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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1475 by mlosch, Fri Jul 15 13:02:32 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/seaice/seaice_growth.F
8      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
9        remove then obsolete STORE directives
10      - fix STORE directives for tice and tices, so that only the
11        appropriate part of the fields are stored (and not the entire
12        field)
13      - cosmetic changes: adjust CPP flags and indentation for better
14        legibilty
15    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
16      Chris Wilson)
17    o pkg/gmredi:
18       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
19       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
20    
21    checkpoint63 (2011/07/11)
22    o pkg/exch2:
23     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
24     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
25       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
26       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
27    o pkg/diagnostics:
28     - deal with pairs of post-processed diags which are computed together; in
29       particular, re-order list of diags within 1 file to save 2nd computation.
30     - add S/R to compute velocity stream-function (called after velocity-potential
31       calculation) from divergence free transport -> new diagnostics "PsiVEL".
32     - add parameter to select grid-point location where PsiVEL == 0.
33    o eesupp/src:
34       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
35       (specific S/R needed with exch2 topology - for now, just print an error msg)
36    o pkg/shelfice
37     - Implement friction velocity-dependent transfer coefficients following
38       Holland and Jenkins, JPO, 1999
39       Original code by M. Losch with small modifs.
40       Enable with CPP option SHI_ALLOW_GAMMAFRICT
41       and runtime flag SHELFICEuseGammaFrict
42    o verification lab_sea & global_ocean.cs32x15:
43     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
44       does not miss some dependencies (but is slower) and also works with many files
45       (default makedepend limitation for AD built).
46     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
47    o pkg/diagnostics:
48     - add run-time parameter "useMissingValue" (def=False) to fill land-point
49        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
50       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
51     - Extend the use of "missing_value" setting from data.diagnostics for the case
52       of counter-diagnostics (where fraction-weight is zero). This applies both to
53       MNC and MDS output files.
54    o pkg/seaice/seaice_growth.F:
55      - add 'a priori' cap of latent heat flux based on actual mass considerations
56        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
57        non-legacy seaice_solve4temp.
58      - add diagnostic of the residual sublimation freshwater flux (the freshwater
59        flux taken from the ocean if the total actual latent heat fluxes exceed
60        the maximum)
61      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
62       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
63      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
64       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
65      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
66      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
67    o verification 1D_ocean_ice_column:
68       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
69       update results
70    o pkg/diagnostics:
71     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
72       which are not filled-up but computed from other diags ; In this case, the mate
73       diag points to the primary (filled-up) diag to used for post processing.
74     - Update Velocity-potential computation using post-processed diag framework.
75     ==> Change the ordering of fields and time-periods in MDS output file
76       when using periodic averaging: now writes one time record with the full set
77       of fields for this time period, then the next time reccord (it used to be
78       one field with the full set of time records then the next field).
79         Note: this is now similar to NetCDF (MNC) output file. <==
80    
81    checkpoint62z (2011/06/21)
82    o adjoint monitor:
83     - Add adjoint monitor output for packages exf, seaice
84       and update relevant testreport output
85    o pkg/seaice:
86     - re-order diags inits so that they appear in order in available_diagnostics.log
87     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
88       area/heff/hsnow preceeding thermodynamic growth/melt.
89     - modified diag: SIdA; output actual effect, as the description states.
90     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
91     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
92       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
93        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
94     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
95     - added diagnostics for seaice generic tracers (SItr*).
96     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
97     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
98     I. Fenty: 18-Jun-2011:
99     Minor changes to seaice package:
100     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
101        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
102       - Differentiated "regularization variables" from "floor variables"
103        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
104        * hiceMin became SEAICE_hice_reg (old hiceMin)
105          (with _reg meaning regularization variable)
106       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
107        so as to ensure energy conservation when going between phases
108      - A22 was not used anywhere
109     2) Changed regularization procedure for heffActual and hsnowActual to ensure
110        well-boundedness and smooth adjoint in seaice_growth.F
111     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
112        because the old regularization always set heffActual >= 0.05 cm
113     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
114        on AREA when HEFF > 0.
115      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
116        requiring that DISABLE_AREA_FLOOR *not* be defined
117     Affected verifications:
118      - 1D_ocean_ice_column (output.txt output_adm.txt)
119      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
120    o pkg/diagnostics:
121      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
122      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
123        (was _RL, now integer) with option = 0 to retrieve all levels.
124      - add pieces of code to compute velocity potential at each level (new diagnostics
125        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
126        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
127      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
128        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
129        and in diagnostics_fract_fill.F (do not need a valid pointer for the
130        diagnostics counter-mate); check that definition of counter-diagnostic
131        includes a valid counter-mate (in diagnostics_set_levels.F).
