/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1321 by dimitri, Wed Oct 27 05:48:33 2010 UTC revision 1.1498 by jmc, Mon Aug 29 19:46:22 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/ebm:
8      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
9      - add multi-threaded test for verification exp. global_ocean_ebm
10    
11    checkpoint63b (2011/08/29)
12    o pkg/ebm:
13      - fix sign of runoff;
14      - update directly forcing fields (Qnet,EmPmR) to use standard
15        external_forcing_surf.F (remove ebm_forcing_surf.F);
16      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
17      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
18        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
19      - update global_ocean_ebm parameters file data and update output (fwd+ad).
20    o verification/matrix_example:
21      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
22        MPI and mutlti-threaded testing.
23    o pkg/matrix:
24      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
25      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
26      - fix for multi-threaded (remove DATA statement);
27      - use standard DIFFERENT_MULTIPLE function;
28      - add MATRIX_OPTIONS.h
29    o verification/matrix_example:
30       To allow to split the domain in several tiles, change the domain size
31        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
32        Western side) of land points.
33    o (*_)write_pickup:
34      - fix few bugs in mypackage_read/write_pickup.F
35      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
36        array of length 1 (was caught by compiler syntax-check).
37    o pkg/diagnostics (velocity potential solver):
38      - fix initialisation of main diagonal matrix (for overlap values)
39    o tools/build_options:
40      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
41        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
42      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
43        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
44        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
45        and use "-devel" testreport option for standard testing on baudelaire.
46    o pkg/grdchk:
47      - Assume that all gradient-check position are within the same tile
48        corresponding to global indices (iGloTile,jGloTile) and that
49        positions (i,j indices or nbeg) are local to this tile;
50      - set tile local-indices and proc. number according to tile global-indices;
51      - remove grdchkwhichproc from namelist (retired param);
52      - send adjoint gradient to all procs so that all procs print it to STDOUT;
53      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
54    o adding package bbl (Bottom Boundary Layer)
55      description in MITgcm/pkg/bbl/bbl_description.tex
56      example/test experiment in MITgcm_contrib/bbl
57    o adjoint verifications
58      - changed 5 experiments to multi-tiles
59        * global_ocean.90x40x15
60        * obcs_ctrl
61        * offline_exf_seaice
62        * tutorial_dic_adjoffline
63        * tutorial_tracer_adjsens
64        changed reference output for those that crossed tile boundaries
65        (changed choices of gradient check positions)
66      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
67      - temporary bug fix in grdchk_loc.F for obcs
68    o genmake2 & testreport
69      - add target "obj" (just for OBJFILES files) to Makefile;
70      - add option to specify FEXTRAFLAGS on command line.
71    o pkg/mypackage:
72      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
73    
74    checkpoint63a (2011/08/02)
75    o pkg/diagnostics (velocity potential):
76      - fix velocity-potential calculation when using OBCS: balance net inflow
77        at each level (new S/R OBCS_DIAG_BALANCE).
78      - fix some of the problems with OBCS in stream-function calculation.
79    o pkg/exf/exf_readparms.F
80      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
81        EXF_NML_OBCS) more consistent, so that you need not have these lists
82        in data.exf when they are not used.
83    o optim/optim_readdata.F:
84      - add some output about obcs variables that might help debugging
85      - add a check about nvarlength
86    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
87    o pkg/diagnostics (velocity potential):
88      - fix mask for OBCS (still problems in stream-function with OBCS);
89      - add specific parameter (default = main code CG2D params) for solver;
90      - in case of poor convergence, use solution corresponding to lowest residual.
91    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
92      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
93      and should be avoided where possible.
94    o model/src (rStar):
95      - include r* effect on reference-state (PhiRef) in totPhiHyd
96        (so that it's really the potential anomaly at the cell center);
97        affect solution only if z* with full pressure in EOS.
98      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
99        update output (because of z* in totPhiHyd and viscA4 changes);
100      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
101        @ constant r) until interpolation at constant r is implemented.
102    o pkg/diagnostics
103      - fix RCENTER diagnostics in case cell center is not at interface middle
104    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
105      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
106      that THETA and SALT are "conservative temperature" and "absolute
107      salinity"
108    o pkg/ctrl
109      - fix computation of endrec in s/r ctrl_init_rec
110      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
111    o pkg/seaice/seaice_growth.F
112      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
113        remove then obsolete STORE directives
114      - fix STORE directives for tice and tices, so that only the
115        appropriate part of the fields are stored (and not the entire
116        field); update global_ocean.cs32x15.seaice AD output.
