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revision 1.1268 by mlosch, Fri May 14 11:35:35 2010 UTC revision 1.1493 by jmc, Wed Aug 24 02:51:20 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/diagnostics (velocity potential solver):
8      - fix initialisation of main diagonal matrix (for overlap values)
9    o tools/build_options:
10      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
11        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
12      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
13        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
14        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
15        and use "-devel" testreport option for standard testing on baudelaire.
16    o pkg/grdchk:
17      - Assume that all gradient-check position are within the same tile
18        corresponding to global indices (iGloTile,jGloTile) and that
19        positions (i,j indices or nbeg) are local to this tile;
20      - set tile local-indices and proc. number according to tile global-indices;
21      - remove grdchkwhichproc from namelist (retired param);
22      - send adjoint gradient to all procs so that all procs print it to STDOUT;
23      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
24    o adding package bbl (Bottom Boundary Layer)
25      description in MITgcm/pkg/bbl/bbl_description.tex
26      example/test experiment in MITgcm_contrib/bbl
27    o adjoint verifications
28      - changed 5 experiments to multi-tiles
29        * global_ocean.90x40x15
30        * obcs_ctrl
31        * offline_exf_seaice
32        * tutorial_dic_adjoffline
33        * tutorial_tracer_adjsens
34        changed reference output for those that crossed tile boundaries
35        (changed choices of gradient check positions)
36      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
37      - temporary bug fix in grdchk_loc.F for obcs
38    o genmake2 & testreport
39      - add target "obj" (just for OBJFILES files) to Makefile;
40      - add option to specify FEXTRAFLAGS on command line.
41    o pkg/mypackage:
42      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
43    
44    checkpoint63a (2011/08/02)
45    o pkg/diagnostics (velocity potential):
46      - fix velocity-potential calculation when using OBCS: balance net inflow
47        at each level (new S/R OBCS_DIAG_BALANCE).
48      - fix some of the problems with OBCS in stream-function calculation.
49    o pkg/exf/exf_readparms.F
50      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
51        EXF_NML_OBCS) more consistent, so that you need not have these lists
52        in data.exf when they are not used.
53    o optim/optim_readdata.F:
54      - add some output about obcs variables that might help debugging
55      - add a check about nvarlength
56    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
57    o pkg/diagnostics (velocity potential):
58      - fix mask for OBCS (still problems in stream-function with OBCS);
59      - add specific parameter (default = main code CG2D params) for solver;
60      - in case of poor convergence, use solution corresponding to lowest residual.
61    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
62      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
63      and should be avoided where possible.
64    o model/src (rStar):
65      - include r* effect on reference-state (PhiRef) in totPhiHyd
66        (so that it's really the potential anomaly at the cell center);
67        affect solution only if z* with full pressure in EOS.
68      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
69        update output (because of z* in totPhiHyd and viscA4 changes);
70      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
71        @ constant r) until interpolation at constant r is implemented.
72    o pkg/diagnostics
73      - fix RCENTER diagnostics in case cell center is not at interface middle
74    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
75      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
76      that THETA and SALT are "conservative temperature" and "absolute
77      salinity"
78    o pkg/ctrl
79      - fix computation of endrec in s/r ctrl_init_rec
80      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
81    o pkg/seaice/seaice_growth.F
82      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
83        remove then obsolete STORE directives
84      - fix STORE directives for tice and tices, so that only the
85        appropriate part of the fields are stored (and not the entire
86        field); update global_ocean.cs32x15.seaice AD output.
87      - cosmetic changes: adjust CPP flags and indentation for better
88        legibilty
89    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
90      Chris Wilson)
91    o pkg/gmredi:
92       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
93       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
94    
95    checkpoint63  (2011/07/11)
96    o pkg/exch2:
97     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
98     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
99       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
100       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
101    o pkg/diagnostics:
102     - deal with pairs of post-processed diags which are computed together; in
103       particular, re-order list of diags within 1 file to save 2nd computation.
104     - add S/R to compute velocity stream-function (called after velocity-potential
105       calculation) from divergence free transport -> new diagnostics "PsiVEL".
106     - add parameter to select grid-point location where PsiVEL == 0.
107    o eesupp/src:
108       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
109       (specific S/R needed with exch2 topology - for now, just print an error msg)
110    o pkg/shelfice
111     - Implement friction velocity-dependent transfer coefficients following
112       Holland and Jenkins, JPO, 1999
113       Original code by M. Losch with small modifs.
114       Enable with CPP option SHI_ALLOW_GAMMAFRICT
115       and runtime flag SHELFICEuseGammaFrict
116    o verification lab_sea & global_ocean.cs32x15:
117     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
118       does not miss some dependencies (but is slower) and also works with many files
119       (default makedepend limitation for AD built).
120     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
121    o pkg/diagnostics:
122     - add run-time parameter "useMissingValue" (def=False) to fill land-point
123        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
124       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
125     - Extend the use of "missing_value" setting from data.diagnostics for the case
126       of counter-diagnostics (where fraction-weight is zero). This applies both to
127       MNC and MDS output files.
128    o pkg/seaice/seaice_growth.F:
129      - add 'a priori' cap of latent heat flux based on actual mass considerations
130        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
131        non-legacy seaice_solve4temp.
132      - add diagnostic of the residual sublimation freshwater flux (the freshwater
133        flux taken from the ocean if the total actual latent heat fluxes exceed
134        the maximum)
135      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
136       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
137      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
138       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
139      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
140      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
141    o verification 1D_ocean_ice_column:
142       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
143       update results
144    o pkg/diagnostics:
145     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
146       which are not filled-up but computed from other diags ; In this case, the mate
147       diag points to the primary (filled-up) diag to used for post processing.