132    o model/src (rStar):
133      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
134        affect solution only if z* with full pressure in EOS;
135        update output of test-exp global_ocean.90x40x15.
136    o pkg/seaice:
137      - introduce siEps=1e-5 parameter
138      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
139      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
140      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
141        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
142        as well as ice cover age and ridging index (attached to AREA).
143        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
144        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
145        Up to SItrMaxNum=3 tracers can be used simultaneously.
146    o pkg/salt_plume:
147      -introduce SPsalFRAC run time parameter that sets the fraction of the
148       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
149       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
150    o model debug options:
151      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
152        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
153      - Refine debug-msg printing selection (3 new levels):
154        debugMode  : controls printing of debug messages (sequence of S/R calls).
155        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
156         debLevZero =  0 ; /* level of disabled aux. msg printing */
157         debLevA =  1 ; /* level of minimum  aux. msg printing */
158         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
159         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
160         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
161         debLevE =  5 ; /* level of extensive debug printing */
162        New debugLevel default: with default debugMode value (=F),
163          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
164          and if debugMode=T, default debugLevel = 4 (debLevD).
165        Relation with previous settings:
166         debLevB (=2) corresponds to former debLevA (=1)
167         debLevD (=4) corresponds to former debLevB (=2)
168        Note:
169         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
170         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
171            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
172      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
173        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
174    o pkg/obcs:
175      - change OBCSfixTopo default from True to False (should not change the results);
176        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
177    o pkg/thsice:
178      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
179        2nd layer seaice sublimation (unlikely to happen)
180      - use Interior mask for OBCS in thsice_advection.F (similar to what is
181        done in gad_advection & seaice_advection).
182    o adjoint:
183      bug fix spotted by Gael Forget:
184      seaice_advection and thsice_advection still had
185      legacy CPP options to avoid CS corner updates for adjoint
186    o pkg/seaice:
187      => Change some of the defaults (2011/05/29):
188         - change SEAICEuseFluxForm default (from False to True)
189         - change DIFF1 default (from 0.004 m/s to 0. m/s)
190         And print warnings if DIFF1 is not set in data.seaice and centered
191          avection scheme is used without any diffusion.
192      also:
193      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
194      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
195      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
196        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
197        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
198      update results of test exp.:
199         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
200             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
201             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
202         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
203         seaice_obcs: output (SEAICEuseFluxForm=T)
204      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
205          for standard fwd & AD lab_sea tests (to keep the same output).
206    o pkg/seaice/seaice_growth.F:
207      - use Ian Fenty's capping formulas for actual ice
208      thickness thoughout EVOLUTION branch.
209      - put treatment pathological case #2) in CPP brackets
210      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
211      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
212    o pkg/seaice:
213      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
214      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
215      also pass fac as a param, which can be 1. (to update the tendency
216      field) or the time step (to update the field itself).
217      - seaice_advdiff.F: for multidim, call seaice_diffusion with
218      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
219      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
220      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
221      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
222    o pkg/seaice:
223      diffusion with centered advection scheme (diffus.F & advect.F):
224      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
225        to just compute the laplacian of input-field.
226      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
227      - fix flux-form version in diffus.F to conserve tracer.
228      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
229       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
230    
231    checkpoint62y (2011/05/26)
232    o pkg/seaice:
233     - seaice_growth.F : in EVOLUTION branch, always include
234       a_QSWbyATM_cover in qnet (as it should be).
235     - verification/global_ocean.cs32x15 : update results accordingly
236       (output.seaice.txt output_adm.seaice.txt).
237    o pkg/seaice + obcs:
238     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
239       equivalent of assuming no tracer gradient outside the OB region.
240       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
241     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
242       after changes above);
243     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
244       only at OB location (instead of over a band of OLx width).
245    o pkg/seaice:
246     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
247       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
248    o pkg/obcs:
249      - split header file "OBCS.h" into 4 separated files:
250        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
251       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
252         (contain no conditional statement which depends on OBCS options).
253      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
254        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
255    o ctrl, cost, grdchk & autodiff pkgs:
256      - make options file more standard (like other {PKG}_OPTIONS.h file but
257        with AD_CONFIG.h); clean-up some of the included header files.
258    o pkg/obcs:
259      - do not mask tracer when applying OB (tracer == 0 could generate problems)
260      - apply tracer OB values to tracer field only at OB location (instead of
261        over a band of OLx width)
262      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
263      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
264        obcs_apply_tloc.F & obcs_apply_sloc.F
265    o obcs in model/src:
266      - call OBCS_APPLY_W only if NonHydrostatic.