117      - cosmetic changes: adjust CPP flags and indentation for better
118        legibilty
119    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
120      Chris Wilson)
121    o pkg/gmredi:
122       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
123       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
124    
125    checkpoint63  (2011/07/11)
126    o pkg/exch2:
127     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
128     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
129       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
130       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
131    o pkg/diagnostics:
132     - deal with pairs of post-processed diags which are computed together; in
133       particular, re-order list of diags within 1 file to save 2nd computation.
134     - add S/R to compute velocity stream-function (called after velocity-potential
135       calculation) from divergence free transport -> new diagnostics "PsiVEL".
136     - add parameter to select grid-point location where PsiVEL == 0.
137    o eesupp/src:
138       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
139       (specific S/R needed with exch2 topology - for now, just print an error msg)
140    o pkg/shelfice
141     - Implement friction velocity-dependent transfer coefficients following
142       Holland and Jenkins, JPO, 1999
143       Original code by M. Losch with small modifs.
144       Enable with CPP option SHI_ALLOW_GAMMAFRICT
145       and runtime flag SHELFICEuseGammaFrict
146    o verification lab_sea & global_ocean.cs32x15:
147     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
148       does not miss some dependencies (but is slower) and also works with many files
149       (default makedepend limitation for AD built).
150     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
151    o pkg/diagnostics:
152     - add run-time parameter "useMissingValue" (def=False) to fill land-point
153        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
154       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
155     - Extend the use of "missing_value" setting from data.diagnostics for the case
156       of counter-diagnostics (where fraction-weight is zero). This applies both to
157       MNC and MDS output files.
158    o pkg/seaice/seaice_growth.F:
159      - add 'a priori' cap of latent heat flux based on actual mass considerations
160        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
161        non-legacy seaice_solve4temp.
162      - add diagnostic of the residual sublimation freshwater flux (the freshwater
163        flux taken from the ocean if the total actual latent heat fluxes exceed
164        the maximum)
165      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
166       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
167      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
168       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
169      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
170      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
171    o verification 1D_ocean_ice_column:
172       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
173       update results
174    o pkg/diagnostics:
175     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
176       which are not filled-up but computed from other diags ; In this case, the mate
177       diag points to the primary (filled-up) diag to used for post processing.
178     - Update Velocity-potential computation using post-processed diag framework.
179     ==> Change the ordering of fields and time-periods in MDS output file
180       when using periodic averaging: now writes one time record with the full set
181       of fields for this time period, then the next time reccord (it used to be
182       one field with the full set of time records then the next field).
183         Note: this is now similar to NetCDF (MNC) output file. <==
184    
185    checkpoint62z (2011/06/21)
186    o adjoint monitor:
187     - Add adjoint monitor output for packages exf, seaice
188       and update relevant testreport output
189    o pkg/seaice:
190     - re-order diags inits so that they appear in order in available_diagnostics.log
191     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
192       area/heff/hsnow preceeding thermodynamic growth/melt.
193     - modified diag: SIdA; output actual effect, as the description states.
194     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
195     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
196       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
197        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
198     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
199     - added diagnostics for seaice generic tracers (SItr*).
200     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
201     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
202     I. Fenty: 18-Jun-2011:
203     Minor changes to seaice package:
204     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
205        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
206       - Differentiated "regularization variables" from "floor variables"
207        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
208        * hiceMin became SEAICE_hice_reg (old hiceMin)
209          (with _reg meaning regularization variable)
210       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
211        so as to ensure energy conservation when going between phases
212      - A22 was not used anywhere
213     2) Changed regularization procedure for heffActual and hsnowActual to ensure
214        well-boundedness and smooth adjoint in seaice_growth.F
215     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
216        because the old regularization always set heffActual >= 0.05 cm
217     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
218        on AREA when HEFF > 0.
219      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
220        requiring that DISABLE_AREA_FLOOR *not* be defined
221     Affected verifications:
222      - 1D_ocean_ice_column (output.txt output_adm.txt)
223      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
224    o pkg/diagnostics:
225      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
226      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
227        (was _RL, now integer) with option = 0 to retrieve all levels.
