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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1479 by jmc, Fri Jul 22 19:55:01 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):
8      - fix mask for OBCS (still problems in stream-function with OBCS);
9      - add specific parameter (default = main code CG2D params) for solver;
10      - in case of poor convergence, use solution corresponding to lowest residual.
11    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
12      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
13      and should be avoided where possible.
14    o model/src (rStar):
15      - include r* effect on reference-state (PhiRef) in totPhiHyd
16        (so that it's really the potential anomaly at the cell center);
17        affect solution only if z* with full pressure in EOS.
18      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
19        update output (because of z* in totPhiHyd and viscA4 changes);
20      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
21        @ constant r) until interpolation at constant r is implemented.
22    o pkg/diagnostics
23      - fix RCENTER diagnostics in case cell center is not at interface middle
24    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
25      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
26      that THETA and SALT are "conservative temperature" and "absolute
27      salinity"
28    o pkg/ctrl
29      - fix computation of endrec in s/r ctrl_init_rec
30      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
31    o pkg/seaice/seaice_growth.F
32      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
33        remove then obsolete STORE directives
34      - fix STORE directives for tice and tices, so that only the
35        appropriate part of the fields are stored (and not the entire
36        field); update global_ocean.cs32x15.seaice AD output.
37      - cosmetic changes: adjust CPP flags and indentation for better
38        legibilty
39    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
40      Chris Wilson)
41    o pkg/gmredi:
42       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
43       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
44    
45    checkpoint63 (2011/07/11)
46    o pkg/exch2:
47     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
48     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
49       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
50       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
51    o pkg/diagnostics:
52     - deal with pairs of post-processed diags which are computed together; in
53       particular, re-order list of diags within 1 file to save 2nd computation.
54     - add S/R to compute velocity stream-function (called after velocity-potential
55       calculation) from divergence free transport -> new diagnostics "PsiVEL".
56     - add parameter to select grid-point location where PsiVEL == 0.
57    o eesupp/src:
58       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
59       (specific S/R needed with exch2 topology - for now, just print an error msg)
60    o pkg/shelfice
61     - Implement friction velocity-dependent transfer coefficients following
62       Holland and Jenkins, JPO, 1999
63       Original code by M. Losch with small modifs.
64       Enable with CPP option SHI_ALLOW_GAMMAFRICT
65       and runtime flag SHELFICEuseGammaFrict
66    o verification lab_sea & global_ocean.cs32x15:
67     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
68       does not miss some dependencies (but is slower) and also works with many files
69       (default makedepend limitation for AD built).
70     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
71    o pkg/diagnostics:
72     - add run-time parameter "useMissingValue" (def=False) to fill land-point
73        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
74       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
75     - Extend the use of "missing_value" setting from data.diagnostics for the case
76       of counter-diagnostics (where fraction-weight is zero). This applies both to
77       MNC and MDS output files.
78    o pkg/seaice/seaice_growth.F:
79      - add 'a priori' cap of latent heat flux based on actual mass considerations
80        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
81        non-legacy seaice_solve4temp.
82      - add diagnostic of the residual sublimation freshwater flux (the freshwater
83        flux taken from the ocean if the total actual latent heat fluxes exceed
84        the maximum)
85      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
86       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
87      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
88       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
89      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
90      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
91    o verification 1D_ocean_ice_column:
92       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
93       update results
94    o pkg/diagnostics:
95     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
96       which are not filled-up but computed from other diags ; In this case, the mate
97       diag points to the primary (filled-up) diag to used for post processing.
98     - Update Velocity-potential computation using post-processed diag framework.
99     ==> Change the ordering of fields and time-periods in MDS output file
100       when using periodic averaging: now writes one time record with the full set
101       of fields for this time period, then the next time reccord (it used to be
102       one field with the full set of time records then the next field).
103         Note: this is now similar to NetCDF (MNC) output file. <==
104    
105    checkpoint62z (2011/06/21)
106    o adjoint monitor:
107     - Add adjoint monitor output for packages exf, seaice
108       and update relevant testreport output
109    o pkg/seaice:
110     - re-order diags inits so that they appear in order in available_diagnostics.log
111     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
112       area/heff/hsnow preceeding thermodynamic growth/melt.
113     - modified diag: SIdA; output actual effect, as the description states.
114     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
115     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
116       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
117        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
118     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
119     - added diagnostics for seaice generic tracers (SItr*).