267      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
268      - reset dEtaHdt and wVel to zero outside OB interior region ;
269      - leave tracer unchanged outside OB interior region: This has no effect
270        on the solution but just to prevent unrealistic tracer value outside OB.
271      - zero out velocity outside OB interior region: This has no effect on
272        the solution but just to prevent unrealistic velocity outside OB.
273    o obcs and non-lin free-surf:
274       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
275       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
276       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
277       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
278       update results of test-exp. exp4(nlfs).
279    o exp4 (nlfs) test-exp:
280       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
281       with NonLin-FreeSurf); update output.nlfs.txt
282    o obcs and 2d/3d solver norm:
283       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
284       and outside OB interior region (will allow to place OB further inside the
285       domain). Depending on the domain, can affects cg2d-Norm (previous
286       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
287       and cg3d-Norm (previous Norm was computed before canceling OB terms),
288       e.g. in tutorial_plume_on_slope.
289      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
290    o pkg rbcs:
291      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
292      - add capability to apply relaxation to horizontal velocity uVel & vVel.
293    o pkg/grdchk: add gradient check for control variable xx_shifwflx
294    o pkg/shelfice/shelfice_init_fixed.F
295      fix CPP-flag combinations
296    o pkg/seaice: Merge iceage code of Pierre Rampal
297      * update/change/correct ice age calculations
298      * add age updates for pathological cases
299      Probably needs more testing...
300    
301    checkpoint62x (2011/05/13)
302    o pkg/mom_vecinv:
303       high-order vorticity scheme: use interior masks (maskInW & S)
304       to zero-out (outside OB) gradient of vorticity.
305    o verification exp.:
306       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
307       hs94.128x64x5 and seaice_obcs ; update results.
308    o pkg/obcs:
309      fix bug in OBeta for YZ sections in obcs_exf_load.F
310    o pkg/ctrl, pkg/shelfice, and optim:
311      - add new control variable xx_shifwflx (fresh water flux underneath ice
312        shelves). This is almost as tedious as obcs-ctrl, because the
313        variables needs its own mask.
314      - add a cost function term that penalizes the deviation of xx_shifwflx
315        from the first guess (zero) in analogy to other control variables
316    o pkg/shelfice:
317      - start basic adjoint
318    o pkg/ctrl:
319      - remove extra 2D field "for good measure" when initializing in
320        ctrl_set_globfld_[xy/xz/yz].F
321      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
322      - improve error messages in ctrl_set_unpack_*
323    o OBC implementation in momentum:
324       use interior masks (maskInC,W & S) in momentum S/R:
325       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
326       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
327       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
328       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
329       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
330        (and also with Leith/Smagorinsky harmonic-viscosity).
331       Update output of experiment dome and exp4 (+nlfs).
332    o exp4 test-exp:
333      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
334        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
335        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
336        time-varying OB at Western-side for wVel (NonHyd); update output.
337      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
338        and biharmonic-viscosity ; also use prescribed time varying OB.
339    o pkg/obcs:
340      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
341    o model/src:
342      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
343      - initialise startTime & nIter0 with unlikely values: allows to set one
344        from the other without ambiguity.
345    o seaice_obcs test-exp.:
346      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
347    o pkg/obcs:
348      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
349        no longer needed with maskInC,W,S in pkg/generic_advdiff.
350    o pkg/seaice:
351      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
352        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
353      - fixed bug in the initialization of sea ice salinity variable HSALT
354        in seaice_init_varia.F  (removed dependence on ICE2WATR)
355    o fizhi-cs test exp.:
356       switch reference output convention for these 2 non-standard test-exp,
357        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
358          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
359       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
360    o model/inc:
361      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
362        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
363    o pkg/seaice:
364      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
365    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
366      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
367        and initial HSALT
368    
369    checkpoint62w (2011/04/26)
370    o pkg/mom_fluxform:
371      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
372      - use parameter "sideDragFactor" in no-slip BC side-drag part.