148     - Update Velocity-potential computation using post-processed diag framework.
149     ==> Change the ordering of fields and time-periods in MDS output file
150       when using periodic averaging: now writes one time record with the full set
151       of fields for this time period, then the next time reccord (it used to be
152       one field with the full set of time records then the next field).
153         Note: this is now similar to NetCDF (MNC) output file. <==
154    
155    checkpoint62z (2011/06/21)
156    o adjoint monitor:
157     - Add adjoint monitor output for packages exf, seaice
158       and update relevant testreport output
159    o pkg/seaice:
160     - re-order diags inits so that they appear in order in available_diagnostics.log
161     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
162       area/heff/hsnow preceeding thermodynamic growth/melt.
163     - modified diag: SIdA; output actual effect, as the description states.
164     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
165     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
166       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
167        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
168     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
169     - added diagnostics for seaice generic tracers (SItr*).
170     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
171     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
172     I. Fenty: 18-Jun-2011:
173     Minor changes to seaice package:
174     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
175        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
176       - Differentiated "regularization variables" from "floor variables"
177        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
178        * hiceMin became SEAICE_hice_reg (old hiceMin)
179          (with _reg meaning regularization variable)
180       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
181        so as to ensure energy conservation when going between phases
182      - A22 was not used anywhere
183     2) Changed regularization procedure for heffActual and hsnowActual to ensure
184        well-boundedness and smooth adjoint in seaice_growth.F
185     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
186        because the old regularization always set heffActual >= 0.05 cm
187     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
188        on AREA when HEFF > 0.
189      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
190        requiring that DISABLE_AREA_FLOOR *not* be defined
191     Affected verifications:
192      - 1D_ocean_ice_column (output.txt output_adm.txt)
193      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
194    o pkg/diagnostics:
195      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
196      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
197        (was _RL, now integer) with option = 0 to retrieve all levels.
198      - add pieces of code to compute velocity potential at each level (new diagnostics
199        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
200        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
201      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
202        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
203        and in diagnostics_fract_fill.F (do not need a valid pointer for the
204        diagnostics counter-mate); check that definition of counter-diagnostic
205        includes a valid counter-mate (in diagnostics_set_levels.F).
206    o model/src (rStar):
207      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
208        affect solution only if z* with full pressure in EOS;
209        update output of test-exp global_ocean.90x40x15.
210    o pkg/seaice:
211      - introduce siEps=1e-5 parameter
212      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
213      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
214      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
215        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
216        as well as ice cover age and ridging index (attached to AREA).
217        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
218        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
219        Up to SItrMaxNum=3 tracers can be used simultaneously.
220    o pkg/salt_plume:
221      -introduce SPsalFRAC run time parameter that sets the fraction of the
222       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
223       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
224    o model debug options:
225      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
226        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
227      - Refine debug-msg printing selection (3 new levels):
228        debugMode  : controls printing of debug messages (sequence of S/R calls).
229        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
230         debLevZero =  0 ; /* level of disabled aux. msg printing */
231         debLevA =  1 ; /* level of minimum  aux. msg printing */
232         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
233         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
234         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
235         debLevE =  5 ; /* level of extensive debug printing */
236        New debugLevel default: with default debugMode value (=F),
237          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
238          and if debugMode=T, default debugLevel = 4 (debLevD).
239        Relation with previous settings:
240         debLevB (=2) corresponds to former debLevA (=1)
241         debLevD (=4) corresponds to former debLevB (=2)
242        Note:
243         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
244         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
245            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
246      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
247        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
248    o pkg/obcs:
249      - change OBCSfixTopo default from True to False (should not change the results);
250        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
251    o pkg/thsice:
252      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
253        2nd layer seaice sublimation (unlikely to happen)
254      - use Interior mask for OBCS in thsice_advection.F (similar to what is
255        done in gad_advection & seaice_advection).
256    o adjoint:
257      bug fix spotted by Gael Forget:
258      seaice_advection and thsice_advection still had
259      legacy CPP options to avoid CS corner updates for adjoint
260    o pkg/seaice:
261      => Change some of the defaults (2011/05/29):
262         - change SEAICEuseFluxForm default (from False to True)
263         - change DIFF1 default (from 0.004 m/s to 0. m/s)
264         And print warnings if DIFF1 is not set in data.seaice and centered
265          avection scheme is used without any diffusion.
266      also:
267      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
268      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
269      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
270        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
271        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
272      update results of test exp.:
273         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
274             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
275             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
276         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
277         seaice_obcs: output (SEAICEuseFluxForm=T)
278      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
279          for standard fwd & AD lab_sea tests (to keep the same output).
280    o pkg/seaice/seaice_growth.F:
281      - use Ian Fenty's capping formulas for actual ice
282      thickness thoughout EVOLUTION branch.
283      - put treatment pathological case #2) in CPP brackets
284      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
285      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
286    o pkg/seaice:
287      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
288      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
289      also pass fac as a param, which can be 1. (to update the tendency
290      field) or the time step (to update the field itself).
291      - seaice_advdiff.F: for multidim, call seaice_diffusion with
292      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
293      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
294      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
295      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
296    o pkg/seaice:
297      diffusion with centered advection scheme (diffus.F & advect.F):
298      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
299        to just compute the laplacian of input-field.
300      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
301      - fix flux-form version in diffus.F to conserve tracer.
