if NonHydrostatic.
383      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
384      - reset dEtaHdt and wVel to zero outside OB interior region ;
385      - leave tracer unchanged outside OB interior region: This has no effect
386        on the solution but just to prevent unrealistic tracer value outside OB.
387      - zero out velocity outside OB interior region: This has no effect on
388        the solution but just to prevent unrealistic velocity outside OB.
389    o obcs and non-lin free-surf:
390       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
391       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
392       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
393       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
394       update results of test-exp. exp4(nlfs).
395    o exp4 (nlfs) test-exp:
396       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
397       with NonLin-FreeSurf); update output.nlfs.txt
398    o obcs and 2d/3d solver norm:
399       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
400       and outside OB interior region (will allow to place OB further inside the
401       domain). Depending on the domain, can affects cg2d-Norm (previous
402       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
403       and cg3d-Norm (previous Norm was computed before canceling OB terms),
404       e.g. in tutorial_plume_on_slope.
405      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
406    o pkg rbcs:
407      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
408      - add capability to apply relaxation to horizontal velocity uVel & vVel.
409    o pkg/grdchk: add gradient check for control variable xx_shifwflx
410    o pkg/shelfice/shelfice_init_fixed.F
411      fix CPP-flag combinations
412    o pkg/seaice: Merge iceage code of Pierre Rampal
413      * update/change/correct ice age calculations
414      * add age updates for pathological cases
415      Probably needs more testing...
416    
417    checkpoint62x (2011/05/13)
418    o pkg/mom_vecinv:
419       high-order vorticity scheme: use interior masks (maskInW & S)
420       to zero-out (outside OB) gradient of vorticity.
421    o verification exp.:
422       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
423       hs94.128x64x5 and seaice_obcs ; update results.
424    o pkg/obcs:
425      fix bug in OBeta for YZ sections in obcs_exf_load.F
426    o pkg/ctrl, pkg/shelfice, and optim:
427      - add new control variable xx_shifwflx (fresh water flux underneath ice
428        shelves). This is almost as tedious as obcs-ctrl, because the
429        variables needs its own mask.
430      - add a cost function term that penalizes the deviation of xx_shifwflx
431        from the first guess (zero) in analogy to other control variables
432    o pkg/shelfice:
433      - start basic adjoint
434    o pkg/ctrl:
435      - remove extra 2D field "for good measure" when initializing in
436        ctrl_set_globfld_[xy/xz/yz].F
437      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
438      - improve error messages in ctrl_set_unpack_*
439    o OBC implementation in momentum:
440       use interior masks (maskInC,W & S) in momentum S/R:
441       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
442       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
443       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
444       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
445       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
446        (and also with Leith/Smagorinsky harmonic-viscosity).
447       Update output of experiment dome and exp4 (+nlfs).
448    o exp4 test-exp:
449      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
450        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
451        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
452        time-varying OB at Western-side for wVel (NonHyd); update output.
453      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
454        and biharmonic-viscosity ; also use prescribed time varying OB.
455    o pkg/obcs:
456      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
457    o model/src:
458      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
459      - initialise startTime & nIter0 with unlikely values: allows to set one
460        from the other without ambiguity.
461    o seaice_obcs test-exp.:
462      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
463    o pkg/obcs:
464      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
465        no longer needed with maskInC,W,S in pkg/generic_advdiff.
466    o pkg/seaice:
467      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
468        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
469      - fixed bug in the initialization of sea ice salinity variable HSALT
470        in seaice_init_varia.F  (removed dependence on ICE2WATR)
471    o fizhi-cs test exp.:
472       switch reference output convention for these 2 non-standard test-exp,
473        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
474          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
475       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
476    o model/inc:
477      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
478        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
479    o pkg/seaice:
480      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
481    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
482      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
483        and initial HSALT
484    
485    checkpoint62w (2011/04/26)
486    o pkg/mom_fluxform:
487      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
488      - use parameter "sideDragFactor" in no-slip BC side-drag part.