373      - update output of exp. global_ocean.90x40x15
374    o pkg/mom_vecinv:
375      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
376    o update seaice exp.:
377      use more consistent parameter values (remove "backward compatability only":
378       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
379      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
380       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
381    o update test-exp global_ocean.90x40x15:
382      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
383      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
384      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
385      o turn on zStar & viscA4 in standard set-up (dir input/)
386        and update output files: output.txt & output.dwnslp.txt
387    o new AD-test experiment: obcs_ctrl
388      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
389    o pkg/dic:
390      fix two bugs in handling water vapour pressure in carbonate chemistry
391      and air-sea fluxes. Found by Val Bennington and Galen McKinley
392      (add DIC Option = WATERVAP_BUG to recover old results)
393      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
394    o adding allowInteriorFreezing option to check for water below freezing point
395      at depth and bring the negative heat anomaly to the surface level
396    o pkgs _fields_load:
397      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
398      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
399        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
400        rbcs to get interpolation weights and time reccord number.
401      - fix multi-threading in aim_fields_load.F
402      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
403    o external_fields_load:
404      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
405       interpolation weights) to use in a periodic time-series ; do not divide by
406       time-step to convert to integer:
407       - this fixes case where externForcingPeriod is not multiple of time-step
408          (Thanks to Christopher L. Wolfe)
409       - this fixes case where externForcingPeriod is an odd multiple of time-step
410         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
411      store index of time-record which is currently loaded:
412       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
413       - needed for the adjoint but not yet used because of extensive recomputations;
414         (to be fixed soon)
415    
416    checkpoint62v (2011/04/02)
417    o verification/1D_ocean_ice_column added to test Ian Fenty's
418      pkg/seaice_growth.F modifications for improving sea ice code differentiability
419    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
420      (new velocity statistics after changing maskInW & maskInS definition)
421    o pkg/generic_advdiff with OBCS:
422      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
423      equivalent to assumption of no tracer gradient outside the OB region.
424      This will affect the results if using obcs+biharmonic diffusion.
425      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
426    o pkg/obcs:
427      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
428      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
429      in Interior region. No impact on solution but affects Velocity monitor stats.
430    o pkg/ptracers (adjoint)
431      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
432      tape file for each tracer
433    o model/inc/src and pkg/autodiff: add parameters that allow to turn
434      of parts of the adjoint code at run time. For now, there are only
435      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
436      parameters are set in data.pkg.
437      This is the lazy coward's version of doing this, but still useful for
438      debugging. In order to do it right, everything needs to be moved to
439      pkg/autodiff.
440    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
441      the end; this fixes the adjoint balancing code for open boundaries.
442    o pkg/ctrl:
443      - change behavior of xx_${varname}period to be analogous to exf-conventions:
444        xx_${varname}period =   0.,  means time-independent control part
445        xx_${varname}period = -12., means one-year-periodic monthly control part
446      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
447        clean up ctrl_init a little, remove unused variables
448      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
449      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
450    
451    checkpoint62u (2011/03/15)
452    o model/src:
453      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
454        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
455      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
456        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
457    o pkg/ctrl/obcs/ecco:
458      - remove obsolete, unused, and partially broken code:
459        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
460        ALLOW_CTRL_OBCS_BALANCE
461      - put a stop statement into ecco/cost_obcsvol.F, but also add
462        cost_obcsvol to ecco_ad_diff.list
463    o pkg/ecco: fix counting cost function contributions for obcs (code
464      by Matt M.) and diffkr for diagnostics
465    o pkg/ecco, pkg/ctrl, pkg/grdchk:
466      add cost penalty terms for initial uvel, vvel, eta controls
467      and I/O for prior error files
468    o pkg/mdsio:
469       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
470       (new argument) to check for tiled file in mdsioLocalDir : this fix the
471       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
472    o pkg/ctrl:
473     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
474       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
475       unused and superfluous variables
476     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
477    o pkg/ecco
478     - enable adjoint of Stevens OB
479    o pkg/ctrl/ecco/grdchk:
480      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
481        Fortunately, we do not have any tests for the numerous cpp-flagged
482        option of "obcs as control parameters" so we will never know
483        if this is an improvement (but at least now things compile).
484      - remove an obsolete initialization from ecco_cost_init_barfiles.F
485      - fix some problems within never used ifdefs to make the code compile
486    o pkg/obcs:
487     - Refine Interior mask definition to work with more complex OB (e.g.
488       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
489       read in Interior mask from file. Check if Interior mask is consistent
490       with OB list of indices.
491    o pkg/seaice
492     - beginning code for a seaice tracer package,
493       but currently only used for seaice age: SEAICE_AGE
494       SEAICE_num = 4
495       iTracer = 1: area-weighted ice age
496               = 2: volume-weighted ice age
497               = 3, 4: template for one-year vs. multi-year ice
498       data.seaice has new namelist SEAICE_PARM03 for arrays related to
499       SEAICE_num
500    
501    checkpoint62t (2011/03/05)
502    o pkg/obcs:
503     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
504       then normal component. This ensures that the normal component is set
505       correctly even when it conficts with tangential setting from an other OB.