120     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
121     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
122     I. Fenty: 18-Jun-2011:
123     Minor changes to seaice package:
124     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
125        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
126       - Differentiated "regularization variables" from "floor variables"
127        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
128        * hiceMin became SEAICE_hice_reg (old hiceMin)
129          (with _reg meaning regularization variable)
130       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
131        so as to ensure energy conservation when going between phases
132      - A22 was not used anywhere
133     2) Changed regularization procedure for heffActual and hsnowActual to ensure
134        well-boundedness and smooth adjoint in seaice_growth.F
135     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
136        because the old regularization always set heffActual >= 0.05 cm
137     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
138        on AREA when HEFF > 0.
139      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
140        requiring that DISABLE_AREA_FLOOR *not* be defined
141     Affected verifications:
142      - 1D_ocean_ice_column (output.txt output_adm.txt)
143      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
144    o pkg/diagnostics:
145      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
146      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
147        (was _RL, now integer) with option = 0 to retrieve all levels.
148      - add pieces of code to compute velocity potential at each level (new diagnostics
149        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
150        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
151      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
152        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
153        and in diagnostics_fract_fill.F (do not need a valid pointer for the
154        diagnostics counter-mate); check that definition of counter-diagnostic
155        includes a valid counter-mate (in diagnostics_set_levels.F).
156    o model/src (rStar):
157      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
158        affect solution only if z* with full pressure in EOS;
159        update output of test-exp global_ocean.90x40x15.
160    o pkg/seaice:
161      - introduce siEps=1e-5 parameter
162      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
163      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
164      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
165        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
166        as well as ice cover age and ridging index (attached to AREA).
167        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
168        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
169        Up to SItrMaxNum=3 tracers can be used simultaneously.
170    o pkg/salt_plume:
171      -introduce SPsalFRAC run time parameter that sets the fraction of the
172       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
173       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
174    o model debug options:
175      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
176        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
177      - Refine debug-msg printing selection (3 new levels):
178        debugMode  : controls printing of debug messages (sequence of S/R calls).
179        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
180         debLevZero =  0 ; /* level of disabled aux. msg printing */
181         debLevA =  1 ; /* level of minimum  aux. msg printing */
182         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
183         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
184         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
185         debLevE =  5 ; /* level of extensive debug printing */
186        New debugLevel default: with default debugMode value (=F),
187          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
188          and if debugMode=T, default debugLevel = 4 (debLevD).
189        Relation with previous settings:
190         debLevB (=2) corresponds to former debLevA (=1)
191         debLevD (=4) corresponds to former debLevB (=2)
192        Note:
193         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
194         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
195            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
196      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
197        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
198    o pkg/obcs:
199      - change OBCSfixTopo default from True to False (should not change the results);
200        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
201    o pkg/thsice:
202      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
203        2nd layer seaice sublimation (unlikely to happen)
204      - use Interior mask for OBCS in thsice_advection.F (similar to what is
205        done in gad_advection & seaice_advection).
206    o adjoint:
207      bug fix spotted by Gael Forget:
208      seaice_advection and thsice_advection still had
209      legacy CPP options to avoid CS corner updates for adjoint
210    o pkg/seaice:
211      => Change some of the defaults (2011/05/29):
212         - change SEAICEuseFluxForm default (from False to True)
213         - change DIFF1 default (from 0.004 m/s to 0. m/s)
214         And print warnings if DIFF1 is not set in data.seaice and centered
215          avection scheme is used without any diffusion.
216      also:
217      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
218      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
219      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
220        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
221        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
222      update results of test exp.:
223         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
224             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
225             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
226         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
227         seaice_obcs: output (SEAICEuseFluxForm=T)
228      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
229          for standard fwd & AD lab_sea tests (to keep the same output).
230    o pkg/seaice/seaice_growth.F:
231      - use Ian Fenty's capping formulas for actual ice
232      thickness thoughout EVOLUTION branch.
233      - put treatment pathological case #2) in CPP brackets
234      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
235      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
236    o pkg/seaice:
237      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
238      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
239      also pass fac as a param, which can be 1. (to update the tendency
240      field) or the time step (to update the field itself).
241      - seaice_advdiff.F: for multidim, call seaice_diffusion with
242      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
243      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
244      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
245      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
246    o pkg/seaice:
247      diffusion with centered advection scheme (diffus.F & advect.F):
248      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
249        to just compute the laplacian of input-field.
250      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
251      - fix flux-form version in diffus.F to conserve tracer.
252      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
253       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
254    
255    checkpoint62y (2011/05/26)
256    o pkg/seaice:
257     - seaice_growth.F : in EVOLUTION branch, always include
258       a_QSWbyATM_cover in qnet (as it should be).
259     - verification/global_ocean.cs32x15 : update results accordingly
260       (output.seaice.txt output_adm.seaice.txt).
261    o pkg/seaice + obcs:
262     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
263       equivalent of assuming no tracer gradient outside the OB region.
264       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
265     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
266       after changes above);
267     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
268       only at OB location (instead of over a band of OLx width).
