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revision 1.1290 by gforget, Fri Aug 6 18:45:41 2010 UTC revision 1.1478 by mlosch, Thu Jul 21 13:45:55 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: small changes that permit vectorizable
8      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
9      and should be avoided where possible.
10    o model/src (rStar):
11      - include r* effect on reference-state (PhiRef) in totPhiHyd
12        (so that it's really the potential anomaly at the cell center);
13        affect solution only if z* with full pressure in EOS.
14      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
15        update output (because of z* in totPhiHyd and viscA4 changes);
16      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
17        @ constant r) until interpolation at constant r is implemented.
18    o pkg/diagnostics
19      - fix RCENTER diagnostics in case cell center is not at interface middle
20    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
21      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
22      that THETA and SALT are "conservative temperature" and "absolute
23      salinity"
24    o pkg/ctrl
25      - fix computation of endrec in s/r ctrl_init_rec
26      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
27    o pkg/seaice/seaice_growth.F
28      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
29        remove then obsolete STORE directives
30      - fix STORE directives for tice and tices, so that only the
31        appropriate part of the fields are stored (and not the entire
32        field); update global_ocean.cs32x15.seaice AD output.
33      - cosmetic changes: adjust CPP flags and indentation for better
34        legibilty
35    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
36      Chris Wilson)
37    o pkg/gmredi:
38       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
39       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
40    
41    checkpoint63 (2011/07/11)
42    o pkg/exch2:
43     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
44     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
45       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
46       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
47    o pkg/diagnostics:
48     - deal with pairs of post-processed diags which are computed together; in
49       particular, re-order list of diags within 1 file to save 2nd computation.
50     - add S/R to compute velocity stream-function (called after velocity-potential
51       calculation) from divergence free transport -> new diagnostics "PsiVEL".
52     - add parameter to select grid-point location where PsiVEL == 0.
53    o eesupp/src:
54       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
55       (specific S/R needed with exch2 topology - for now, just print an error msg)
56    o pkg/shelfice
57     - Implement friction velocity-dependent transfer coefficients following
58       Holland and Jenkins, JPO, 1999
59       Original code by M. Losch with small modifs.
60       Enable with CPP option SHI_ALLOW_GAMMAFRICT
61       and runtime flag SHELFICEuseGammaFrict
62    o verification lab_sea & global_ocean.cs32x15:
63     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
64       does not miss some dependencies (but is slower) and also works with many files
65       (default makedepend limitation for AD built).
66     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
67    o pkg/diagnostics:
68     - add run-time parameter "useMissingValue" (def=False) to fill land-point
69        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
70       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
71     - Extend the use of "missing_value" setting from data.diagnostics for the case
72       of counter-diagnostics (where fraction-weight is zero). This applies both to
73       MNC and MDS output files.
74    o pkg/seaice/seaice_growth.F:
75      - add 'a priori' cap of latent heat flux based on actual mass considerations
76        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
77        non-legacy seaice_solve4temp.
78      - add diagnostic of the residual sublimation freshwater flux (the freshwater
79        flux taken from the ocean if the total actual latent heat fluxes exceed
80        the maximum)
81      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
82       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
83      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
84       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
85      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
86      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
87    o verification 1D_ocean_ice_column:
88       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
89       update results
90    o pkg/diagnostics:
91     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
92       which are not filled-up but computed from other diags ; In this case, the mate
93       diag points to the primary (filled-up) diag to used for post processing.
94     - Update Velocity-potential computation using post-processed diag framework.
95     ==> Change the ordering of fields and time-periods in MDS output file
96       when using periodic averaging: now writes one time record with the full set
97       of fields for this time period, then the next time reccord (it used to be
98       one field with the full set of time records then the next field).
99         Note: this is now similar to NetCDF (MNC) output file. <==
100    
101    checkpoint62z (2011/06/21)
102    o adjoint monitor:
103     - Add adjoint monitor output for packages exf, seaice
104       and update relevant testreport output
105    o pkg/seaice:
106     - re-order diags inits so that they appear in order in available_diagnostics.log
107     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
108       area/heff/hsnow preceeding thermodynamic growth/melt.
109     - modified diag: SIdA; output actual effect, as the description states.
110     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
111     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
112       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
113        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
114     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
115     - added diagnostics for seaice generic tracers (SItr*).