506       Affects results of test-experiment seaice_obcs: update the output.txt
507    o pkg/obcs:
508     - add code to monitor statistics of dynamical fields at OB.
509     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
510       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
511       - change default: balance the Net inflow through all OB (instead of balancing
512         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
513     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
514       to match Nortern OB inflow (OBCS_balanceFacN=0).
515    o pkg/seaice:
516     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
517    o pkg/seaice (seaice_growth v 1.113):
518     - reverting seaice_growth to v 1.111 in order to have code with exact bit
519       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
520       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
521       runtime flag SEAICEareaFormula is kept but is inactive
522    o model/src:
523     - add new param to scale curvilinear grid distance and area when using
524       a different sphere radius from the grid-files.
525     - test/check multi-threads EXCH applied to local variable (cg2d_x)
526    o adjoint:
527     - enable adjoint of Stevens OB
528     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
529       (a bit delicate because of potentially modified adj. common block structure;
530       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
531    
532    checkpoint62s (2011/02/15)
533    o pkg/seaice (seaice_growth v 1.112):
534     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
535       computing the ice cover tendency from effective thickness tendencies. Include
536       Ian Fenty's formula.
537     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
538       SEAICEareaFormula.
539     - simplify notations for the various d_HEFF/d_AREA terms.
540    o pkg/gmredi:
541     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
542       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
543       add a verification test-run (front_relax.bvp) to test GM_useBVP.
544    o pkg/seaice (seaice_growth v 1.111):
545     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
546     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
547       also melt ice.
548    o pkg/seaice:
549     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
550     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
551    o pkg/cheapaml:
552     - from Nico Wienders: New version of this package.
553    o pkg/flt:
554     - add CPP options to prevent floats to re-enter the opposite side of
555       a periodic domain (default: keep periodicity)
556    o pkg/gmredi:
557     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
558       (needed for multi-dim advection).
559     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
560    o model/src:
561     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
562    o tutorial_tracer_adjsens
563     - extend to NLFS and replace maskC by hFacC
564       (change reference output accordingly)
565    
566    checkpoint62r (2011/01/24)
567    o testreport:
568     - add option -deloutp (-do) to remove output file after successful run
569     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
570       extract exact list of procs from this file ; adjust COMMAND by
571       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
572    o pkg/ecco: replace old ineffective way of penalizing deviations from
573      first guess (of obcs) with code by Matt Mazloff
574    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
575      exf/cal
576      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
577        and handle case of obcs?period == 0
578        Not affected by these changes: There is still an inconsistency in
579        the computation of start/endrec for the obcs variables for ALLOW_CAL
580        defined (see comment by Menemenlis, 7-Mar-2003)
581      - make S/R ctrl_get_gen_rec return something meaningful even if
582        ALLOW_CAL is not defined
583      - ctrl_getobcs?: simplify code so that it does not need to use
584                       S/R exf_swapfields
585    o testreport:
586       allow to test MPI with different number of processors for each experiment:
587       create file "SIZE.h.mpi" in each build dir.
588       Note: update of "-command" argument not yet implemented.
589    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
590      alleviate the need for additional 3D tapes when using
591      the non-inear free surface in the adjoint. This is done
592      by adding an 'update' of hfacc etc. to their current
593      value at the beginning of forward_step.F.
594    o pkg/seaice
595      seaice_lsr: move stress-divergence computations out of outer pseudo-
596      timestepping loop
597    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
598      up, so that the calls of the ctrl_* subroutines are really at the end
599      of the routine.
600    o pkg/gmredi:
601      allow to specify a 2-D horizontal map and a 1-D vertical profil
602      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
603    o pkg/seaice:
604      move lsr iterations from seaice_dynsolver to seaice_lsr.
605    o pkg/seaice:
606      reduce memory footprint of seaice mutldim advection tapes,
607      by using a 2D tape independent of the generic_advdiff ones,
608      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
609    
610    checkpoint62q (2010/12/29)
611    o model/src:
612      - check horizontal grid-spacing for unset or zero/negative values.
613      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
614    o pkg/flt:
615      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
616      - precision of input and output files set according to readBinaryPrec
617        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
618      - initial float position from tiled file was not converted to index space
619        (looks like a bug): fixed to make it similar to initial pos. global file.
620    o global_ocean.cs32x15:
621       change SIZE.h of AD set-up to get same tiling as with MPI.