269    o pkg/seaice:
270     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
271       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
272    o pkg/obcs:
273      - split header file "OBCS.h" into 4 separated files:
274        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
275       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
276         (contain no conditional statement which depends on OBCS options).
277      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
278        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
279    o ctrl, cost, grdchk & autodiff pkgs:
280      - make options file more standard (like other {PKG}_OPTIONS.h file but
281        with AD_CONFIG.h); clean-up some of the included header files.
282    o pkg/obcs:
283      - do not mask tracer when applying OB (tracer == 0 could generate problems)
284      - apply tracer OB values to tracer field only at OB location (instead of
285        over a band of OLx width)
286      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
287      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
288        obcs_apply_tloc.F & obcs_apply_sloc.F
289    o obcs in model/src:
290      - call OBCS_APPLY_W only if NonHydrostatic.
291      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
292      - reset dEtaHdt and wVel to zero outside OB interior region ;
293      - leave tracer unchanged outside OB interior region: This has no effect
294        on the solution but just to prevent unrealistic tracer value outside OB.
295      - zero out velocity outside OB interior region: This has no effect on
296        the solution but just to prevent unrealistic velocity outside OB.
297    o obcs and non-lin free-surf:
298       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
299       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
300       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
301       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
302       update results of test-exp. exp4(nlfs).
303    o exp4 (nlfs) test-exp:
304       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
305       with NonLin-FreeSurf); update output.nlfs.txt
306    o obcs and 2d/3d solver norm:
307       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
308       and outside OB interior region (will allow to place OB further inside the
309       domain). Depending on the domain, can affects cg2d-Norm (previous
310       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
311       and cg3d-Norm (previous Norm was computed before canceling OB terms),
312       e.g. in tutorial_plume_on_slope.
313      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
314    o pkg rbcs:
315      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
316      - add capability to apply relaxation to horizontal velocity uVel & vVel.
317    o pkg/grdchk: add gradient check for control variable xx_shifwflx
318    o pkg/shelfice/shelfice_init_fixed.F
319      fix CPP-flag combinations
320    o pkg/seaice: Merge iceage code of Pierre Rampal
321      * update/change/correct ice age calculations
322      * add age updates for pathological cases
323      Probably needs more testing...
324    
325    checkpoint62x (2011/05/13)
326    o pkg/mom_vecinv:
327       high-order vorticity scheme: use interior masks (maskInW & S)
328       to zero-out (outside OB) gradient of vorticity.
329    o verification exp.:
330       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
331       hs94.128x64x5 and seaice_obcs ; update results.
332    o pkg/obcs:
333      fix bug in OBeta for YZ sections in obcs_exf_load.F
334    o pkg/ctrl, pkg/shelfice, and optim:
335      - add new control variable xx_shifwflx (fresh water flux underneath ice
336        shelves). This is almost as tedious as obcs-ctrl, because the
337        variables needs its own mask.
338      - add a cost function term that penalizes the deviation of xx_shifwflx
339        from the first guess (zero) in analogy to other control variables
340    o pkg/shelfice:
341      - start basic adjoint
342    o pkg/ctrl:
343      - remove extra 2D field "for good measure" when initializing in
344        ctrl_set_globfld_[xy/xz/yz].F
345      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
346      - improve error messages in ctrl_set_unpack_*
347    o OBC implementation in momentum:
348       use interior masks (maskInC,W & S) in momentum S/R:
349       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
350       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
351       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
352       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
353       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
354        (and also with Leith/Smagorinsky harmonic-viscosity).
355       Update output of experiment dome and exp4 (+nlfs).
356    o exp4 test-exp:
357      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
358        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
359        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
360        time-varying OB at Western-side for wVel (NonHyd); update output.
361      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
362        and biharmonic-viscosity ; also use prescribed time varying OB.
363    o pkg/obcs:
364      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
365    o model/src:
366      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
367      - initialise startTime & nIter0 with unlikely values: allows to set one
368        from the other without ambiguity.
369    o seaice_obcs test-exp.:
370      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
371    o pkg/obcs:
372      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
373        no longer needed with maskInC,W,S in pkg/generic_advdiff.
374    o pkg/seaice:
375      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
376        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
377      - fixed bug in the initialization of sea ice salinity variable HSALT
378        in seaice_init_varia.F  (removed dependence on ICE2WATR)
379    o fizhi-cs test exp.:
380       switch reference output convention for these 2 non-standard test-exp,
381        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
382          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
383       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
384    o model/inc:
385      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
386        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
387    o pkg/seaice:
388      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
389    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
390      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
391        and initial HSALT
392    
393    checkpoint62w (2011/04/26)
394    o pkg/mom_fluxform:
395      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
396      - use parameter "sideDragFactor" in no-slip BC side-drag part.