489      - update output of exp. global_ocean.90x40x15
490    o pkg/mom_vecinv:
491      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
492    o update seaice exp.:
493      use more consistent parameter values (remove "backward compatability only":
494       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
495      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
496       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
497    o update test-exp global_ocean.90x40x15:
498      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
499      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
500      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
501      o turn on zStar & viscA4 in standard set-up (dir input/)
502        and update output files: output.txt & output.dwnslp.txt
503    o new AD-test experiment: obcs_ctrl
504      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
505    o pkg/dic:
506      fix two bugs in handling water vapour pressure in carbonate chemistry
507      and air-sea fluxes. Found by Val Bennington and Galen McKinley
508      (add DIC Option = WATERVAP_BUG to recover old results)
509      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
510    o adding allowInteriorFreezing option to check for water below freezing point
511      at depth and bring the negative heat anomaly to the surface level
512    o pkgs _fields_load:
513      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
514      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
515        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
516        rbcs to get interpolation weights and time reccord number.
517      - fix multi-threading in aim_fields_load.F
518      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
519    o external_fields_load:
520      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
521       interpolation weights) to use in a periodic time-series ; do not divide by
522       time-step to convert to integer:
523       - this fixes case where externForcingPeriod is not multiple of time-step
524          (Thanks to Christopher L. Wolfe)
525       - this fixes case where externForcingPeriod is an odd multiple of time-step
526         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
527      store index of time-record which is currently loaded:
528       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
529       - needed for the adjoint but not yet used because of extensive recomputations;
530         (to be fixed soon)
531    
532    checkpoint62v (2011/04/02)
533    o verification/1D_ocean_ice_column added to test Ian Fenty's
534      pkg/seaice_growth.F modifications for improving sea ice code differentiability
535    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
536      (new velocity statistics after changing maskInW & maskInS definition)
537    o pkg/generic_advdiff with OBCS:
538      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
539      equivalent to assumption of no tracer gradient outside the OB region.
540      This will affect the results if using obcs+biharmonic diffusion.
541      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
542    o pkg/obcs:
543      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
544      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
545      in Interior region. No impact on solution but affects Velocity monitor stats.
546    o pkg/ptracers (adjoint)
547      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
548      tape file for each tracer
549    o model/inc/src and pkg/autodiff: add parameters that allow to turn
550      of parts of the adjoint code at run time. For now, there are only
551      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
552      parameters are set in data.pkg.
553      This is the lazy coward's version of doing this, but still useful for
554      debugging. In order to do it right, everything needs to be moved to
555      pkg/autodiff.
556    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
557      the end; this fixes the adjoint balancing code for open boundaries.
558    o pkg/ctrl:
559      - change behavior of xx_${varname}period to be analogous to exf-conventions:
560        xx_${varname}period =   0.,  means time-independent control part
561        xx_${varname}period = -12., means one-year-periodic monthly control part
562      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
563        clean up ctrl_init a little, remove unused variables
564      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
565      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
566    
567    checkpoint62u (2011/03/15)
568    o model/src:
569      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
570        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
571      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
572        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
573    o pkg/ctrl/obcs/ecco:
574      - remove obsolete, unused, and partially broken code:
575        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
576        ALLOW_CTRL_OBCS_BALANCE
577      - put a stop statement into ecco/cost_obcsvol.F, but also add
578        cost_obcsvol to ecco_ad_diff.list
579    o pkg/ecco: fix counting cost function contributions for obcs (code
580      by Matt M.) and diffkr for diagnostics
581    o pkg/ecco, pkg/ctrl, pkg/grdchk:
582      add cost penalty terms for initial uvel, vvel, eta controls
583      and I/O for prior error files
584    o pkg/mdsio:
585       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
586       (new argument) to check for tiled file in mdsioLocalDir : this fix the
587       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
588    o pkg/ctrl:
589     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
590       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
591       unused and superfluous variables
592     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
593    o pkg/ecco
594     - enable adjoint of Stevens OB
595    o pkg/ctrl/ecco/grdchk:
596      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
597        Fortunately, we do not have any tests for the numerous cpp-flagged
598        option of "obcs as control parameters" so we will never know
599        if this is an improvement (but at least now things compile).
600      - remove an obsolete initialization from ecco_cost_init_barfiles.F
601      - fix some problems within never used ifdefs to make the code compile
602    o pkg/obcs:
603     - Refine Interior mask definition to work with more complex OB (e.g.
604       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
605       read in Interior mask from file. Check if Interior mask is consistent
606       with OB list of indices.