116     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
117     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
118     I. Fenty: 18-Jun-2011:
119     Minor changes to seaice package:
120     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
121        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
122       - Differentiated "regularization variables" from "floor variables"
123        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
124        * hiceMin became SEAICE_hice_reg (old hiceMin)
125          (with _reg meaning regularization variable)
126       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
127        so as to ensure energy conservation when going between phases
128      - A22 was not used anywhere
129     2) Changed regularization procedure for heffActual and hsnowActual to ensure
130        well-boundedness and smooth adjoint in seaice_growth.F
131     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
132        because the old regularization always set heffActual >= 0.05 cm
133     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
134        on AREA when HEFF > 0.
135      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
136        requiring that DISABLE_AREA_FLOOR *not* be defined
137     Affected verifications:
138      - 1D_ocean_ice_column (output.txt output_adm.txt)
139      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
140    o pkg/diagnostics:
141      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
142      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
143        (was _RL, now integer) with option = 0 to retrieve all levels.
144      - add pieces of code to compute velocity potential at each level (new diagnostics
145        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
146        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
147      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
148        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
149        and in diagnostics_fract_fill.F (do not need a valid pointer for the
150        diagnostics counter-mate); check that definition of counter-diagnostic
151        includes a valid counter-mate (in diagnostics_set_levels.F).
152    o model/src (rStar):
153      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
154        affect solution only if z* with full pressure in EOS;
155        update output of test-exp global_ocean.90x40x15.
156    o pkg/seaice:
157      - introduce siEps=1e-5 parameter
158      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
159      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
160      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
161        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
162        as well as ice cover age and ridging index (attached to AREA).
163        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
164        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
165        Up to SItrMaxNum=3 tracers can be used simultaneously.
166    o pkg/salt_plume:
167      -introduce SPsalFRAC run time parameter that sets the fraction of the
168       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
169       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
170    o model debug options:
171      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
172        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
173      - Refine debug-msg printing selection (3 new levels):
174        debugMode  : controls printing of debug messages (sequence of S/R calls).
175        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
176         debLevZero =  0 ; /* level of disabled aux. msg printing */
177         debLevA =  1 ; /* level of minimum  aux. msg printing */
178         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
179         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
180         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
181         debLevE =  5 ; /* level of extensive debug printing */
182        New debugLevel default: with default debugMode value (=F),
183          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
184          and if debugMode=T, default debugLevel = 4 (debLevD).
185        Relation with previous settings:
186         debLevB (=2) corresponds to former debLevA (=1)
187         debLevD (=4) corresponds to former debLevB (=2)
188        Note:
189         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
190         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
191            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
192      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
193        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
194    o pkg/obcs:
195      - change OBCSfixTopo default from True to False (should not change the results);
196        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
197    o pkg/thsice:
198      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
199        2nd layer seaice sublimation (unlikely to happen)
200      - use Interior mask for OBCS in thsice_advection.F (similar to what is
201        done in gad_advection & seaice_advection).
202    o adjoint:
203      bug fix spotted by Gael Forget:
204      seaice_advection and thsice_advection still had
205      legacy CPP options to avoid CS corner updates for adjoint
206    o pkg/seaice:
207      => Change some of the defaults (2011/05/29):
208         - change SEAICEuseFluxForm default (from False to True)
209         - change DIFF1 default (from 0.004 m/s to 0. m/s)
210         And print warnings if DIFF1 is not set in data.seaice and centered
211          avection scheme is used without any diffusion.
212      also:
213      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
214      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
215      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
216        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
217        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
218      update results of test exp.:
219         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
220             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
221             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
222         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
223         seaice_obcs: output (SEAICEuseFluxForm=T)
224      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
225          for standard fwd & AD lab_sea tests (to keep the same output).
226    o pkg/seaice/seaice_growth.F:
227      - use Ian Fenty's capping formulas for actual ice
228      thickness thoughout EVOLUTION branch.
229      - put treatment pathological case #2) in CPP brackets
230      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
231      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
232    o pkg/seaice:
233      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
234      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
235      also pass fac as a param, which can be 1. (to update the tendency
236      field) or the time step (to update the field itself).
237      - seaice_advdiff.F: for multidim, call seaice_diffusion with
238      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
239      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
240      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
241      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
242    o pkg/seaice:
243      diffusion with centered advection scheme (diffus.F & advect.F):
244      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
245        to just compute the laplacian of input-field.
246      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
247      - fix flux-form version in diffus.F to conserve tracer.