302      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
303       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
304    
305    checkpoint62y (2011/05/26)
306    o pkg/seaice:
307     - seaice_growth.F : in EVOLUTION branch, always include
308       a_QSWbyATM_cover in qnet (as it should be).
309     - verification/global_ocean.cs32x15 : update results accordingly
310       (output.seaice.txt output_adm.seaice.txt).
311    o pkg/seaice + obcs:
312     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
313       equivalent of assuming no tracer gradient outside the OB region.
314       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
315     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
316       after changes above);
317     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
318       only at OB location (instead of over a band of OLx width).
319    o pkg/seaice:
320     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
321       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
322    o pkg/obcs:
323      - split header file "OBCS.h" into 4 separated files:
324        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
325       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
326         (contain no conditional statement which depends on OBCS options).
327      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
328        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
329    o ctrl, cost, grdchk & autodiff pkgs:
330      - make options file more standard (like other {PKG}_OPTIONS.h file but
331        with AD_CONFIG.h); clean-up some of the included header files.
332    o pkg/obcs:
333      - do not mask tracer when applying OB (tracer == 0 could generate problems)
334      - apply tracer OB values to tracer field only at OB location (instead of
335        over a band of OLx width)
336      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
337      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
338        obcs_apply_tloc.F & obcs_apply_sloc.F
339    o obcs in model/src:
340      - call OBCS_APPLY_W only if NonHydrostatic.
341      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
342      - reset dEtaHdt and wVel to zero outside OB interior region ;
343      - leave tracer unchanged outside OB interior region: This has no effect
344        on the solution but just to prevent unrealistic tracer value outside OB.
345      - zero out velocity outside OB interior region: This has no effect on
346        the solution but just to prevent unrealistic velocity outside OB.
347    o obcs and non-lin free-surf:
348       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
349       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
350       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
351       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
352       update results of test-exp. exp4(nlfs).
353    o exp4 (nlfs) test-exp:
354       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
355       with NonLin-FreeSurf); update output.nlfs.txt
356    o obcs and 2d/3d solver norm:
357       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
358       and outside OB interior region (will allow to place OB further inside the
359       domain). Depending on the domain, can affects cg2d-Norm (previous
360       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
361       and cg3d-Norm (previous Norm was computed before canceling OB terms),
362       e.g. in tutorial_plume_on_slope.
363      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
364    o pkg rbcs:
365      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
366      - add capability to apply relaxation to horizontal velocity uVel & vVel.
367    o pkg/grdchk: add gradient check for control variable xx_shifwflx
368    o pkg/shelfice/shelfice_init_fixed.F
369      fix CPP-flag combinations
370    o pkg/seaice: Merge iceage code of Pierre Rampal
371      * update/change/correct ice age calculations
372      * add age updates for pathological cases
373      Probably needs more testing...
374    
375    checkpoint62x (2011/05/13)
376    o pkg/mom_vecinv:
377       high-order vorticity scheme: use interior masks (maskInW & S)
378       to zero-out (outside OB) gradient of vorticity.
379    o verification exp.:
380       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
381       hs94.128x64x5 and seaice_obcs ; update results.
382    o pkg/obcs:
383      fix bug in OBeta for YZ sections in obcs_exf_load.F
384    o pkg/ctrl, pkg/shelfice, and optim:
385      - add new control variable xx_shifwflx (fresh water flux underneath ice
386        shelves). This is almost as tedious as obcs-ctrl, because the
387        variables needs its own mask.
388      - add a cost function term that penalizes the deviation of xx_shifwflx
389        from the first guess (zero) in analogy to other control variables
390    o pkg/shelfice:
391      - start basic adjoint
392    o pkg/ctrl:
393      - remove extra 2D field "for good measure" when initializing in
394        ctrl_set_globfld_[xy/xz/yz].F
395      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
396      - improve error messages in ctrl_set_unpack_*
397    o OBC implementation in momentum:
398       use interior masks (maskInC,W & S) in momentum S/R:
399       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
400       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
401       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
402       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
403       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
404        (and also with Leith/Smagorinsky harmonic-viscosity).
405       Update output of experiment dome and exp4 (+nlfs).
406    o exp4 test-exp:
407      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
408        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
409        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
410        time-varying OB at Western-side for wVel (NonHyd); update output.
411      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
412        and biharmonic-viscosity ; also use prescribed time varying OB.
413    o pkg/obcs:
414      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
415    o model/src:
416      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
417      - initialise startTime & nIter0 with unlikely values: allows to set one
418        from the other without ambiguity.
419    o seaice_obcs test-exp.:
420      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
421    o pkg/obcs:
422      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
423        no longer needed with maskInC,W,S in pkg/generic_advdiff.
424    o pkg/seaice:
425      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
426        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
427      - fixed bug in the initialization of sea ice salinity variable HSALT
428        in seaice_init_varia.F  (removed dependence on ICE2WATR)
429    o fizhi-cs test exp.:
430       switch reference output convention for these 2 non-standard test-exp,
431        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
432          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
433       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
434    o model/inc:
435      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
436        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
437    o pkg/seaice:
438      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
439    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
440      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
441        and initial HSALT
442    
443    checkpoint62w (2011/04/26)
444    o pkg/mom_fluxform:
445      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
446      - use parameter "sideDragFactor" in no-slip BC side-drag part.