397      - update output of exp. global_ocean.90x40x15
398    o pkg/mom_vecinv:
399      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
400    o update seaice exp.:
401      use more consistent parameter values (remove "backward compatability only":
402       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
403      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
404       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
405    o update test-exp global_ocean.90x40x15:
406      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
407      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
408      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
409      o turn on zStar & viscA4 in standard set-up (dir input/)
410        and update output files: output.txt & output.dwnslp.txt
411    o new AD-test experiment: obcs_ctrl
412      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
413    o pkg/dic:
414      fix two bugs in handling water vapour pressure in carbonate chemistry
415      and air-sea fluxes. Found by Val Bennington and Galen McKinley
416      (add DIC Option = WATERVAP_BUG to recover old results)
417      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
418    o adding allowInteriorFreezing option to check for water below freezing point
419      at depth and bring the negative heat anomaly to the surface level
420    o pkgs _fields_load:
421      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
422      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
423        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
424        rbcs to get interpolation weights and time reccord number.
425      - fix multi-threading in aim_fields_load.F
426      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
427    o external_fields_load:
428      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
429       interpolation weights) to use in a periodic time-series ; do not divide by
430       time-step to convert to integer:
431       - this fixes case where externForcingPeriod is not multiple of time-step
432          (Thanks to Christopher L. Wolfe)
433       - this fixes case where externForcingPeriod is an odd multiple of time-step
434         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
435      store index of time-record which is currently loaded:
436       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
437       - needed for the adjoint but not yet used because of extensive recomputations;
438         (to be fixed soon)
439    
440    checkpoint62v (2011/04/02)
441    o verification/1D_ocean_ice_column added to test Ian Fenty's
442      pkg/seaice_growth.F modifications for improving sea ice code differentiability
443    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
444      (new velocity statistics after changing maskInW & maskInS definition)
445    o pkg/generic_advdiff with OBCS:
446      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
447      equivalent to assumption of no tracer gradient outside the OB region.
448      This will affect the results if using obcs+biharmonic diffusion.
449      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
450    o pkg/obcs:
451      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
452      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
453      in Interior region. No impact on solution but affects Velocity monitor stats.
454    o pkg/ptracers (adjoint)
455      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
456      tape file for each tracer
457    o model/inc/src and pkg/autodiff: add parameters that allow to turn
458      of parts of the adjoint code at run time. For now, there are only
459      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
460      parameters are set in data.pkg.
461      This is the lazy coward's version of doing this, but still useful for
462      debugging. In order to do it right, everything needs to be moved to
463      pkg/autodiff.
464    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
465      the end; this fixes the adjoint balancing code for open boundaries.
466    o pkg/ctrl:
467      - change behavior of xx_${varname}period to be analogous to exf-conventions:
468        xx_${varname}period =   0.,  means time-independent control part
469        xx_${varname}period = -12., means one-year-periodic monthly control part
470      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
471        clean up ctrl_init a little, remove unused variables
472      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
473      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
474    
475    checkpoint62u (2011/03/15)
476    o model/src:
477      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
478        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
479      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
480        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
481    o pkg/ctrl/obcs/ecco:
482      - remove obsolete, unused, and partially broken code:
483        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
484        ALLOW_CTRL_OBCS_BALANCE
485      - put a stop statement into ecco/cost_obcsvol.F, but also add
486        cost_obcsvol to ecco_ad_diff.list
487    o pkg/ecco: fix counting cost function contributions for obcs (code
488      by Matt M.) and diffkr for diagnostics
489    o pkg/ecco, pkg/ctrl, pkg/grdchk:
490      add cost penalty terms for initial uvel, vvel, eta controls
491      and I/O for prior error files
492    o pkg/mdsio:
493       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
494       (new argument) to check for tiled file in mdsioLocalDir : this fix the
495       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
496    o pkg/ctrl:
497     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
498       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
499       unused and superfluous variables
500     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
501    o pkg/ecco
502     - enable adjoint of Stevens OB
503    o pkg/ctrl/ecco/grdchk:
504      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
505        Fortunately, we do not have any tests for the numerous cpp-flagged
506        option of "obcs as control parameters" so we will never know
507        if this is an improvement (but at least now things compile).
508      - remove an obsolete initialization from ecco_cost_init_barfiles.F
509      - fix some problems within never used ifdefs to make the code compile
510    o pkg/obcs:
511     - Refine Interior mask definition to work with more complex OB (e.g.
512       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
513       read in Interior mask from file. Check if Interior mask is consistent
514       with OB list of indices.