607    o pkg/seaice
608     - beginning code for a seaice tracer package,
609       but currently only used for seaice age: SEAICE_AGE
610       SEAICE_num = 4
611       iTracer = 1: area-weighted ice age
612               = 2: volume-weighted ice age
613               = 3, 4: template for one-year vs. multi-year ice
614       data.seaice has new namelist SEAICE_PARM03 for arrays related to
615       SEAICE_num
616    
617    checkpoint62t (2011/03/05)
618    o pkg/obcs:
619     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
620       then normal component. This ensures that the normal component is set
621       correctly even when it conficts with tangential setting from an other OB.
622       Affects results of test-experiment seaice_obcs: update the output.txt
623    o pkg/obcs:
624     - add code to monitor statistics of dynamical fields at OB.
625     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
626       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
627       - change default: balance the Net inflow through all OB (instead of balancing
628         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
629     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
630       to match Nortern OB inflow (OBCS_balanceFacN=0).
631    o pkg/seaice:
632     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
633    o pkg/seaice (seaice_growth v 1.113):
634     - reverting seaice_growth to v 1.111 in order to have code with exact bit
635       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
636       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
637       runtime flag SEAICEareaFormula is kept but is inactive
638    o model/src:
639     - add new param to scale curvilinear grid distance and area when using
640       a different sphere radius from the grid-files.
641     - test/check multi-threads EXCH applied to local variable (cg2d_x)
642    o adjoint:
643     - enable adjoint of Stevens OB
644     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
645       (a bit delicate because of potentially modified adj. common block structure;
646       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
647    
648    checkpoint62s (2011/02/15)
649    o pkg/seaice (seaice_growth v 1.112):
650     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
651       computing the ice cover tendency from effective thickness tendencies. Include
652       Ian Fenty's formula.
653     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
654       SEAICEareaFormula.
655     - simplify notations for the various d_HEFF/d_AREA terms.
656    o pkg/gmredi:
657     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
658       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
659       add a verification test-run (front_relax.bvp) to test GM_useBVP.
660    o pkg/seaice (seaice_growth v 1.111):
661     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
662     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
663       also melt ice.
664    o pkg/seaice:
665     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
666     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
667    o pkg/cheapaml:
668     - from Nico Wienders: New version of this package.
669    o pkg/flt:
670     - add CPP options to prevent floats to re-enter the opposite side of
671       a periodic domain (default: keep periodicity)
672    o pkg/gmredi:
673     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
674       (needed for multi-dim advection).
675     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
676    o model/src:
677     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
678    o tutorial_tracer_adjsens
679     - extend to NLFS and replace maskC by hFacC
680       (change reference output accordingly)
681    
682    checkpoint62r (2011/01/24)
683    o testreport:
684     - add option -deloutp (-do) to remove output file after successful run
685     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
686       extract exact list of procs from this file ; adjust COMMAND by
687       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
688    o pkg/ecco: replace old ineffective way of penalizing deviations from
689      first guess (of obcs) with code by Matt Mazloff
690    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
691      exf/cal
692      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
693        and handle case of obcs?period == 0
694        Not affected by these changes: There is still an inconsistency in
695        the computation of start/endrec for the obcs variables for ALLOW_CAL
696        defined (see comment by Menemenlis, 7-Mar-2003)
697      - make S/R ctrl_get_gen_rec return something meaningful even if
698        ALLOW_CAL is not defined
699      - ctrl_getobcs?: simplify code so that it does not need to use
700                       S/R exf_swapfields
701    o testreport:
702       allow to test MPI with different number of processors for each experiment:
703       create file "SIZE.h.mpi" in each build dir.
704       Note: update of "-command" argument not yet implemented.
705    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
706      alleviate the need for additional 3D tapes when using
707      the non-inear free surface in the adjoint. This is done
708      by adding an 'update' of hfacc etc. to their current
709      value at the beginning of forward_step.F.
710    o pkg/seaice
711      seaice_lsr: move stress-divergence computations out of outer pseudo-
712      timestepping loop
713    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
714      up, so that the calls of the ctrl_* subroutines are really at the end
715      of the routine.
716    o pkg/gmredi:
717      allow to specify a 2-D horizontal map and a 1-D vertical profil
718      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
719    o pkg/seaice:
720      move lsr iterations from seaice_dynsolver to seaice_lsr.