447      - update output of exp. global_ocean.90x40x15
448    o pkg/mom_vecinv:
449      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
450    o update seaice exp.:
451      use more consistent parameter values (remove "backward compatability only":
452       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
453      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
454       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
455    o update test-exp global_ocean.90x40x15:
456      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
457      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
458      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
459      o turn on zStar & viscA4 in standard set-up (dir input/)
460        and update output files: output.txt & output.dwnslp.txt
461    o new AD-test experiment: obcs_ctrl
462      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
463    o pkg/dic:
464      fix two bugs in handling water vapour pressure in carbonate chemistry
465      and air-sea fluxes. Found by Val Bennington and Galen McKinley
466      (add DIC Option = WATERVAP_BUG to recover old results)
467      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
468    o adding allowInteriorFreezing option to check for water below freezing point
469      at depth and bring the negative heat anomaly to the surface level
470    o pkgs _fields_load:
471      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
472      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
473        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
474        rbcs to get interpolation weights and time reccord number.
475      - fix multi-threading in aim_fields_load.F
476      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
477    o external_fields_load:
478      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
479       interpolation weights) to use in a periodic time-series ; do not divide by
480       time-step to convert to integer:
481       - this fixes case where externForcingPeriod is not multiple of time-step
482          (Thanks to Christopher L. Wolfe)
483       - this fixes case where externForcingPeriod is an odd multiple of time-step
484         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
485      store index of time-record which is currently loaded:
486       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
487       - needed for the adjoint but not yet used because of extensive recomputations;
488         (to be fixed soon)
489    
490    checkpoint62v (2011/04/02)
491    o verification/1D_ocean_ice_column added to test Ian Fenty's
492      pkg/seaice_growth.F modifications for improving sea ice code differentiability
493    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
494      (new velocity statistics after changing maskInW & maskInS definition)
495    o pkg/generic_advdiff with OBCS:
496      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
497      equivalent to assumption of no tracer gradient outside the OB region.
498      This will affect the results if using obcs+biharmonic diffusion.
499      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
500    o pkg/obcs:
501      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
502      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
503      in Interior region. No impact on solution but affects Velocity monitor stats.
504    o pkg/ptracers (adjoint)
505      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
506      tape file for each tracer
507    o model/inc/src and pkg/autodiff: add parameters that allow to turn
508      of parts of the adjoint code at run time. For now, there are only
509      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
510      parameters are set in data.pkg.
511      This is the lazy coward's version of doing this, but still useful for
512      debugging. In order to do it right, everything needs to be moved to
513      pkg/autodiff.
514    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
515      the end; this fixes the adjoint balancing code for open boundaries.
516    o pkg/ctrl:
517      - change behavior of xx_${varname}period to be analogous to exf-conventions:
518        xx_${varname}period =   0.,  means time-independent control part
519        xx_${varname}period = -12., means one-year-periodic monthly control part
520      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
521        clean up ctrl_init a little, remove unused variables
522      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
523      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
524    
525    checkpoint62u (2011/03/15)
526    o model/src:
527      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
528        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
529      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
530        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
531    o pkg/ctrl/obcs/ecco:
532      - remove obsolete, unused, and partially broken code:
533        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
534        ALLOW_CTRL_OBCS_BALANCE
535      - put a stop statement into ecco/cost_obcsvol.F, but also add
536        cost_obcsvol to ecco_ad_diff.list
537    o pkg/ecco: fix counting cost function contributions for obcs (code
538      by Matt M.) and diffkr for diagnostics
539    o pkg/ecco, pkg/ctrl, pkg/grdchk:
540      add cost penalty terms for initial uvel, vvel, eta controls
541      and I/O for prior error files
542    o pkg/mdsio:
543       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
544       (new argument) to check for tiled file in mdsioLocalDir : this fix the
545       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
546    o pkg/ctrl:
547     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
548       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
549       unused and superfluous variables
550     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
551    o pkg/ecco
552     - enable adjoint of Stevens OB
553    o pkg/ctrl/ecco/grdchk:
554      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
555        Fortunately, we do not have any tests for the numerous cpp-flagged
556        option of "obcs as control parameters" so we will never know
557        if this is an improvement (but at least now things compile).
558      - remove an obsolete initialization from ecco_cost_init_barfiles.F
559      - fix some problems within never used ifdefs to make the code compile
560    o pkg/obcs:
561     - Refine Interior mask definition to work with more complex OB (e.g.
562       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
563       read in Interior mask from file. Check if Interior mask is consistent
564       with OB list of indices.
565    o pkg/seaice
566     - beginning code for a seaice tracer package,
567       but currently only used for seaice age: SEAICE_AGE
568       SEAICE_num = 4
569       iTracer = 1: area-weighted ice age
570               = 2: volume-weighted ice age
571               = 3, 4: template for one-year vs. multi-year ice
572       data.seaice has new namelist SEAICE_PARM03 for arrays related to
573       SEAICE_num
574    
575    checkpoint62t (2011/03/05)
576    o pkg/obcs:
577     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
578       then normal component. This ensures that the normal component is set
579       correctly even when it conficts with tangential setting from an other OB.
580       Affects results of test-experiment seaice_obcs: update the output.txt
581    o pkg/obcs:
582     - add code to monitor statistics of dynamical fields at OB.
583     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
584       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
585       - change default: balance the Net inflow through all OB (instead of balancing
586         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
587     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
588       to match Nortern OB inflow (OBCS_balanceFacN=0).
589    o pkg/seaice:
590     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
591    o pkg/seaice (seaice_growth v 1.113):
592     - reverting seaice_growth to v 1.111 in order to have code with exact bit
593       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
594       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
595       runtime flag SEAICEareaFormula is kept but is inactive
596    o model/src:
597     - add new param to scale curvilinear grid distance and area when using
598       a different sphere radius from the grid-files.