228      - add pieces of code to compute velocity potential at each level (new diagnostics
229        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
230        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
231      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
232        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
233        and in diagnostics_fract_fill.F (do not need a valid pointer for the
234        diagnostics counter-mate); check that definition of counter-diagnostic
235        includes a valid counter-mate (in diagnostics_set_levels.F).
236    o model/src (rStar):
237      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
238        affect solution only if z* with full pressure in EOS;
239        update output of test-exp global_ocean.90x40x15.
240    o pkg/seaice:
241      - introduce siEps=1e-5 parameter
242      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
243      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
244      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
245        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
246        as well as ice cover age and ridging index (attached to AREA).
247        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
248        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
249        Up to SItrMaxNum=3 tracers can be used simultaneously.
250    o pkg/salt_plume:
251      -introduce SPsalFRAC run time parameter that sets the fraction of the
252       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
253       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
254    o model debug options:
255      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
256        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
257      - Refine debug-msg printing selection (3 new levels):
258        debugMode  : controls printing of debug messages (sequence of S/R calls).
259        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
260         debLevZero =  0 ; /* level of disabled aux. msg printing */
261         debLevA =  1 ; /* level of minimum  aux. msg printing */
262         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
263         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
264         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
265         debLevE =  5 ; /* level of extensive debug printing */
266        New debugLevel default: with default debugMode value (=F),
267          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
268          and if debugMode=T, default debugLevel = 4 (debLevD).
269        Relation with previous settings:
270         debLevB (=2) corresponds to former debLevA (=1)
271         debLevD (=4) corresponds to former debLevB (=2)
272        Note:
273         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
274         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
275            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
276      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
277        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
278    o pkg/obcs:
279      - change OBCSfixTopo default from True to False (should not change the results);
280        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
281    o pkg/thsice:
282      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
283        2nd layer seaice sublimation (unlikely to happen)
284      - use Interior mask for OBCS in thsice_advection.F (similar to what is
285        done in gad_advection & seaice_advection).
286    o adjoint:
287      bug fix spotted by Gael Forget:
288      seaice_advection and thsice_advection still had
289      legacy CPP options to avoid CS corner updates for adjoint
290    o pkg/seaice:
291      => Change some of the defaults (2011/05/29):
292         - change SEAICEuseFluxForm default (from False to True)
293         - change DIFF1 default (from 0.004 m/s to 0. m/s)
294         And print warnings if DIFF1 is not set in data.seaice and centered
295          avection scheme is used without any diffusion.
296      also:
297      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
298      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
299      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
300        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
301        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
302      update results of test exp.:
303         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
304             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
305             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
306         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
307         seaice_obcs: output (SEAICEuseFluxForm=T)
308      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
309          for standard fwd & AD lab_sea tests (to keep the same output).
310    o pkg/seaice/seaice_growth.F:
311      - use Ian Fenty's capping formulas for actual ice
312      thickness thoughout EVOLUTION branch.
313      - put treatment pathological case #2) in CPP brackets
314      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
315      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
316    o pkg/seaice:
317      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
318      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
319      also pass fac as a param, which can be 1. (to update the tendency
320      field) or the time step (to update the field itself).
321      - seaice_advdiff.F: for multidim, call seaice_diffusion with
322      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
323      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
324      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
325      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
326    o pkg/seaice:
327      diffusion with centered advection scheme (diffus.F & advect.F):
328      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
329        to just compute the laplacian of input-field.
330      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
331      - fix flux-form version in diffus.F to conserve tracer.
332      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
333       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
334    
335    checkpoint62y (2011/05/26)
336    o pkg/seaice:
337     - seaice_growth.F : in EVOLUTION branch, always include
338       a_QSWbyATM_cover in qnet (as it should be).
339     - verification/global_ocean.cs32x15 : update results accordingly
340       (output.seaice.txt output_adm.seaice.txt).
341    o pkg/seaice + obcs:
342     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
343       equivalent of assuming no tracer gradient outside the OB region.
344       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
345     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
346       after changes above);
347     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
348       only at OB location (instead of over a band of OLx width).
349    o pkg/seaice:
350     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
351       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
352    o pkg/obcs:
353      - split header file "OBCS.h" into 4 separated files:
354        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
355       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
356         (contain no conditional statement which depends on OBCS options).
357      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
358        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
359    o ctrl, cost, grdchk & autodiff pkgs:
360      - make options file more standard (like other {PKG}_OPTIONS.h file but
361        with AD_CONFIG.h); clean-up some of the included header files.