248      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
249       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
250    
251    checkpoint62y (2011/05/26)
252    o pkg/seaice:
253     - seaice_growth.F : in EVOLUTION branch, always include
254       a_QSWbyATM_cover in qnet (as it should be).
255     - verification/global_ocean.cs32x15 : update results accordingly
256       (output.seaice.txt output_adm.seaice.txt).
257    o pkg/seaice + obcs:
258     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
259       equivalent of assuming no tracer gradient outside the OB region.
260       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
261     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
262       after changes above);
263     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
264       only at OB location (instead of over a band of OLx width).
265    o pkg/seaice:
266     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
267       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
268    o pkg/obcs:
269      - split header file "OBCS.h" into 4 separated files:
270        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
271       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
272         (contain no conditional statement which depends on OBCS options).
273      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
274        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
275    o ctrl, cost, grdchk & autodiff pkgs:
276      - make options file more standard (like other {PKG}_OPTIONS.h file but
277        with AD_CONFIG.h); clean-up some of the included header files.
278    o pkg/obcs:
279      - do not mask tracer when applying OB (tracer == 0 could generate problems)
280      - apply tracer OB values to tracer field only at OB location (instead of
281        over a band of OLx width)
282      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
283      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
284        obcs_apply_tloc.F & obcs_apply_sloc.F
285    o obcs in model/src:
286      - call OBCS_APPLY_W only if NonHydrostatic.
287      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
288      - reset dEtaHdt and wVel to zero outside OB interior region ;
289      - leave tracer unchanged outside OB interior region: This has no effect
290        on the solution but just to prevent unrealistic tracer value outside OB.
291      - zero out velocity outside OB interior region: This has no effect on
292        the solution but just to prevent unrealistic velocity outside OB.
293    o obcs and non-lin free-surf:
294       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
295       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
296       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
297       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
298       update results of test-exp. exp4(nlfs).
299    o exp4 (nlfs) test-exp:
300       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
301       with NonLin-FreeSurf); update output.nlfs.txt
302    o obcs and 2d/3d solver norm:
303       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
304       and outside OB interior region (will allow to place OB further inside the
305       domain). Depending on the domain, can affects cg2d-Norm (previous
306       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
307       and cg3d-Norm (previous Norm was computed before canceling OB terms),
308       e.g. in tutorial_plume_on_slope.
309      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
310    o pkg rbcs:
311      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
312      - add capability to apply relaxation to horizontal velocity uVel & vVel.
313    o pkg/grdchk: add gradient check for control variable xx_shifwflx
314    o pkg/shelfice/shelfice_init_fixed.F
315      fix CPP-flag combinations
316    o pkg/seaice: Merge iceage code of Pierre Rampal
317      * update/change/correct ice age calculations
318      * add age updates for pathological cases
319      Probably needs more testing...
320    
321    checkpoint62x (2011/05/13)
322    o pkg/mom_vecinv:
323       high-order vorticity scheme: use interior masks (maskInW & S)
324       to zero-out (outside OB) gradient of vorticity.
325    o verification exp.:
326       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
327       hs94.128x64x5 and seaice_obcs ; update results.
328    o pkg/obcs:
329      fix bug in OBeta for YZ sections in obcs_exf_load.F
330    o pkg/ctrl, pkg/shelfice, and optim:
331      - add new control variable xx_shifwflx (fresh water flux underneath ice
332        shelves). This is almost as tedious as obcs-ctrl, because the
333        variables needs its own mask.
334      - add a cost function term that penalizes the deviation of xx_shifwflx
335        from the first guess (zero) in analogy to other control variables
336    o pkg/shelfice:
337      - start basic adjoint
338    o pkg/ctrl:
339      - remove extra 2D field "for good measure" when initializing in
340        ctrl_set_globfld_[xy/xz/yz].F
341      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
342      - improve error messages in ctrl_set_unpack_*
343    o OBC implementation in momentum:
344       use interior masks (maskInC,W & S) in momentum S/R:
345       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
346       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
347       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
348       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
349       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
350        (and also with Leith/Smagorinsky harmonic-viscosity).
351       Update output of experiment dome and exp4 (+nlfs).
352    o exp4 test-exp:
353      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
354        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
355        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
356        time-varying OB at Western-side for wVel (NonHyd); update output.
357      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
358        and biharmonic-viscosity ; also use prescribed time varying OB.