599     - test/check multi-threads EXCH applied to local variable (cg2d_x)
600    o adjoint:
601     - enable adjoint of Stevens OB
602     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
603       (a bit delicate because of potentially modified adj. common block structure;
604       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
605    
606    checkpoint62s (2011/02/15)
607    o pkg/seaice (seaice_growth v 1.112):
608     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
609       computing the ice cover tendency from effective thickness tendencies. Include
610       Ian Fenty's formula.
611     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
612       SEAICEareaFormula.
613     - simplify notations for the various d_HEFF/d_AREA terms.
614    o pkg/gmredi:
615     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
616       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
617       add a verification test-run (front_relax.bvp) to test GM_useBVP.
618    o pkg/seaice (seaice_growth v 1.111):
619     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
620     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
621       also melt ice.
622    o pkg/seaice:
623     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
624     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
625    o pkg/cheapaml:
626     - from Nico Wienders: New version of this package.
627    o pkg/flt:
628     - add CPP options to prevent floats to re-enter the opposite side of
629       a periodic domain (default: keep periodicity)
630    o pkg/gmredi:
631     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
632       (needed for multi-dim advection).
633     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
634    o model/src:
635     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
636    o tutorial_tracer_adjsens
637     - extend to NLFS and replace maskC by hFacC
638       (change reference output accordingly)
639    
640    checkpoint62r (2011/01/24)
641    o testreport:
642     - add option -deloutp (-do) to remove output file after successful run
643     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
644       extract exact list of procs from this file ; adjust COMMAND by
645       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
646    o pkg/ecco: replace old ineffective way of penalizing deviations from
647      first guess (of obcs) with code by Matt Mazloff
648    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
649      exf/cal
650      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
651        and handle case of obcs?period == 0
652        Not affected by these changes: There is still an inconsistency in
653        the computation of start/endrec for the obcs variables for ALLOW_CAL
654        defined (see comment by Menemenlis, 7-Mar-2003)
655      - make S/R ctrl_get_gen_rec return something meaningful even if
656        ALLOW_CAL is not defined
657      - ctrl_getobcs?: simplify code so that it does not need to use
658                       S/R exf_swapfields
659    o testreport:
660       allow to test MPI with different number of processors for each experiment:
661       create file "SIZE.h.mpi" in each build dir.
662       Note: update of "-command" argument not yet implemented.
663    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
664      alleviate the need for additional 3D tapes when using
665      the non-inear free surface in the adjoint. This is done
666      by adding an 'update' of hfacc etc. to their current
667      value at the beginning of forward_step.F.
668    o pkg/seaice
669      seaice_lsr: move stress-divergence computations out of outer pseudo-
670      timestepping loop
671    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
672      up, so that the calls of the ctrl_* subroutines are really at the end
673      of the routine.
674    o pkg/gmredi:
675      allow to specify a 2-D horizontal map and a 1-D vertical profil
676      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
677    o pkg/seaice:
678      move lsr iterations from seaice_dynsolver to seaice_lsr.
679    o pkg/seaice:
680      reduce memory footprint of seaice mutldim advection tapes,
681      by using a 2D tape independent of the generic_advdiff ones,
682      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
683    
684    checkpoint62q (2010/12/29)
685    o model/src:
686      - check horizontal grid-spacing for unset or zero/negative values.
687      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
688    o pkg/flt:
689      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
690      - precision of input and output files set according to readBinaryPrec
691        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
692      - initial float position from tiled file was not converted to index space
693        (looks like a bug): fixed to make it similar to initial pos. global file.
694    o global_ocean.cs32x15:
695       change SIZE.h of AD set-up to get same tiling as with MPI.
696       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
697    o model/src:
698       add flag to control printing of domain fields (bathymetry, hFac ...) in
699       ini_mask_etc (call to plot_fieds_xy*).
700    o pkg/thsice:
701       if useEXF, some forcing fields are not valid in overlap: fixed by computing
702       over the interior only + apply EXCH at the end (like with SEAICE advection).
703    o pkg/mdsio:
704      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
705        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
706      - change barrier call for safe multi-threads access to 3-D shared buffer.
707      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
708      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
709        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
710    o pkg/flt:
711      - add fourth-order Runge-Kutta integration
712      - add basic exch2 support (only 1 facet supported so far!)
713    o pkg/mdsio+rw:
714      new S/R to read local (or tile independent) vector (read counterpart of
715       mds_writevec_loc, and front-end write_glvec_rl/rs).
716    o global_ocean.cs32x15: additional input_ad.seaice experiment
717        that uses pkg/seaice rather than pkg/thsice.
718        (using multidim advection for seaice)
719    o towards more F95 syntax for array specification in namelist:
720      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
721        of all verification experiments.
722           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
723          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
724      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
725    o global_ocean.cs32x15: additional input.seaice experiment
726        that uses pkg/seaice rather than pkg/thsice.
727    
728    checkpoint62p (2010/12/17)
729    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
730        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
731    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
732        allow for use of multim. advection in seaice adjoint.
733    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
734      - first attempt to close budgets by taking into account the freshwater
735        flux implied by the sublimation of snow and ice. So far only the
736        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
737        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
738    o eesupp/src:
739      new S/R with new option (NML_EXTENDED_F77) to change array specification
740      from F95 standard to commonly accepted extended F77 form.