515    o pkg/seaice
516     - beginning code for a seaice tracer package,
517       but currently only used for seaice age: SEAICE_AGE
518       SEAICE_num = 4
519       iTracer = 1: area-weighted ice age
520               = 2: volume-weighted ice age
521               = 3, 4: template for one-year vs. multi-year ice
522       data.seaice has new namelist SEAICE_PARM03 for arrays related to
523       SEAICE_num
524    
525    checkpoint62t (2011/03/05)
526    o pkg/obcs:
527     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
528       then normal component. This ensures that the normal component is set
529       correctly even when it conficts with tangential setting from an other OB.
530       Affects results of test-experiment seaice_obcs: update the output.txt
531    o pkg/obcs:
532     - add code to monitor statistics of dynamical fields at OB.
533     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
534       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
535       - change default: balance the Net inflow through all OB (instead of balancing
536         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
537     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
538       to match Nortern OB inflow (OBCS_balanceFacN=0).
539    o pkg/seaice:
540     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
541    o pkg/seaice (seaice_growth v 1.113):
542     - reverting seaice_growth to v 1.111 in order to have code with exact bit
543       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
544       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
545       runtime flag SEAICEareaFormula is kept but is inactive
546    o model/src:
547     - add new param to scale curvilinear grid distance and area when using
548       a different sphere radius from the grid-files.
549     - test/check multi-threads EXCH applied to local variable (cg2d_x)
550    o adjoint:
551     - enable adjoint of Stevens OB
552     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
553       (a bit delicate because of potentially modified adj. common block structure;
554       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
555    
556    checkpoint62s (2011/02/15)
557    o pkg/seaice (seaice_growth v 1.112):
558     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
559       computing the ice cover tendency from effective thickness tendencies. Include
560       Ian Fenty's formula.
561     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
562       SEAICEareaFormula.
563     - simplify notations for the various d_HEFF/d_AREA terms.
564    o pkg/gmredi:
565     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
566       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
567       add a verification test-run (front_relax.bvp) to test GM_useBVP.
568    o pkg/seaice (seaice_growth v 1.111):
569     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
570     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
571       also melt ice.
572    o pkg/seaice:
573     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
574     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
575    o pkg/cheapaml:
576     - from Nico Wienders: New version of this package.
577    o pkg/flt:
578     - add CPP options to prevent floats to re-enter the opposite side of
579       a periodic domain (default: keep periodicity)
580    o pkg/gmredi:
581     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
582       (needed for multi-dim advection).
583     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
584    o model/src:
585     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
586    o tutorial_tracer_adjsens
587     - extend to NLFS and replace maskC by hFacC
588       (change reference output accordingly)
589    
590    checkpoint62r (2011/01/24)
591    o testreport:
592     - add option -deloutp (-do) to remove output file after successful run
593     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
594       extract exact list of procs from this file ; adjust COMMAND by
595       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
596    o pkg/ecco: replace old ineffective way of penalizing deviations from
597      first guess (of obcs) with code by Matt Mazloff
598    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
599      exf/cal
600      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
601        and handle case of obcs?period == 0
602        Not affected by these changes: There is still an inconsistency in
603        the computation of start/endrec for the obcs variables for ALLOW_CAL
604        defined (see comment by Menemenlis, 7-Mar-2003)
605      - make S/R ctrl_get_gen_rec return something meaningful even if
606        ALLOW_CAL is not defined
607      - ctrl_getobcs?: simplify code so that it does not need to use
608                       S/R exf_swapfields
609    o testreport:
610       allow to test MPI with different number of processors for each experiment:
611       create file "SIZE.h.mpi" in each build dir.
612       Note: update of "-command" argument not yet implemented.
613    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
614      alleviate the need for additional 3D tapes when using
615      the non-inear free surface in the adjoint. This is done
616      by adding an 'update' of hfacc etc. to their current
617      value at the beginning of forward_step.F.
618    o pkg/seaice
619      seaice_lsr: move stress-divergence computations out of outer pseudo-
620      timestepping loop
621    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
622      up, so that the calls of the ctrl_* subroutines are really at the end
623      of the routine.
624    o pkg/gmredi:
625      allow to specify a 2-D horizontal map and a 1-D vertical profil
626      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
627    o pkg/seaice:
628      move lsr iterations from seaice_dynsolver to seaice_lsr.
629    o pkg/seaice:
630      reduce memory footprint of seaice mutldim advection tapes,
631      by using a 2D tape independent of the generic_advdiff ones,
632      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
633    
634    checkpoint62q (2010/12/29)
635    o model/src:
636      - check horizontal grid-spacing for unset or zero/negative values.
637      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
638    o pkg/flt:
639      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
640      - precision of input and output files set according to readBinaryPrec
641        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
642      - initial float position from tiled file was not converted to index space
643        (looks like a bug): fixed to make it similar to initial pos. global file.