362    o pkg/obcs:
363      - do not mask tracer when applying OB (tracer == 0 could generate problems)
364      - apply tracer OB values to tracer field only at OB location (instead of
365        over a band of OLx width)
366      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
367      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
368        obcs_apply_tloc.F & obcs_apply_sloc.F
369    o obcs in model/src:
370      - call OBCS_APPLY_W only if NonHydrostatic.
371      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
372      - reset dEtaHdt and wVel to zero outside OB interior region ;
373      - leave tracer unchanged outside OB interior region: This has no effect
374        on the solution but just to prevent unrealistic tracer value outside OB.
375      - zero out velocity outside OB interior region: This has no effect on
376        the solution but just to prevent unrealistic velocity outside OB.
377    o obcs and non-lin free-surf:
378       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
379       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
380       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
381       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
382       update results of test-exp. exp4(nlfs).
383    o exp4 (nlfs) test-exp:
384       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
385       with NonLin-FreeSurf); update output.nlfs.txt
386    o obcs and 2d/3d solver norm:
387       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
388       and outside OB interior region (will allow to place OB further inside the
389       domain). Depending on the domain, can affects cg2d-Norm (previous
390       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
391       and cg3d-Norm (previous Norm was computed before canceling OB terms),
392       e.g. in tutorial_plume_on_slope.
393      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
394    o pkg rbcs:
395      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
396      - add capability to apply relaxation to horizontal velocity uVel & vVel.
397    o pkg/grdchk: add gradient check for control variable xx_shifwflx
398    o pkg/shelfice/shelfice_init_fixed.F
399      fix CPP-flag combinations
400    o pkg/seaice: Merge iceage code of Pierre Rampal
401      * update/change/correct ice age calculations
402      * add age updates for pathological cases
403      Probably needs more testing...
404    
405    checkpoint62x (2011/05/13)
406    o pkg/mom_vecinv:
407       high-order vorticity scheme: use interior masks (maskInW & S)
408       to zero-out (outside OB) gradient of vorticity.
409    o verification exp.:
410       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
411       hs94.128x64x5 and seaice_obcs ; update results.
412    o pkg/obcs:
413      fix bug in OBeta for YZ sections in obcs_exf_load.F
414    o pkg/ctrl, pkg/shelfice, and optim:
415      - add new control variable xx_shifwflx (fresh water flux underneath ice
416        shelves). This is almost as tedious as obcs-ctrl, because the
417        variables needs its own mask.
418      - add a cost function term that penalizes the deviation of xx_shifwflx
419        from the first guess (zero) in analogy to other control variables
420    o pkg/shelfice:
421      - start basic adjoint
422    o pkg/ctrl:
423      - remove extra 2D field "for good measure" when initializing in
424        ctrl_set_globfld_[xy/xz/yz].F
425      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
426      - improve error messages in ctrl_set_unpack_*
427    o OBC implementation in momentum:
428       use interior masks (maskInC,W & S) in momentum S/R:
429       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
430       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
431       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
432       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
433       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
434        (and also with Leith/Smagorinsky harmonic-viscosity).
435       Update output of experiment dome and exp4 (+nlfs).
436    o exp4 test-exp:
437      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
438        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
439        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
440        time-varying OB at Western-side for wVel (NonHyd); update output.
441      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
442        and biharmonic-viscosity ; also use prescribed time varying OB.
443    o pkg/obcs:
444      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
445    o model/src:
446      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
447      - initialise startTime & nIter0 with unlikely values: allows to set one
448        from the other without ambiguity.
449    o seaice_obcs test-exp.:
450      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
451    o pkg/obcs:
452      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
453        no longer needed with maskInC,W,S in pkg/generic_advdiff.
454    o pkg/seaice:
455      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
456        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
457      - fixed bug in the initialization of sea ice salinity variable HSALT
458        in seaice_init_varia.F  (removed dependence on ICE2WATR)
459    o fizhi-cs test exp.:
460       switch reference output convention for these 2 non-standard test-exp,
461        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
462          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
463       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
464    o model/inc:
465      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
466        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
467    o pkg/seaice:
468      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
469    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
470      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
471        and initial HSALT
472    
473    checkpoint62w (2011/04/26)
474    o pkg/mom_fluxform:
475      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
476      - use parameter "sideDragFactor" in no-slip BC side-drag part.