741      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
742      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
743      for less tolerant f77 compiler (e.g., pgf77, g77).
744    o globalFiles:
745      commented out in parameter file "data" since it's not safe with MPI
746      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
747      in this case); no longer commented out in restart test (tst_2+2).
748    o add adTapeDir to specify a special directory where adjoint tapes are
749      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
750      and cannot be used together with mdsioLocalDir.
751    o nesting pkgs:
752      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
753      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
754      - add parameter files + utils dir + output from short run on beagle.
755    o pkg/seaice:
756        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
757    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
758      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
759    
760    checkpoint62o (2010/11/25)
761    o pkg/exf:
762      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
763    o pkg/seaice:
764      - seaice_ocean_stress: split a loop for better vectorization of the
765        adjoint code
766      - seaice_growth.F: fix bug in conservation of freshwater connected to
767        capping of heff, put contribution into d_HEFFbyNEG
768      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
769        by something more sensible (parameters that are what their name implies)
770      - change some defaults, so that by default exf-parameters are used for
771        things like rhoAir, cpAir,latent/sensible heat parameters, in order
772        to reproduce the old results, many data.seaice now contain funny values
773        for cpAir and latent heat of sublimation
774    o packages_readparms.F: move exf_readparms up in line so that
775        exf-parameters are visible for other packages (e.g. seaice)
776    o debugMode & debugLevel=2:
777      - differentiate between debugMode & debugLevel=2:
778        debugMode: controls printing of debug messages (sequence of S/R calls).
779        debugLevel: controls printing of algorithm intermediate results and stats.
780      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
781        => allows to print debug-stats without all sequence of call messages.
782      - switch control of debug print from debugLevel to debugMode in many S/R.
783    o pkg/obcs (obcs-sponge):
784        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
785        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
786    o pkg/generic_advdiff:
787      - record overlap minimum size for each advection scheme;
788      - refine criteria on overlap minimum size;
789      - check and stop (in gad_check) if overlap size is too small.
790    o pkg/obcs:
791      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
792        once, in ptracers_implicit.F)
793      - with seaice: remove test on empty file name in obcs_apply_seaice (always
794        apply OB values when tile has OB)
795    o model/src, coriolis setting:
796      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
797        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
798        files (selectCoriMap=3) with any grid.
799      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
800    o pkg/seaice/seaice_growth.F:
801        a few cosmetic changes that reduce the number of lines of code
802    o pkg/obcs: add boundary conditions following Stevens (1990)
803      - the code follows old MOM/NAOSIM code
804      - so far it is only implemented for the eastern and western boundaries
805        and NOT for pTracers
806    o pkg/rbcs:
807      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
808        beginning of the first rbcs forcing period.
809      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
810        offline package, i.e., one file per time, labeled by iteration number;
811        deltaTrbcs sets the timestep with which the data was generated;
812        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
813      - rbcsForcingCycle=0 makes forcing non-cyclic.
814      - make arithmetic safe for negative times and odd forcing periods.
815    
816    checkpoint62n (2010/11/09)
817    o pkg/seaice:
818        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
819    o pkg/obcs:
820       New S/R to copy tracer value from the OB location to narrow band region
821        (width = same as overlap) beyond the OB: preserve OB value (needed for
822        high-order scheme) which were overwritten by EXCH call if in overlap
823        region. Applied to theta, salt, ptracer and advected seaice variables.
824       With seaice: use maskInC in similar way as in gad_advection.F,
825        in seaice_advection.F and advect.F.
826       Update output of experiment seaice_obcs and change exp4 to test OBCS with
827        4th order Adv.Scheme. for pasive salt and ptracer.
828    o tools/genmake2:
829      - when looking for an optfile (not specified), only search for Fortran compiler
830        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
831      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
832        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
833      - set default for CPP to "cpp -traditional -P" (was the case without specifying
834        an optfile, but otherwise default was just "cpp".
835      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
836      - when "CC" is not set in the optfile, look for possible C compiler
837        (instead of just setting CC=cc)
838      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
839        => add a ".F" to ".o" rule for source files with no "#include" (such as
840           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
841      - move gfortran before g77 in list of possible Fortran compiler (consistent
842        with reference compiler switch from g77 to gfortran)
843    o pkg/seaice:
844      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
845        seaice_check that stops the model, when the CPP flag is used.
846      o seaice_growth.F: make capping of ice volume conserving by returning the
847        capped ice as freshwater to EmPmR. This does not change the verification
848        experiments but will change runs where the capping is acutally active
849    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
850      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
851         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
852         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
853    o tools/genmake2:
854      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
855      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
856      - clean previous genmake log files before anything else.
857      - change Makefile to remove testreport log files (*.tr_log) and genmake log
858        files only with "CLEAN" target (instead of "Clean");
859    o pkg/generic_advdiff:
860      Change OBCS in multiDim advection (gad_advection.F):
861       Use maskInC to prevent intermediate update of tracer-field in OB regions,
862       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
863       which were applying future time-step OB values.
864      This way, all explicit calculations use current-time-step OB values
865       (simpler and more consistent).
866      Affects results when set-up uses time-varying OBC and multi-dim advection;
867       update output of experiment seaice_obcs.
868    o pkg/seaice:
869      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
870       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
871         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
872      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
873       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
874       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
875    o pkg aim (2010/10/26):
876      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
877        formulation with obliquity, eccentricity, ... as run-time parameters,
878      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
879        upward shortwave radition at the surface (all-sky and clear-sky).