721    o pkg/seaice:
722      reduce memory footprint of seaice mutldim advection tapes,
723      by using a 2D tape independent of the generic_advdiff ones,
724      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
725    
726    checkpoint62q (2010/12/29)
727    o model/src:
728      - check horizontal grid-spacing for unset or zero/negative values.
729      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
730    o pkg/flt:
731      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
732      - precision of input and output files set according to readBinaryPrec
733        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
734      - initial float position from tiled file was not converted to index space
735        (looks like a bug): fixed to make it similar to initial pos. global file.
736    o global_ocean.cs32x15:
737       change SIZE.h of AD set-up to get same tiling as with MPI.
738       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
739    o model/src:
740       add flag to control printing of domain fields (bathymetry, hFac ...) in
741       ini_mask_etc (call to plot_fieds_xy*).
742    o pkg/thsice:
743       if useEXF, some forcing fields are not valid in overlap: fixed by computing
744       over the interior only + apply EXCH at the end (like with SEAICE advection).
745    o pkg/mdsio:
746      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
747        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
748      - change barrier call for safe multi-threads access to 3-D shared buffer.
749      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
750      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
751        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
752    o pkg/flt:
753      - add fourth-order Runge-Kutta integration
754      - add basic exch2 support (only 1 facet supported so far!)
755    o pkg/mdsio+rw:
756      new S/R to read local (or tile independent) vector (read counterpart of
757       mds_writevec_loc, and front-end write_glvec_rl/rs).
758    o global_ocean.cs32x15: additional input_ad.seaice experiment
759        that uses pkg/seaice rather than pkg/thsice.
760        (using multidim advection for seaice)
761    o towards more F95 syntax for array specification in namelist:
762      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
763        of all verification experiments.
764           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
765          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
766      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
767    o global_ocean.cs32x15: additional input.seaice experiment
768        that uses pkg/seaice rather than pkg/thsice.
769    
770    checkpoint62p (2010/12/17)
771    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
772        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
773    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
774        allow for use of multim. advection in seaice adjoint.
775    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
776      - first attempt to close budgets by taking into account the freshwater
777        flux implied by the sublimation of snow and ice. So far only the
778        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
779        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
780    o eesupp/src:
781      new S/R with new option (NML_EXTENDED_F77) to change array specification
782      from F95 standard to commonly accepted extended F77 form.
783      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
784      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
785      for less tolerant f77 compiler (e.g., pgf77, g77).
786    o globalFiles:
787      commented out in parameter file "data" since it's not safe with MPI
788      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
789      in this case); no longer commented out in restart test (tst_2+2).
790    o add adTapeDir to specify a special directory where adjoint tapes are
791      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
792      and cannot be used together with mdsioLocalDir.
793    o nesting pkgs:
794      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
795      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
796      - add parameter files + utils dir + output from short run on beagle.
797    o pkg/seaice:
798        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
799    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
800      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
801    
802    checkpoint62o (2010/11/25)
803    o pkg/exf:
804      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
805    o pkg/seaice:
806      - seaice_ocean_stress: split a loop for better vectorization of the
807        adjoint code
808      - seaice_growth.F: fix bug in conservation of freshwater connected to
809        capping of heff, put contribution into d_HEFFbyNEG
810      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
811        by something more sensible (parameters that are what their name implies)
812      - change some defaults, so that by default exf-parameters are used for
813        things like rhoAir, cpAir,latent/sensible heat parameters, in order
814        to reproduce the old results, many data.seaice now contain funny values
815        for cpAir and latent heat of sublimation
816    o packages_readparms.F: move exf_readparms up in line so that
817        exf-parameters are visible for other packages (e.g. seaice)
818    o debugMode & debugLevel=2:
819      - differentiate between debugMode & debugLevel=2:
820        debugMode: controls printing of debug messages (sequence of S/R calls).
821        debugLevel: controls printing of algorithm intermediate results and stats.
822      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
823        => allows to print debug-stats without all sequence of call messages.
824      - switch control of debug print from debugLevel to debugMode in many S/R.