477      - update output of exp. global_ocean.90x40x15
478    o pkg/mom_vecinv:
479      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
480    o update seaice exp.:
481      use more consistent parameter values (remove "backward compatability only":
482       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
483      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
484       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
485    o update test-exp global_ocean.90x40x15:
486      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
487      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
488      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
489      o turn on zStar & viscA4 in standard set-up (dir input/)
490        and update output files: output.txt & output.dwnslp.txt
491    o new AD-test experiment: obcs_ctrl
492      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
493    o pkg/dic:
494      fix two bugs in handling water vapour pressure in carbonate chemistry
495      and air-sea fluxes. Found by Val Bennington and Galen McKinley
496      (add DIC Option = WATERVAP_BUG to recover old results)
497      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
498    o adding allowInteriorFreezing option to check for water below freezing point
499      at depth and bring the negative heat anomaly to the surface level
500    o pkgs _fields_load:
501      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
502      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
503        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
504        rbcs to get interpolation weights and time reccord number.
505      - fix multi-threading in aim_fields_load.F
506      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
507    o external_fields_load:
508      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
509       interpolation weights) to use in a periodic time-series ; do not divide by
510       time-step to convert to integer:
511       - this fixes case where externForcingPeriod is not multiple of time-step
512          (Thanks to Christopher L. Wolfe)
513       - this fixes case where externForcingPeriod is an odd multiple of time-step
514         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
515      store index of time-record which is currently loaded:
516       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
517       - needed for the adjoint but not yet used because of extensive recomputations;
518         (to be fixed soon)
519    
520    checkpoint62v (2011/04/02)
521    o verification/1D_ocean_ice_column added to test Ian Fenty's
522      pkg/seaice_growth.F modifications for improving sea ice code differentiability
523    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
524      (new velocity statistics after changing maskInW & maskInS definition)
525    o pkg/generic_advdiff with OBCS:
526      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
527      equivalent to assumption of no tracer gradient outside the OB region.
528      This will affect the results if using obcs+biharmonic diffusion.
529      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
530    o pkg/obcs:
531      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
532      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
533      in Interior region. No impact on solution but affects Velocity monitor stats.
534    o pkg/ptracers (adjoint)
535      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
536      tape file for each tracer
537    o model/inc/src and pkg/autodiff: add parameters that allow to turn
538      of parts of the adjoint code at run time. For now, there are only
539      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
540      parameters are set in data.pkg.
541      This is the lazy coward's version of doing this, but still useful for
542      debugging. In order to do it right, everything needs to be moved to
543      pkg/autodiff.
544    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
545      the end; this fixes the adjoint balancing code for open boundaries.
546    o pkg/ctrl:
547      - change behavior of xx_${varname}period to be analogous to exf-conventions:
548        xx_${varname}period =   0.,  means time-independent control part
549        xx_${varname}period = -12., means one-year-periodic monthly control part
550      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
551        clean up ctrl_init a little, remove unused variables
552      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
553      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
554    
555    checkpoint62u (2011/03/15)
556    o model/src:
557      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
558        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
559      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
560        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
561    o pkg/ctrl/obcs/ecco:
562      - remove obsolete, unused, and partially broken code:
563        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
564        ALLOW_CTRL_OBCS_BALANCE
565      - put a stop statement into ecco/cost_obcsvol.F, but also add
566        cost_obcsvol to ecco_ad_diff.list
567    o pkg/ecco: fix counting cost function contributions for obcs (code
568      by Matt M.) and diffkr for diagnostics
569    o pkg/ecco, pkg/ctrl, pkg/grdchk:
570      add cost penalty terms for initial uvel, vvel, eta controls
571      and I/O for prior error files
572    o pkg/mdsio:
573       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
574       (new argument) to check for tiled file in mdsioLocalDir : this fix the
575       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
576    o pkg/ctrl:
577     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
578       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
579       unused and superfluous variables
580     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
581    o pkg/ecco
582     - enable adjoint of Stevens OB
583    o pkg/ctrl/ecco/grdchk:
584      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
585        Fortunately, we do not have any tests for the numerous cpp-flagged
586        option of "obcs as control parameters" so we will never know
587        if this is an improvement (but at least now things compile).