644    o global_ocean.cs32x15:
645       change SIZE.h of AD set-up to get same tiling as with MPI.
646       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
647    o model/src:
648       add flag to control printing of domain fields (bathymetry, hFac ...) in
649       ini_mask_etc (call to plot_fieds_xy*).
650    o pkg/thsice:
651       if useEXF, some forcing fields are not valid in overlap: fixed by computing
652       over the interior only + apply EXCH at the end (like with SEAICE advection).
653    o pkg/mdsio:
654      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
655        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
656      - change barrier call for safe multi-threads access to 3-D shared buffer.
657      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
658      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
659        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
660    o pkg/flt:
661      - add fourth-order Runge-Kutta integration
662      - add basic exch2 support (only 1 facet supported so far!)
663    o pkg/mdsio+rw:
664      new S/R to read local (or tile independent) vector (read counterpart of
665       mds_writevec_loc, and front-end write_glvec_rl/rs).
666    o global_ocean.cs32x15: additional input_ad.seaice experiment
667        that uses pkg/seaice rather than pkg/thsice.
668        (using multidim advection for seaice)
669    o towards more F95 syntax for array specification in namelist:
670      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
671        of all verification experiments.
672           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
673          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
674      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
675    o global_ocean.cs32x15: additional input.seaice experiment
676        that uses pkg/seaice rather than pkg/thsice.
677    
678    checkpoint62p (2010/12/17)
679    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
680        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
681    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
682        allow for use of multim. advection in seaice adjoint.
683    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
684      - first attempt to close budgets by taking into account the freshwater
685        flux implied by the sublimation of snow and ice. So far only the
686        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
687        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
688    o eesupp/src:
689      new S/R with new option (NML_EXTENDED_F77) to change array specification
690      from F95 standard to commonly accepted extended F77 form.
691      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
692      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
693      for less tolerant f77 compiler (e.g., pgf77, g77).
694    o globalFiles:
695      commented out in parameter file "data" since it's not safe with MPI
696      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
697      in this case); no longer commented out in restart test (tst_2+2).
698    o add adTapeDir to specify a special directory where adjoint tapes are
699      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
700      and cannot be used together with mdsioLocalDir.
701    o nesting pkgs:
702      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
703      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
704      - add parameter files + utils dir + output from short run on beagle.
705    o pkg/seaice:
706        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
707    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
708      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
709    
710    checkpoint62o (2010/11/25)
711    o pkg/exf:
712      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
713    o pkg/seaice:
714      - seaice_ocean_stress: split a loop for better vectorization of the
715        adjoint code
716      - seaice_growth.F: fix bug in conservation of freshwater connected to
717        capping of heff, put contribution into d_HEFFbyNEG
718      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
719        by something more sensible (parameters that are what their name implies)
720      - change some defaults, so that by default exf-parameters are used for
721        things like rhoAir, cpAir,latent/sensible heat parameters, in order
722        to reproduce the old results, many data.seaice now contain funny values
723        for cpAir and latent heat of sublimation
724    o packages_readparms.F: move exf_readparms up in line so that
725        exf-parameters are visible for other packages (e.g. seaice)
726    o debugMode & debugLevel=2:
727      - differentiate between debugMode & debugLevel=2:
728        debugMode: controls printing of debug messages (sequence of S/R calls).
729        debugLevel: controls printing of algorithm intermediate results and stats.
730      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
731        => allows to print debug-stats without all sequence of call messages.
732      - switch control of debug print from debugLevel to debugMode in many S/R.
733    o pkg/obcs (obcs-sponge):
734        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
735        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
736    o pkg/generic_advdiff:
737      - record overlap minimum size for each advection scheme;
738      - refine criteria on overlap minimum size;
739      - check and stop (in gad_check) if overlap size is too small.
740    o pkg/obcs:
741      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
742        once, in ptracers_implicit.F)
743      - with seaice: remove test on empty file name in obcs_apply_seaice (always
744        apply OB values when tile has OB)
745    o model/src, coriolis setting:
746      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
747        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
748        files (selectCoriMap=3) with any grid.
749      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
750    o pkg/seaice/seaice_growth.F:
751        a few cosmetic changes that reduce the number of lines of code
752    o pkg/obcs: add boundary conditions following Stevens (1990)
753      - the code follows old MOM/NAOSIM code
754      - so far it is only implemented for the eastern and western boundaries
755        and NOT for pTracers
756    o pkg/rbcs:
757      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
758        beginning of the first rbcs forcing period.
759      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
760        offline package, i.e., one file per time, labeled by iteration number;
761        deltaTrbcs sets the timestep with which the data was generated;
762        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
763      - rbcsForcingCycle=0 makes forcing non-cyclic.