359    o pkg/obcs:
360      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
361    o model/src:
362      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
363      - initialise startTime & nIter0 with unlikely values: allows to set one
364        from the other without ambiguity.
365    o seaice_obcs test-exp.:
366      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
367    o pkg/obcs:
368      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
369        no longer needed with maskInC,W,S in pkg/generic_advdiff.
370    o pkg/seaice:
371      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
372        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
373      - fixed bug in the initialization of sea ice salinity variable HSALT
374        in seaice_init_varia.F  (removed dependence on ICE2WATR)
375    o fizhi-cs test exp.:
376       switch reference output convention for these 2 non-standard test-exp,
377        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
378          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
379       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
380    o model/inc:
381      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
382        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
383    o pkg/seaice:
384      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
385    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
386      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
387        and initial HSALT
388    
389    checkpoint62w (2011/04/26)
390    o pkg/mom_fluxform:
391      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
392      - use parameter "sideDragFactor" in no-slip BC side-drag part.
393      - update output of exp. global_ocean.90x40x15
394    o pkg/mom_vecinv:
395      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
396    o update seaice exp.:
397      use more consistent parameter values (remove "backward compatability only":
398       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
399      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
400       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
401    o update test-exp global_ocean.90x40x15:
402      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
403      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
404      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
405      o turn on zStar & viscA4 in standard set-up (dir input/)
406        and update output files: output.txt & output.dwnslp.txt
407    o new AD-test experiment: obcs_ctrl
408      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
409    o pkg/dic:
410      fix two bugs in handling water vapour pressure in carbonate chemistry
411      and air-sea fluxes. Found by Val Bennington and Galen McKinley
412      (add DIC Option = WATERVAP_BUG to recover old results)
413      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
414    o adding allowInteriorFreezing option to check for water below freezing point
415      at depth and bring the negative heat anomaly to the surface level
416    o pkgs _fields_load:
417      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
418      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
419        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
420        rbcs to get interpolation weights and time reccord number.
421      - fix multi-threading in aim_fields_load.F
422      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
423    o external_fields_load:
424      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
425       interpolation weights) to use in a periodic time-series ; do not divide by
426       time-step to convert to integer:
427       - this fixes case where externForcingPeriod is not multiple of time-step
428          (Thanks to Christopher L. Wolfe)
429       - this fixes case where externForcingPeriod is an odd multiple of time-step
430         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
431      store index of time-record which is currently loaded:
432       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
433       - needed for the adjoint but not yet used because of extensive recomputations;
434         (to be fixed soon)
435    
436    checkpoint62v (2011/04/02)
437    o verification/1D_ocean_ice_column added to test Ian Fenty's
438      pkg/seaice_growth.F modifications for improving sea ice code differentiability
439    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
440      (new velocity statistics after changing maskInW & maskInS definition)
441    o pkg/generic_advdiff with OBCS:
442      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
443      equivalent to assumption of no tracer gradient outside the OB region.
444      This will affect the results if using obcs+biharmonic diffusion.
445      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
446    o pkg/obcs:
447      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
448      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
449      in Interior region. No impact on solution but affects Velocity monitor stats.
450    o pkg/ptracers (adjoint)
451      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
452      tape file for each tracer
453    o model/inc/src and pkg/autodiff: add parameters that allow to turn
454      of parts of the adjoint code at run time. For now, there are only
455      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
456      parameters are set in data.pkg.
457      This is the lazy coward's version of doing this, but still useful for
458      debugging. In order to do it right, everything needs to be moved to
459      pkg/autodiff.
460    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
461      the end; this fixes the adjoint balancing code for open boundaries.