588      - remove an obsolete initialization from ecco_cost_init_barfiles.F
589      - fix some problems within never used ifdefs to make the code compile
590    o pkg/obcs:
591     - Refine Interior mask definition to work with more complex OB (e.g.
592       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
593       read in Interior mask from file. Check if Interior mask is consistent
594       with OB list of indices.
595    o pkg/seaice
596     - beginning code for a seaice tracer package,
597       but currently only used for seaice age: SEAICE_AGE
598       SEAICE_num = 4
599       iTracer = 1: area-weighted ice age
600               = 2: volume-weighted ice age
601               = 3, 4: template for one-year vs. multi-year ice
602       data.seaice has new namelist SEAICE_PARM03 for arrays related to
603       SEAICE_num
604    
605    checkpoint62t (2011/03/05)
606    o pkg/obcs:
607     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
608       then normal component. This ensures that the normal component is set
609       correctly even when it conficts with tangential setting from an other OB.
610       Affects results of test-experiment seaice_obcs: update the output.txt
611    o pkg/obcs:
612     - add code to monitor statistics of dynamical fields at OB.
613     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
614       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
615       - change default: balance the Net inflow through all OB (instead of balancing
616         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
617     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
618       to match Nortern OB inflow (OBCS_balanceFacN=0).
619    o pkg/seaice:
620     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
621    o pkg/seaice (seaice_growth v 1.113):
622     - reverting seaice_growth to v 1.111 in order to have code with exact bit
623       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
624       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
625       runtime flag SEAICEareaFormula is kept but is inactive
626    o model/src:
627     - add new param to scale curvilinear grid distance and area when using
628       a different sphere radius from the grid-files.
629     - test/check multi-threads EXCH applied to local variable (cg2d_x)
630    o adjoint:
631     - enable adjoint of Stevens OB
632     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
633       (a bit delicate because of potentially modified adj. common block structure;
634       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
635    
636    checkpoint62s (2011/02/15)
637    o pkg/seaice (seaice_growth v 1.112):
638     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
639       computing the ice cover tendency from effective thickness tendencies. Include
640       Ian Fenty's formula.
641     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
642       SEAICEareaFormula.
643     - simplify notations for the various d_HEFF/d_AREA terms.
644    o pkg/gmredi:
645     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
646       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
647       add a verification test-run (front_relax.bvp) to test GM_useBVP.
648    o pkg/seaice (seaice_growth v 1.111):
649     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
650     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
651       also melt ice.
652    o pkg/seaice:
653     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
654     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
655    o pkg/cheapaml:
656     - from Nico Wienders: New version of this package.
657    o pkg/flt:
658     - add CPP options to prevent floats to re-enter the opposite side of
659       a periodic domain (default: keep periodicity)
660    o pkg/gmredi:
661     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
662       (needed for multi-dim advection).
663     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
664    o model/src:
665     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
666    o tutorial_tracer_adjsens
667     - extend to NLFS and replace maskC by hFacC
668       (change reference output accordingly)
669    
670    checkpoint62r (2011/01/24)
671    o testreport:
672     - add option -deloutp (-do) to remove output file after successful run
673     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
674       extract exact list of procs from this file ; adjust COMMAND by
675       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
676    o pkg/ecco: replace old ineffective way of penalizing deviations from
677      first guess (of obcs) with code by Matt Mazloff
678    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
679      exf/cal
680      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
681        and handle case of obcs?period == 0
682        Not affected by these changes: There is still an inconsistency in
683        the computation of start/endrec for the obcs variables for ALLOW_CAL
684        defined (see comment by Menemenlis, 7-Mar-2003)
685      - make S/R ctrl_get_gen_rec return something meaningful even if
686        ALLOW_CAL is not defined
687      - ctrl_getobcs?: simplify code so that it does not need to use
688                       S/R exf_swapfields
689    o testreport:
690       allow to test MPI with different number of processors for each experiment:
691       create file "SIZE.h.mpi" in each build dir.
692       Note: update of "-command" argument not yet implemented.
693    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
694      alleviate the need for additional 3D tapes when using
695      the non-inear free surface in the adjoint. This is done
696      by adding an 'update' of hfacc etc. to their current
697      value at the beginning of forward_step.F.
698    o pkg/seaice
699      seaice_lsr: move stress-divergence computations out of outer pseudo-
700      timestepping loop
701    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
702      up, so that the calls of the ctrl_* subroutines are really at the end
703      of the routine.