622       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
623    o model/src:
624       add flag to control printing of domain fields (bathymetry, hFac ...) in
625       ini_mask_etc (call to plot_fieds_xy*).
626    o pkg/thsice:
627       if useEXF, some forcing fields are not valid in overlap: fixed by computing
628       over the interior only + apply EXCH at the end (like with SEAICE advection).
629    o pkg/mdsio:
630      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
631        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
632      - change barrier call for safe multi-threads access to 3-D shared buffer.
633      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
634      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
635        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
636    o pkg/flt:
637      - add fourth-order Runge-Kutta integration
638      - add basic exch2 support (only 1 facet supported so far!)
639    o pkg/mdsio+rw:
640      new S/R to read local (or tile independent) vector (read counterpart of
641       mds_writevec_loc, and front-end write_glvec_rl/rs).
642    o global_ocean.cs32x15: additional input_ad.seaice experiment
643        that uses pkg/seaice rather than pkg/thsice.
644        (using multidim advection for seaice)
645    o towards more F95 syntax for array specification in namelist:
646      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
647        of all verification experiments.
648           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
649          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
650      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
651    o global_ocean.cs32x15: additional input.seaice experiment
652        that uses pkg/seaice rather than pkg/thsice.
653    
654    checkpoint62p (2010/12/17)
655    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
656        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
657    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
658        allow for use of multim. advection in seaice adjoint.
659    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
660      - first attempt to close budgets by taking into account the freshwater
661        flux implied by the sublimation of snow and ice. So far only the
662        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
663        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
664    o eesupp/src:
665      new S/R with new option (NML_EXTENDED_F77) to change array specification
666      from F95 standard to commonly accepted extended F77 form.
667      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
668      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
669      for less tolerant f77 compiler (e.g., pgf77, g77).
670    o globalFiles:
671      commented out in parameter file "data" since it's not safe with MPI
672      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
673      in this case); no longer commented out in restart test (tst_2+2).
674    o add adTapeDir to specify a special directory where adjoint tapes are
675      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
676      and cannot be used together with mdsioLocalDir.
677    o nesting pkgs:
678      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
679      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
680      - add parameter files + utils dir + output from short run on beagle.
681    o pkg/seaice:
682        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
683    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
684      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
685    
686    checkpoint62o (2010/11/25)
687    o pkg/exf:
688      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
689    o pkg/seaice:
690      - seaice_ocean_stress: split a loop for better vectorization of the
691        adjoint code
692      - seaice_growth.F: fix bug in conservation of freshwater connected to
693        capping of heff, put contribution into d_HEFFbyNEG
694      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
695        by something more sensible (parameters that are what their name implies)
696      - change some defaults, so that by default exf-parameters are used for
697        things like rhoAir, cpAir,latent/sensible heat parameters, in order
698        to reproduce the old results, many data.seaice now contain funny values
699        for cpAir and latent heat of sublimation
700    o packages_readparms.F: move exf_readparms up in line so that
701        exf-parameters are visible for other packages (e.g. seaice)
702    o debugMode & debugLevel=2:
703      - differentiate between debugMode & debugLevel=2:
704        debugMode: controls printing of debug messages (sequence of S/R calls).
705        debugLevel: controls printing of algorithm intermediate results and stats.
706      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
707        => allows to print debug-stats without all sequence of call messages.
708      - switch control of debug print from debugLevel to debugMode in many S/R.
709    o pkg/obcs (obcs-sponge):
710        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
711        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
712    o pkg/generic_advdiff:
713      - record overlap minimum size for each advection scheme;
714      - refine criteria on overlap minimum size;
715      - check and stop (in gad_check) if overlap size is too small.
716    o pkg/obcs:
717      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
718        once, in ptracers_implicit.F)
719      - with seaice: remove test on empty file name in obcs_apply_seaice (always
720        apply OB values when tile has OB)
721    o model/src, coriolis setting:
722      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
723        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
724        files (selectCoriMap=3) with any grid.
725      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
726    o pkg/seaice/seaice_growth.F:
727        a few cosmetic changes that reduce the number of lines of code
728    o pkg/obcs: add boundary conditions following Stevens (1990)
729      - the code follows old MOM/NAOSIM code
730      - so far it is only implemented for the eastern and western boundaries
731        and NOT for pTracers
732    o pkg/rbcs:
733      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
734        beginning of the first rbcs forcing period.
735      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
736        offline package, i.e., one file per time, labeled by iteration number;
737        deltaTrbcs sets the timestep with which the data was generated;
738        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
739      - rbcsForcingCycle=0 makes forcing non-cyclic.