764      - make arithmetic safe for negative times and odd forcing periods.
765    
766    checkpoint62n (2010/11/09)
767    o pkg/seaice:
768        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
769    o pkg/obcs:
770       New S/R to copy tracer value from the OB location to narrow band region
771        (width = same as overlap) beyond the OB: preserve OB value (needed for
772        high-order scheme) which were overwritten by EXCH call if in overlap
773        region. Applied to theta, salt, ptracer and advected seaice variables.
774       With seaice: use maskInC in similar way as in gad_advection.F,
775        in seaice_advection.F and advect.F.
776       Update output of experiment seaice_obcs and change exp4 to test OBCS with
777        4th order Adv.Scheme. for pasive salt and ptracer.
778    o tools/genmake2:
779      - when looking for an optfile (not specified), only search for Fortran compiler
780        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
781      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
782        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
783      - set default for CPP to "cpp -traditional -P" (was the case without specifying
784        an optfile, but otherwise default was just "cpp".
785      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
786      - when "CC" is not set in the optfile, look for possible C compiler
787        (instead of just setting CC=cc)
788      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
789        => add a ".F" to ".o" rule for source files with no "#include" (such as
790           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
791      - move gfortran before g77 in list of possible Fortran compiler (consistent
792        with reference compiler switch from g77 to gfortran)
793    o pkg/seaice:
794      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
795        seaice_check that stops the model, when the CPP flag is used.
796      o seaice_growth.F: make capping of ice volume conserving by returning the
797        capped ice as freshwater to EmPmR. This does not change the verification
798        experiments but will change runs where the capping is acutally active
799    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
800      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
801         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
802         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
803    o tools/genmake2:
804      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
805      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
806      - clean previous genmake log files before anything else.
807      - change Makefile to remove testreport log files (*.tr_log) and genmake log
808        files only with "CLEAN" target (instead of "Clean");
809    o pkg/generic_advdiff:
810      Change OBCS in multiDim advection (gad_advection.F):
811       Use maskInC to prevent intermediate update of tracer-field in OB regions,
812       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
813       which were applying future time-step OB values.
814      This way, all explicit calculations use current-time-step OB values
815       (simpler and more consistent).
816      Affects results when set-up uses time-varying OBC and multi-dim advection;
817       update output of experiment seaice_obcs.
818    o pkg/seaice:
819      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
820       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
821         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
822      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
823       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
824       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
825    o pkg aim (2010/10/26):
826      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
827        formulation with obliquity, eccentricity, ... as run-time parameters,
828      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
829        upward shortwave radition at the surface (all-sky and clear-sky).
830    o pkg/obcs:
831      - writing sections with globalFiles=T does not work: switch to tiled-files
832        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
833      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
834      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
835    
836    checkpoint62m (2010/10/21)
837    o pkg/seaice: vectorize seaice_solve4temp.F
838      - move iterations loops outside of i/j-loops
839      - requires 2D arrays for TB and effConduct
840      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
841        modified in this routine
842      - a little bit of clean up, adjusting indentation, etc.
843      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
844        performance and '**TWO' by '**2' (because TWO is a float),
845        replaced ONE, ZERO
846    o eesupp/src:
847       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
848    o pkg/seaice/seaice_growth.F
849      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
850      merging process. The merged routine has two branches, and one activates the 'evolution'
851      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
852      In summary, here is what the '10/10 revision' did consist of
853        part 1: seaice_growth.F revisions 1.71 to 1.75
854          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
855            The emphasis here was on improving readability (e.g. by trying to use meaningful
856            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
857        part 1.5:
858          - revising the lab_sea experiment to make it a more useful (i.e. stable
859            and representative of an actual model run). This was done by generating a
860            (winter) pickup to start from, switching back the main experiment dynamic
861            solver from evp to lsr, having one of the experiments use the free drift solution.
862        part 2: seaice_growth.F revisions 1.76 to 1.85
863          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
864          - Sorting out the various fields units and sign (set early on and reset at the end)
865            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
866            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
867          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
868            and simplifying logical expressions to further improve readibility.
869        part 3: seaice_growth.F revisions 1.86 to 1.89
870          - Re-organize the blocks of code more logically.
871          - Merging the '_if.F' pieces that add something new.
872    o pkg/thsice:
873      - vectorize thsice_solve4temp and thsice_get_exf.