462    o pkg/ctrl:
463      - change behavior of xx_${varname}period to be analogous to exf-conventions:
464        xx_${varname}period =   0.,  means time-independent control part
465        xx_${varname}period = -12., means one-year-periodic monthly control part
466      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
467        clean up ctrl_init a little, remove unused variables
468      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
469      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
470    
471    checkpoint62u (2011/03/15)
472    o model/src:
473      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
474        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
475      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
476        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
477    o pkg/ctrl/obcs/ecco:
478      - remove obsolete, unused, and partially broken code:
479        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
480        ALLOW_CTRL_OBCS_BALANCE
481      - put a stop statement into ecco/cost_obcsvol.F, but also add
482        cost_obcsvol to ecco_ad_diff.list
483    o pkg/ecco: fix counting cost function contributions for obcs (code
484      by Matt M.) and diffkr for diagnostics
485    o pkg/ecco, pkg/ctrl, pkg/grdchk:
486      add cost penalty terms for initial uvel, vvel, eta controls
487      and I/O for prior error files
488    o pkg/mdsio:
489       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
490       (new argument) to check for tiled file in mdsioLocalDir : this fix the
491       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
492    o pkg/ctrl:
493     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
494       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
495       unused and superfluous variables
496     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
497    o pkg/ecco
498     - enable adjoint of Stevens OB
499    o pkg/ctrl/ecco/grdchk:
500      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
501        Fortunately, we do not have any tests for the numerous cpp-flagged
502        option of "obcs as control parameters" so we will never know
503        if this is an improvement (but at least now things compile).
504      - remove an obsolete initialization from ecco_cost_init_barfiles.F
505      - fix some problems within never used ifdefs to make the code compile
506    o pkg/obcs:
507     - Refine Interior mask definition to work with more complex OB (e.g.
508       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
509       read in Interior mask from file. Check if Interior mask is consistent
510       with OB list of indices.
511    o pkg/seaice
512     - beginning code for a seaice tracer package,
513       but currently only used for seaice age: SEAICE_AGE
514       SEAICE_num = 4
515       iTracer = 1: area-weighted ice age
516               = 2: volume-weighted ice age
517               = 3, 4: template for one-year vs. multi-year ice
518       data.seaice has new namelist SEAICE_PARM03 for arrays related to
519       SEAICE_num
520    
521    checkpoint62t (2011/03/05)
522    o pkg/obcs:
523     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
524       then normal component. This ensures that the normal component is set
525       correctly even when it conficts with tangential setting from an other OB.
526       Affects results of test-experiment seaice_obcs: update the output.txt
527    o pkg/obcs:
528     - add code to monitor statistics of dynamical fields at OB.
529     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
530       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
531       - change default: balance the Net inflow through all OB (instead of balancing
532         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
533     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
534       to match Nortern OB inflow (OBCS_balanceFacN=0).
535    o pkg/seaice:
536     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
537    o pkg/seaice (seaice_growth v 1.113):
538     - reverting seaice_growth to v 1.111 in order to have code with exact bit
539       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
540       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
541       runtime flag SEAICEareaFormula is kept but is inactive
542    o model/src:
543     - add new param to scale curvilinear grid distance and area when using
544       a different sphere radius from the grid-files.
545     - test/check multi-threads EXCH applied to local variable (cg2d_x)
546    o adjoint:
547     - enable adjoint of Stevens OB
548     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
549       (a bit delicate because of potentially modified adj. common block structure;
550       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
551    
552    checkpoint62s (2011/02/15)
553    o pkg/seaice (seaice_growth v 1.112):
554     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
555       computing the ice cover tendency from effective thickness tendencies. Include
556       Ian Fenty's formula.
557     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
558       SEAICEareaFormula.
559     - simplify notations for the various d_HEFF/d_AREA terms.
560    o pkg/gmredi:
561     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
562       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
563       add a verification test-run (front_relax.bvp) to test GM_useBVP.
564    o pkg/seaice (seaice_growth v 1.111):
565     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
566     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
567       also melt ice.
568    o pkg/seaice:
569     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
570     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
571    o pkg/cheapaml:
572     - from Nico Wienders: New version of this package.
573    o pkg/flt:
574     - add CPP options to prevent floats to re-enter the opposite side of
575       a periodic domain (default: keep periodicity)
576    o pkg/gmredi:
577     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
578       (needed for multi-dim advection).
579     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
580    o model/src:
581     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
582    o tutorial_tracer_adjsens
583     - extend to NLFS and replace maskC by hFacC
584       (change reference output accordingly)
585    
586    checkpoint62r (2011/01/24)
587    o testreport:
588     - add option -deloutp (-do) to remove output file after successful run
589     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
590       extract exact list of procs from this file ; adjust COMMAND by
591       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
592    o pkg/ecco: replace old ineffective way of penalizing deviations from
593      first guess (of obcs) with code by Matt Mazloff
594    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
595      exf/cal
596      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
597        and handle case of obcs?period == 0
598        Not affected by these changes: There is still an inconsistency in
599        the computation of start/endrec for the obcs variables for ALLOW_CAL
600        defined (see comment by Menemenlis, 7-Mar-2003)
601      - make S/R ctrl_get_gen_rec return something meaningful even if
602        ALLOW_CAL is not defined
603      - ctrl_getobcs?: simplify code so that it does not need to use
604                       S/R exf_swapfields
605    o testreport:
606       allow to test MPI with different number of processors for each experiment:
607       create file "SIZE.h.mpi" in each build dir.