740      - make arithmetic safe for negative times and odd forcing periods.
741    
742    checkpoint62n (2010/11/09)
743    o pkg/seaice:
744        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
745    o pkg/obcs:
746       New S/R to copy tracer value from the OB location to narrow band region
747        (width = same as overlap) beyond the OB: preserve OB value (needed for
748        high-order scheme) which were overwritten by EXCH call if in overlap
749        region. Applied to theta, salt, ptracer and advected seaice variables.
750       With seaice: use maskInC in similar way as in gad_advection.F,
751        in seaice_advection.F and advect.F.
752       Update output of experiment seaice_obcs and change exp4 to test OBCS with
753        4th order Adv.Scheme. for pasive salt and ptracer.
754    o tools/genmake2:
755      - when looking for an optfile (not specified), only search for Fortran compiler
756        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
757      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
758        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
759      - set default for CPP to "cpp -traditional -P" (was the case without specifying
760        an optfile, but otherwise default was just "cpp".
761      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
762      - when "CC" is not set in the optfile, look for possible C compiler
763        (instead of just setting CC=cc)
764      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
765        => add a ".F" to ".o" rule for source files with no "#include" (such as
766           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
767      - move gfortran before g77 in list of possible Fortran compiler (consistent
768        with reference compiler switch from g77 to gfortran)
769    o pkg/seaice:
770      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
771        seaice_check that stops the model, when the CPP flag is used.
772      o seaice_growth.F: make capping of ice volume conserving by returning the
773        capped ice as freshwater to EmPmR. This does not change the verification
774        experiments but will change runs where the capping is acutally active
775    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
776      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
777         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
778         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
779    o tools/genmake2:
780      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
781      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
782      - clean previous genmake log files before anything else.
783      - change Makefile to remove testreport log files (*.tr_log) and genmake log
784        files only with "CLEAN" target (instead of "Clean");
785    o pkg/generic_advdiff:
786      Change OBCS in multiDim advection (gad_advection.F):
787       Use maskInC to prevent intermediate update of tracer-field in OB regions,
788       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
789       which were applying future time-step OB values.
790      This way, all explicit calculations use current-time-step OB values
791       (simpler and more consistent).
792      Affects results when set-up uses time-varying OBC and multi-dim advection;
793       update output of experiment seaice_obcs.
794    o pkg/seaice:
795      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
796       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
797         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
798      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
799       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
800       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
801    o pkg aim (2010/10/26):
802      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
803        formulation with obliquity, eccentricity, ... as run-time parameters,
804      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
805        upward shortwave radition at the surface (all-sky and clear-sky).
806    o pkg/obcs:
807      - writing sections with globalFiles=T does not work: switch to tiled-files
808        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
809      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
810      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
811    
812    checkpoint62m (2010/10/21)
813    o pkg/seaice: vectorize seaice_solve4temp.F
814      - move iterations loops outside of i/j-loops
815      - requires 2D arrays for TB and effConduct
816      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
817        modified in this routine
818      - a little bit of clean up, adjusting indentation, etc.
819      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
820        performance and '**TWO' by '**2' (because TWO is a float),
821        replaced ONE, ZERO
822    o eesupp/src:
823       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
824    o pkg/seaice/seaice_growth.F
825      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
826      merging process. The merged routine has two branches, and one activates the 'evolution'
827      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
828      In summary, here is what the '10/10 revision' did consist of
829        part 1: seaice_growth.F revisions 1.71 to 1.75
830          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
831            The emphasis here was on improving readability (e.g. by trying to use meaningful
832            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
833        part 1.5:
834          - revising the lab_sea experiment to make it a more useful (i.e. stable
835            and representative of an actual model run). This was done by generating a
836            (winter) pickup to start from, switching back the main experiment dynamic
837            solver from evp to lsr, having one of the experiments use the free drift solution.
838        part 2: seaice_growth.F revisions 1.76 to 1.85
839          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
840          - Sorting out the various fields units and sign (set early on and reset at the end)
841            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
842            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
843          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
844            and simplifying logical expressions to further improve readibility.
845        part 3: seaice_growth.F revisions 1.86 to 1.89
846          - Re-organize the blocks of code more logically.
847          - Merging the '_if.F' pieces that add something new.
848    o pkg/thsice:
849      - vectorize thsice_solve4temp and thsice_get_exf.