880    o pkg/obcs:
881      - writing sections with globalFiles=T does not work: switch to tiled-files
882        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
883      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
884      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
885    
886    checkpoint62m (2010/10/21)
887    o pkg/seaice: vectorize seaice_solve4temp.F
888      - move iterations loops outside of i/j-loops
889      - requires 2D arrays for TB and effConduct
890      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
891        modified in this routine
892      - a little bit of clean up, adjusting indentation, etc.
893      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
894        performance and '**TWO' by '**2' (because TWO is a float),
895        replaced ONE, ZERO
896    o eesupp/src:
897       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
898    o pkg/seaice/seaice_growth.F
899      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
900      merging process. The merged routine has two branches, and one activates the 'evolution'
901      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
902      In summary, here is what the '10/10 revision' did consist of
903        part 1: seaice_growth.F revisions 1.71 to 1.75
904          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
905            The emphasis here was on improving readability (e.g. by trying to use meaningful
906            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
907        part 1.5:
908          - revising the lab_sea experiment to make it a more useful (i.e. stable
909            and representative of an actual model run). This was done by generating a
910            (winter) pickup to start from, switching back the main experiment dynamic
911            solver from evp to lsr, having one of the experiments use the free drift solution.
912        part 2: seaice_growth.F revisions 1.76 to 1.85
913          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
914          - Sorting out the various fields units and sign (set early on and reset at the end)
915            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
916            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
917          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
918            and simplifying logical expressions to further improve readibility.
919        part 3: seaice_growth.F revisions 1.86 to 1.89
920          - Re-organize the blocks of code more logically.
921          - Merging the '_if.F' pieces that add something new.
922    o pkg/thsice:
923      - vectorize thsice_solve4temp and thsice_get_exf.
924        Problem: thsice_solve4temp has an unvectorizable statement that
925        might also be problematic for TAF
926      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
927        does not change the verifcation experiment, but will change all
928        experiments that have this flag undefined (not tested in verification);
929        a little reorganization to save a few 2D fields and recomputations
930      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
931      - 2nd step:  fix some store dirs
932        o seems to work somewhat, i.e. using ifort but not g77
933        o likely cause are incomplete init. or recomputation
934        o start verification/global_ocean.cs32x15/input_ad.thsice
935    o pkg/obcs: add support for exch2
936      - the position of the boundary and prescribed values are specified using
937        a global domain with exch2 facets stacked
938        - in x for N,S boundaries (like W2_mapIO=-1)
939        - in y for E,W boundaries (so E,W boundaries do not overlap)
940    o pkg/mdsio: add support for writing global sections with exch2
941        file layout is as for obcs described above:
942        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
943        - for y-z sections, facets are stacked in y
944    o pkg/thsice:
945       - change a few routines for better vectorization: thsice_albedo.F,
946         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
947         not affected, but in particular the latter routine has changed
948         dramatically (not necessarily easier to read now).
949       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
950       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
951    o verification/lab_sea:
952      - overhaul of the forward model experiments. The main motivation
953        for this revision is that lab_sea has proven quite fragile (when
954        changing the sea-ice code, and switching platforms) to a point
955        when failures were very hard to attribute to specific code problems.
956      - the suspected reason for this fragility is noise amplification by evp so,
957        to start with, we decided to replace evp with lsr in the main experiment.
958      - the input.lsr experiment thus became obsolete and was removed.
959      - it was replaced with the input.fd experiment that uses an
960        analytical "free drift" solution as the ice velocity field.
961      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
962        will hopefully allow us to discriminate problems due to dynamic solvers
963        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
964        us to test additional options, along with the salt plume package.
965      - Finally a pickup was generated (at the end of a one year run) to
966        make the tests more representative of an actual model run. Previously
967        the tests starting point was a 1m thickness of ice everywhere.
968    o pkg/seaice:
969      - introducing S\R seaice_freedrift.F that compute the
970        analytical solution to an approximate ice momentum
971        equation (i.e. the simple stress/coriolis balance).
972      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
973        of the free drift velocity field, and enable its use.
974        To actually use the free drift solution as the model ice
975        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
976    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
977    
978    checkpoint62l (2010/10/04)
979    o pkg/seaice:
980      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
981      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
982       version (with USE_ORIGINAL_SBI undef);
983    o add hooks for new packages OASIS, the package will follow
984      (hooks exclude the seaice pkg for now)
985    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
986      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
987      rather than mdsio_readvector.F/mdsio_writevector.F, within
988      adread_adwrite.F to read/write adjoint-related tapes to disk.
989    o eesupp and pkg/mdsio: ALLOW_WHIO
990      Option to write/read 2D fields to files including tiles halos.
991      The main purpose is for adjoint related "tape I/O".
992      The secondary purpose is for debugging phases.
993      A word on those rather specifically intended purposes.
994      The code was meant to be stripped down to the bare minimum.
995      Typically, there is a unique and basic mapping to the global
996      buffer (tile by tile, then proc by proc, then level by level), and
997      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
998      meant to generate user friendly outputs of various shapes and forms.
999      Rather it is intended, for the knowledgeabale developers,
1000      to be largely independent of the many mdsio options, to allow
1001      outputs of tiles+halos in debugging phases and in adjoint runs,
1002      and to allow some flexibility in tuning (adoint) I/O depending on each
1003      file system behavior. With regard to tuning, most of the potential knobs
1004      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1005      to specify directories, to specify the typical size of I/O calls, etc.)
1006      are not yet included, and will be added if they prove useful.