704    o pkg/gmredi:
705      allow to specify a 2-D horizontal map and a 1-D vertical profil
706      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
707    o pkg/seaice:
708      move lsr iterations from seaice_dynsolver to seaice_lsr.
709    o pkg/seaice:
710      reduce memory footprint of seaice mutldim advection tapes,
711      by using a 2D tape independent of the generic_advdiff ones,
712      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
713    
714    checkpoint62q (2010/12/29)
715    o model/src:
716      - check horizontal grid-spacing for unset or zero/negative values.
717      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
718    o pkg/flt:
719      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
720      - precision of input and output files set according to readBinaryPrec
721        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
722      - initial float position from tiled file was not converted to index space
723        (looks like a bug): fixed to make it similar to initial pos. global file.
724    o global_ocean.cs32x15:
725       change SIZE.h of AD set-up to get same tiling as with MPI.
726       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
727    o model/src:
728       add flag to control printing of domain fields (bathymetry, hFac ...) in
729       ini_mask_etc (call to plot_fieds_xy*).
730    o pkg/thsice:
731       if useEXF, some forcing fields are not valid in overlap: fixed by computing
732       over the interior only + apply EXCH at the end (like with SEAICE advection).
733    o pkg/mdsio:
734      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
735        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
736      - change barrier call for safe multi-threads access to 3-D shared buffer.
737      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
738      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
739        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
740    o pkg/flt:
741      - add fourth-order Runge-Kutta integration
742      - add basic exch2 support (only 1 facet supported so far!)
743    o pkg/mdsio+rw:
744      new S/R to read local (or tile independent) vector (read counterpart of
745       mds_writevec_loc, and front-end write_glvec_rl/rs).
746    o global_ocean.cs32x15: additional input_ad.seaice experiment
747        that uses pkg/seaice rather than pkg/thsice.
748        (using multidim advection for seaice)
749    o towards more F95 syntax for array specification in namelist:
750      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
751        of all verification experiments.
752           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
753          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
754      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
755    o global_ocean.cs32x15: additional input.seaice experiment
756        that uses pkg/seaice rather than pkg/thsice.
757    
758    checkpoint62p (2010/12/17)
759    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
760        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
761    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
762        allow for use of multim. advection in seaice adjoint.
763    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
764      - first attempt to close budgets by taking into account the freshwater
765        flux implied by the sublimation of snow and ice. So far only the
766        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
767        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
768    o eesupp/src:
769      new S/R with new option (NML_EXTENDED_F77) to change array specification
770      from F95 standard to commonly accepted extended F77 form.
771      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
772      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
773      for less tolerant f77 compiler (e.g., pgf77, g77).
774    o globalFiles:
775      commented out in parameter file "data" since it's not safe with MPI
776      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
777      in this case); no longer commented out in restart test (tst_2+2).
778    o add adTapeDir to specify a special directory where adjoint tapes are
779      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
780      and cannot be used together with mdsioLocalDir.
781    o nesting pkgs:
782      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
783      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
784      - add parameter files + utils dir + output from short run on beagle.
785    o pkg/seaice:
786        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
787    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
788      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
789    
790    checkpoint62o (2010/11/25)
791    o pkg/exf:
792      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
793    o pkg/seaice:
794      - seaice_ocean_stress: split a loop for better vectorization of the
795        adjoint code
796      - seaice_growth.F: fix bug in conservation of freshwater connected to
797        capping of heff, put contribution into d_HEFFbyNEG
798      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
799        by something more sensible (parameters that are what their name implies)
800      - change some defaults, so that by default exf-parameters are used for
801        things like rhoAir, cpAir,latent/sensible heat parameters, in order
802        to reproduce the old results, many data.seaice now contain funny values
803        for cpAir and latent heat of sublimation
804    o packages_readparms.F: move exf_readparms up in line so that
805        exf-parameters are visible for other packages (e.g. seaice)
806    o debugMode & debugLevel=2:
807      - differentiate between debugMode & debugLevel=2:
808        debugMode: controls printing of debug messages (sequence of S/R calls).
809        debugLevel: controls printing of algorithm intermediate results and stats.
810      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
811        => allows to print debug-stats without all sequence of call messages.
812      - switch control of debug print from debugLevel to debugMode in many S/R.