825    o pkg/obcs (obcs-sponge):
826        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
827        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
828    o pkg/generic_advdiff:
829      - record overlap minimum size for each advection scheme;
830      - refine criteria on overlap minimum size;
831      - check and stop (in gad_check) if overlap size is too small.
832    o pkg/obcs:
833      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
834        once, in ptracers_implicit.F)
835      - with seaice: remove test on empty file name in obcs_apply_seaice (always
836        apply OB values when tile has OB)
837    o model/src, coriolis setting:
838      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
839        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
840        files (selectCoriMap=3) with any grid.
841      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
842    o pkg/seaice/seaice_growth.F:
843        a few cosmetic changes that reduce the number of lines of code
844    o pkg/obcs: add boundary conditions following Stevens (1990)
845      - the code follows old MOM/NAOSIM code
846      - so far it is only implemented for the eastern and western boundaries
847        and NOT for pTracers
848    o pkg/rbcs:
849      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
850        beginning of the first rbcs forcing period.
851      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
852        offline package, i.e., one file per time, labeled by iteration number;
853        deltaTrbcs sets the timestep with which the data was generated;
854        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
855      - rbcsForcingCycle=0 makes forcing non-cyclic.
856      - make arithmetic safe for negative times and odd forcing periods.
857    
858    checkpoint62n (2010/11/09)
859    o pkg/seaice:
860        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
861    o pkg/obcs:
862       New S/R to copy tracer value from the OB location to narrow band region
863        (width = same as overlap) beyond the OB: preserve OB value (needed for
864        high-order scheme) which were overwritten by EXCH call if in overlap
865        region. Applied to theta, salt, ptracer and advected seaice variables.
866       With seaice: use maskInC in similar way as in gad_advection.F,
867        in seaice_advection.F and advect.F.
868       Update output of experiment seaice_obcs and change exp4 to test OBCS with
869        4th order Adv.Scheme. for pasive salt and ptracer.
870    o tools/genmake2:
871      - when looking for an optfile (not specified), only search for Fortran compiler
872        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
873      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
874        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
875      - set default for CPP to "cpp -traditional -P" (was the case without specifying
876        an optfile, but otherwise default was just "cpp".
877      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
878      - when "CC" is not set in the optfile, look for possible C compiler
879        (instead of just setting CC=cc)
880      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
881        => add a ".F" to ".o" rule for source files with no "#include" (such as
882           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
883      - move gfortran before g77 in list of possible Fortran compiler (consistent
884        with reference compiler switch from g77 to gfortran)
885    o pkg/seaice:
886      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
887        seaice_check that stops the model, when the CPP flag is used.
888      o seaice_growth.F: make capping of ice volume conserving by returning the
889        capped ice as freshwater to EmPmR. This does not change the verification
890        experiments but will change runs where the capping is acutally active
891    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
892      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
893         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
894         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
895    o tools/genmake2:
896      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
897      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
898      - clean previous genmake log files before anything else.
899      - change Makefile to remove testreport log files (*.tr_log) and genmake log
900        files only with "CLEAN" target (instead of "Clean");
901    o pkg/generic_advdiff:
902      Change OBCS in multiDim advection (gad_advection.F):
903       Use maskInC to prevent intermediate update of tracer-field in OB regions,
904       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
905       which were applying future time-step OB values.
906      This way, all explicit calculations use current-time-step OB values
907       (simpler and more consistent).
908      Affects results when set-up uses time-varying OBC and multi-dim advection;
909       update output of experiment seaice_obcs.
910    o pkg/seaice:
911      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
912       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
913         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
914      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
915       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
916       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
917    o pkg aim (2010/10/26):
918      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
919        formulation with obliquity, eccentricity, ... as run-time parameters,
920      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
921        upward shortwave radition at the surface (all-sky and clear-sky).
922  o pkg/obcs:  o pkg/obcs:
923    - writing sections with globalFiles=T does not work: switch to tiled-files    - writing sections with globalFiles=T does not work: switch to tiled-files
924      when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).      when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
# Line 420  o tools/build_options: Line 1335  o tools/build_options:
1335      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1336  o pkg/ecco  o pkg/ecco
1337    - allow user defined cost function contributions    - allow user defined cost function contributions
1338          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1339          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1340    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1341        the two options are complementary.        the two options are complementary.
1342  o pkg/smooth  o pkg/smooth
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