1007    o pkg/seaice:
1008       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1009    o pkg/seaice:
1010       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1011       code (seaice_budget_ice_if.F) which enable to recover old standard
1012       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1013       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1014    o model/src (rStar):
1015       use simple average (not area weighted) of rStarFac at U,V point when using
1016       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1017       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1018    
1019    checkpoint62k (2010/09/17)
1020    o adjoint
1021       * changed verification/global_ocean.cs32x15 ; adjoint now tests
1022         Adams-Bashforth 3 + NLFS + RSTAR
1023       * some more modifs required for ECCO-GODAE v4
1024    o pkg/seaice
1025       add SEAICE_AGE_VOL option to use volume instead of area for
1026       integrating SEAICE_AGE
1027    o model/src:
1028       first check-in of sigma & hybrid-sigma coordinate code ; also includes
1029       non-linear free-surface parts ; but pressure-gradient not yet coded.
1030    o pkg/ptracers:
1031       option for ptracer to convert Salt Relax into additional EmP.
1032        tested in exp. global_ocean.90x40x15.dwnslp (update output)
1033    
1034    checkpoint62j (2010/08/25)
1035    o pkg/ggl90:
1036       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1037    o pkg/dic: car_flux.F, phos_flux.F
1038      - reduce number of exp-calls in order to improve performance
1039      - clean up a little (replace fields by their macros, etc., fix
1040        typo in CPP-flag)
1041    o pkg/ggl90: minor changes
1042      - GGL90diffKrS was removed --> always use GGL90diffKr
1043      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1044      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1045        (commented out for now)
1046      - change in max/min operations to ensure that smoothing is ok
1047      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1048      - always use diffKrNrT as background profile (i.e. never use diffKr field)
1049    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1050    o pkg/dic:
1051      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1052        vectorization
1053      - small bug fix in insol for the unlikely case of a cartesian grid
1054      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1055        + now vectorize, which also removes adjoint recomputations;
1056        + replace integer maksp1 by _RL maskp1
1057        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1058    
1059    checkpoint62i (2010/07/21)
1060    o pkg/flt:
1061      - with OBCS: stop floats which enter the OB region
1062    o model/src:
1063      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1064        for implicit vertical advection.
1065    o pkg/seaice:
1066     - account for melting in seaice age evolution.
1067     - remove double counting of seaice ridging effect on seaice age.
1068    
1069    checkpoint62h (2010/06/18)
1070    o pkg/exch2:
1071     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1072    o tools/genmake2
1073      - remove "-pdefault" option: redundant with the use of "packages.conf";
1074      - remove file pkg/pkg_default : set the default as a pkg group
1075        ("default_pkg_list") defined in pkg/pkg_groups;
1076      - fix for case pkg/pkg_depend is missing (was hanging before);
1077      - add option "-pgroups" to specify a different pkg_groups than the default.
1078    o verification/adjustment.cs-32x32x1:
1079       add a "minimal" set-up test (code_min & input_min) which only compiles
1080       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1081    o tools/genmake2
1082      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1083      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1084    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1085      files are nearly the same anyway.
1086      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1087       - redefinition of tau(i,i) (by a factor of ustar)
1088       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1089       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1090       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1091       - replace
1092         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1093         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1094         by
1095         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1096         (changes results)
1097       -> exf_bulkformulae v1.22,
1098          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1099          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1100                    output.txt 1.63
1101           offline_exf_seaice: output.seaicetd.txt 1.7
1102           seaice_obcs: output.txt 1.10)
1103      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1104       -> exf_bulkformulae v1.23,
1105          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1106          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1107      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1108    o adjoint of exch-1:
1109     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1110       (note: was already like this when using EXCH-2) and remove flow dir
1111       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1112     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1113     - update pkg/exch2 diff list.
1114    
1115    checkpoint62g (2010/05/19)
1116    o eesupp/src (exch-1):
1117     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1118       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1119       (renamed to exch1_*rx_cube.F).
1120     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1121       to call new exch1 S/R ; update Makefile and .cvsignore.
1122     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1123       exch2_xy_rx later)
1124      Note: after updating your code, need to run "make clean" in eesupp/src
1125    o test experiment bottom_ctrl_5x5:
1126       new output_adm.txt with fewer grdchk & less monitor output.
1127    o model/src:
1128      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1129       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1130       beeing treated in the same way (ini_grid is not called a 2nd time).
1131    o pkg/exf:
1132      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1133      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1134      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1135      - cosmetic changes to exf_bulkformulae.F to make it look more like
1136        exf_bulk_largeyeager04.F
1137    o eesupp/src (exch-1):
1138      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1139      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1140        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1141        (even without using MPI).
1142      - Message mode: move RecvAck setting (indicator of buffer being ready)
1143        from send_put to recv_get S/R (was useless before, but not sure if
1144        it's much more useful now);
1145      - Switch the order of sync: MPI-proc 1rst and then threads;
1146      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1147      - fix AD code for communication mode ='get' (but not used).
1148    o model/src:
1149      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1150      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1151  o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API  o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1152  o pkg/ctrl: require a specific set of control variables and exf-flags for  o pkg/ctrl: require a specific set of control variables and exf-flags for
1153    adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)    adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
# Line 149  o tools/build_options: Line 1293  o tools/build_options:
1293      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1294  o pkg/ecco  o pkg/ecco
1295    - allow user defined cost function contributions    - allow user defined cost function contributions
1296          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1297          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1298    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1299        the two options are complementary.        the two options are complementary.
1300  o pkg/smooth  o pkg/smooth
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