850        Problem: thsice_solve4temp has an unvectorizable statement that
851        might also be problematic for TAF
852      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
853        does not change the verifcation experiment, but will change all
854        experiments that have this flag undefined (not tested in verification);
855        a little reorganization to save a few 2D fields and recomputations
856      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
857      - 2nd step:  fix some store dirs
858        o seems to work somewhat, i.e. using ifort but not g77
859        o likely cause are incomplete init. or recomputation
860        o start verification/global_ocean.cs32x15/input_ad.thsice
861    o pkg/obcs: add support for exch2
862      - the position of the boundary and prescribed values are specified using
863        a global domain with exch2 facets stacked
864        - in x for N,S boundaries (like W2_mapIO=-1)
865        - in y for E,W boundaries (so E,W boundaries do not overlap)
866    o pkg/mdsio: add support for writing global sections with exch2
867        file layout is as for obcs described above:
868        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
869        - for y-z sections, facets are stacked in y
870    o pkg/thsice:
871       - change a few routines for better vectorization: thsice_albedo.F,
872         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
873         not affected, but in particular the latter routine has changed
874         dramatically (not necessarily easier to read now).
875       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
876       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
877    o verification/lab_sea:
878      - overhaul of the forward model experiments. The main motivation
879        for this revision is that lab_sea has proven quite fragile (when
880        changing the sea-ice code, and switching platforms) to a point
881        when failures were very hard to attribute to specific code problems.
882      - the suspected reason for this fragility is noise amplification by evp so,
883        to start with, we decided to replace evp with lsr in the main experiment.
884      - the input.lsr experiment thus became obsolete and was removed.
885      - it was replaced with the input.fd experiment that uses an
886        analytical "free drift" solution as the ice velocity field.
887      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
888        will hopefully allow us to discriminate problems due to dynamic solvers
889        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
890        us to test additional options, along with the salt plume package.
891      - Finally a pickup was generated (at the end of a one year run) to
892        make the tests more representative of an actual model run. Previously
893        the tests starting point was a 1m thickness of ice everywhere.
894    o pkg/seaice:
895      - introducing S\R seaice_freedrift.F that compute the
896        analytical solution to an approximate ice momentum
897        equation (i.e. the simple stress/coriolis balance).
898      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
899        of the free drift velocity field, and enable its use.
900        To actually use the free drift solution as the model ice
901        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
902    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
903    
904    checkpoint62l (2010/10/04)
905    o pkg/seaice:
906      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
907      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
908       version (with USE_ORIGINAL_SBI undef);
909    o add hooks for new packages OASIS, the package will follow
910      (hooks exclude the seaice pkg for now)
911    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
912      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
913      rather than mdsio_readvector.F/mdsio_writevector.F, within
914      adread_adwrite.F to read/write adjoint-related tapes to disk.
915    o eesupp and pkg/mdsio: ALLOW_WHIO
916      Option to write/read 2D fields to files including tiles halos.
917      The main purpose is for adjoint related "tape I/O".
918      The secondary purpose is for debugging phases.
919      A word on those rather specifically intended purposes.
920      The code was meant to be stripped down to the bare minimum.
921      Typically, there is a unique and basic mapping to the global
922      buffer (tile by tile, then proc by proc, then level by level), and
923      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
924      meant to generate user friendly outputs of various shapes and forms.
925      Rather it is intended, for the knowledgeabale developers,
926      to be largely independent of the many mdsio options, to allow
927      outputs of tiles+halos in debugging phases and in adjoint runs,
928      and to allow some flexibility in tuning (adoint) I/O depending on each
929      file system behavior. With regard to tuning, most of the potential knobs
930      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
931      to specify directories, to specify the typical size of I/O calls, etc.)
932      are not yet included, and will be added if they prove useful.
933    o pkg/seaice:
934       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
935    o pkg/seaice:
936       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
937       code (seaice_budget_ice_if.F) which enable to recover old standard
938       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
939       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
940    o model/src (rStar):
941       use simple average (not area weighted) of rStarFac at U,V point when using
942       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
943       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
944    
945    checkpoint62k (2010/09/17)
946    o adjoint
947       * changed verification/global_ocean.cs32x15 ; adjoint now tests
948         Adams-Bashforth 3 + NLFS + RSTAR
949       * some more modifs required for ECCO-GODAE v4
950    o pkg/seaice
951       add SEAICE_AGE_VOL option to use volume instead of area for
952       integrating SEAICE_AGE
953  o model/src:  o model/src:
954     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
955     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 1219  o tools/build_options:
1219      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1220  o pkg/ecco  o pkg/ecco
1221    - allow user defined cost function contributions    - allow user defined cost function contributions
1222          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1223          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1224    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1225        the two options are complementary.        the two options are complementary.
1226  o pkg/smooth  o pkg/smooth
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