874        Problem: thsice_solve4temp has an unvectorizable statement that
875        might also be problematic for TAF
876      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
877        does not change the verifcation experiment, but will change all
878        experiments that have this flag undefined (not tested in verification);
879        a little reorganization to save a few 2D fields and recomputations
880      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
881      - 2nd step:  fix some store dirs
882        o seems to work somewhat, i.e. using ifort but not g77
883        o likely cause are incomplete init. or recomputation
884        o start verification/global_ocean.cs32x15/input_ad.thsice
885    o pkg/obcs: add support for exch2
886      - the position of the boundary and prescribed values are specified using
887        a global domain with exch2 facets stacked
888        - in x for N,S boundaries (like W2_mapIO=-1)
889        - in y for E,W boundaries (so E,W boundaries do not overlap)
890    o pkg/mdsio: add support for writing global sections with exch2
891        file layout is as for obcs described above:
892        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
893        - for y-z sections, facets are stacked in y
894    o pkg/thsice:
895       - change a few routines for better vectorization: thsice_albedo.F,
896         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
897         not affected, but in particular the latter routine has changed
898         dramatically (not necessarily easier to read now).
899       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
900       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
901    o verification/lab_sea:
902      - overhaul of the forward model experiments. The main motivation
903        for this revision is that lab_sea has proven quite fragile (when
904        changing the sea-ice code, and switching platforms) to a point
905        when failures were very hard to attribute to specific code problems.
906      - the suspected reason for this fragility is noise amplification by evp so,
907        to start with, we decided to replace evp with lsr in the main experiment.
908      - the input.lsr experiment thus became obsolete and was removed.
909      - it was replaced with the input.fd experiment that uses an
910        analytical "free drift" solution as the ice velocity field.
911      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
912        will hopefully allow us to discriminate problems due to dynamic solvers
913        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
914        us to test additional options, along with the salt plume package.
915      - Finally a pickup was generated (at the end of a one year run) to
916        make the tests more representative of an actual model run. Previously
917        the tests starting point was a 1m thickness of ice everywhere.
918    o pkg/seaice:
919      - introducing S\R seaice_freedrift.F that compute the
920        analytical solution to an approximate ice momentum
921        equation (i.e. the simple stress/coriolis balance).
922      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
923        of the free drift velocity field, and enable its use.
924        To actually use the free drift solution as the model ice
925        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
926    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
927    
928    checkpoint62l (2010/10/04)
929    o pkg/seaice:
930      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
931      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
932       version (with USE_ORIGINAL_SBI undef);
933    o add hooks for new packages OASIS, the package will follow
934      (hooks exclude the seaice pkg for now)
935    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
936      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
937      rather than mdsio_readvector.F/mdsio_writevector.F, within
938      adread_adwrite.F to read/write adjoint-related tapes to disk.
939    o eesupp and pkg/mdsio: ALLOW_WHIO
940      Option to write/read 2D fields to files including tiles halos.
941      The main purpose is for adjoint related "tape I/O".
942      The secondary purpose is for debugging phases.
943      A word on those rather specifically intended purposes.
944      The code was meant to be stripped down to the bare minimum.
945      Typically, there is a unique and basic mapping to the global
946      buffer (tile by tile, then proc by proc, then level by level), and
947      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
948      meant to generate user friendly outputs of various shapes and forms.
949      Rather it is intended, for the knowledgeabale developers,
950      to be largely independent of the many mdsio options, to allow
951      outputs of tiles+halos in debugging phases and in adjoint runs,
952      and to allow some flexibility in tuning (adoint) I/O depending on each
953      file system behavior. With regard to tuning, most of the potential knobs
954      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
955      to specify directories, to specify the typical size of I/O calls, etc.)
956      are not yet included, and will be added if they prove useful.
957    o pkg/seaice:
958       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
959    o pkg/seaice:
960       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
961       code (seaice_budget_ice_if.F) which enable to recover old standard
962       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
963       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
964    o model/src (rStar):
965       use simple average (not area weighted) of rStarFac at U,V point when using
966       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
967       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
968    
969    checkpoint62k (2010/09/17)
970    o adjoint
971       * changed verification/global_ocean.cs32x15 ; adjoint now tests
972         Adams-Bashforth 3 + NLFS + RSTAR
973       * some more modifs required for ECCO-GODAE v4
974    o pkg/seaice
975       add SEAICE_AGE_VOL option to use volume instead of area for
976       integrating SEAICE_AGE
977  o model/src:  o model/src:
978     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
979     non-linear free-surface parts ; but pressure-gradient not yet coded.     non-linear free-surface parts ; but pressure-gradient not yet coded.
# Line 273  o tools/build_options: Line 1243  o tools/build_options:
1243      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1244  o pkg/ecco  o pkg/ecco
1245    - allow user defined cost function contributions    - allow user defined cost function contributions
1246          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1247          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1248    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1249        the two options are complementary.        the two options are complementary.
1250  o pkg/smooth  o pkg/smooth
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