813    o pkg/obcs (obcs-sponge):
814        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
815        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
816    o pkg/generic_advdiff:
817      - record overlap minimum size for each advection scheme;
818      - refine criteria on overlap minimum size;
819      - check and stop (in gad_check) if overlap size is too small.
820    o pkg/obcs:
821      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
822        once, in ptracers_implicit.F)
823      - with seaice: remove test on empty file name in obcs_apply_seaice (always
824        apply OB values when tile has OB)
825    o model/src, coriolis setting:
826      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
827        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
828        files (selectCoriMap=3) with any grid.
829      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
830    o pkg/seaice/seaice_growth.F:
831        a few cosmetic changes that reduce the number of lines of code
832    o pkg/obcs: add boundary conditions following Stevens (1990)
833      - the code follows old MOM/NAOSIM code
834      - so far it is only implemented for the eastern and western boundaries
835        and NOT for pTracers
836    o pkg/rbcs:
837      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
838        beginning of the first rbcs forcing period.
839      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
840        offline package, i.e., one file per time, labeled by iteration number;
841        deltaTrbcs sets the timestep with which the data was generated;
842        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
843      - rbcsForcingCycle=0 makes forcing non-cyclic.
844      - make arithmetic safe for negative times and odd forcing periods.
845    
846    checkpoint62n (2010/11/09)
847    o pkg/seaice:
848        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
849    o pkg/obcs:
850       New S/R to copy tracer value from the OB location to narrow band region
851        (width = same as overlap) beyond the OB: preserve OB value (needed for
852        high-order scheme) which were overwritten by EXCH call if in overlap
853        region. Applied to theta, salt, ptracer and advected seaice variables.
854       With seaice: use maskInC in similar way as in gad_advection.F,
855        in seaice_advection.F and advect.F.
856       Update output of experiment seaice_obcs and change exp4 to test OBCS with
857        4th order Adv.Scheme. for pasive salt and ptracer.
858    o tools/genmake2:
859      - when looking for an optfile (not specified), only search for Fortran compiler
860        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
861      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
862        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
863      - set default for CPP to "cpp -traditional -P" (was the case without specifying
864        an optfile, but otherwise default was just "cpp".
865      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
866      - when "CC" is not set in the optfile, look for possible C compiler
867        (instead of just setting CC=cc)
868      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
869        => add a ".F" to ".o" rule for source files with no "#include" (such as
870           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
871      - move gfortran before g77 in list of possible Fortran compiler (consistent
872        with reference compiler switch from g77 to gfortran)
873    o pkg/seaice:
874      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
875        seaice_check that stops the model, when the CPP flag is used.
876      o seaice_growth.F: make capping of ice volume conserving by returning the
877        capped ice as freshwater to EmPmR. This does not change the verification
878        experiments but will change runs where the capping is acutally active
879    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
880      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
881         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
882         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
883    o tools/genmake2:
884      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
885      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
886      - clean previous genmake log files before anything else.
887      - change Makefile to remove testreport log files (*.tr_log) and genmake log
888        files only with "CLEAN" target (instead of "Clean");
889    o pkg/generic_advdiff:
890      Change OBCS in multiDim advection (gad_advection.F):
891       Use maskInC to prevent intermediate update of tracer-field in OB regions,
892       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
893       which were applying future time-step OB values.
894      This way, all explicit calculations use current-time-step OB values
895       (simpler and more consistent).
896      Affects results when set-up uses time-varying OBC and multi-dim advection;
897       update output of experiment seaice_obcs.
898    o pkg/seaice:
899      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
900       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
901         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
902      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
903       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
904       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
905    o pkg aim (2010/10/26):
906      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
907        formulation with obliquity, eccentricity, ... as run-time parameters,
908      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
909        upward shortwave radition at the surface (all-sky and clear-sky).
910  o pkg/obcs:  o pkg/obcs:
911    - writing sections with globalFiles=T does not work: switch to tiled-files    - writing sections with globalFiles=T does not work: switch to tiled-files
912      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 1323  o tools/build_options:
1323      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1324  o pkg/ecco  o pkg/ecco
1325    - allow user defined cost function contributions    - allow user defined cost function contributions
1326          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1327          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1328    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1329        the two options are complementary.        the two options are complementary.
1330  o pkg/smooth  o pkg/smooth
Legend:
Removed from v.1.1321  
changed lines
  Added in v.1.1498
  ViewVC Help
Powered by ViewVC 1.1.22