608       Note: update of "-command" argument not yet implemented.
609    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
610      alleviate the need for additional 3D tapes when using
611      the non-inear free surface in the adjoint. This is done
612      by adding an 'update' of hfacc etc. to their current
613      value at the beginning of forward_step.F.
614    o pkg/seaice
615      seaice_lsr: move stress-divergence computations out of outer pseudo-
616      timestepping loop
617    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
618      up, so that the calls of the ctrl_* subroutines are really at the end
619      of the routine.
620    o pkg/gmredi:
621      allow to specify a 2-D horizontal map and a 1-D vertical profil
622      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
623    o pkg/seaice:
624      move lsr iterations from seaice_dynsolver to seaice_lsr.
625    o pkg/seaice:
626      reduce memory footprint of seaice mutldim advection tapes,
627      by using a 2D tape independent of the generic_advdiff ones,
628      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
629    
630    checkpoint62q (2010/12/29)
631    o model/src:
632      - check horizontal grid-spacing for unset or zero/negative values.
633      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
634    o pkg/flt:
635      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
636      - precision of input and output files set according to readBinaryPrec
637        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
638      - initial float position from tiled file was not converted to index space
639        (looks like a bug): fixed to make it similar to initial pos. global file.
640    o global_ocean.cs32x15:
641       change SIZE.h of AD set-up to get same tiling as with MPI.
642       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
643    o model/src:
644       add flag to control printing of domain fields (bathymetry, hFac ...) in
645       ini_mask_etc (call to plot_fieds_xy*).
646    o pkg/thsice:
647       if useEXF, some forcing fields are not valid in overlap: fixed by computing
648       over the interior only + apply EXCH at the end (like with SEAICE advection).
649    o pkg/mdsio:
650      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
651        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
652      - change barrier call for safe multi-threads access to 3-D shared buffer.
653      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
654      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
655        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
656    o pkg/flt:
657      - add fourth-order Runge-Kutta integration
658      - add basic exch2 support (only 1 facet supported so far!)
659    o pkg/mdsio+rw:
660      new S/R to read local (or tile independent) vector (read counterpart of
661       mds_writevec_loc, and front-end write_glvec_rl/rs).
662    o global_ocean.cs32x15: additional input_ad.seaice experiment
663        that uses pkg/seaice rather than pkg/thsice.
664        (using multidim advection for seaice)
665    o towards more F95 syntax for array specification in namelist:
666      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
667        of all verification experiments.
668           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
669          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
670      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
671    o global_ocean.cs32x15: additional input.seaice experiment
672        that uses pkg/seaice rather than pkg/thsice.
673    
674    checkpoint62p (2010/12/17)
675    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
676        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
677    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
678        allow for use of multim. advection in seaice adjoint.
679    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
680      - first attempt to close budgets by taking into account the freshwater
681        flux implied by the sublimation of snow and ice. So far only the
682        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
683        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
684    o eesupp/src:
685      new S/R with new option (NML_EXTENDED_F77) to change array specification
686      from F95 standard to commonly accepted extended F77 form.
687      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
688      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
689      for less tolerant f77 compiler (e.g., pgf77, g77).
690    o globalFiles:
691      commented out in parameter file "data" since it's not safe with MPI
692      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
693      in this case); no longer commented out in restart test (tst_2+2).
694    o add adTapeDir to specify a special directory where adjoint tapes are
695      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
696      and cannot be used together with mdsioLocalDir.
697    o nesting pkgs:
698      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
699      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
700      - add parameter files + utils dir + output from short run on beagle.
701    o pkg/seaice:
702        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
703    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
704      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
705    
706    checkpoint62o (2010/11/25)
707    o pkg/exf:
708      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
709    o pkg/seaice:
710      - seaice_ocean_stress: split a loop for better vectorization of the
711        adjoint code
712      - seaice_growth.F: fix bug in conservation of freshwater connected to
713        capping of heff, put contribution into d_HEFFbyNEG
714      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
715        by something more sensible (parameters that are what their name implies)
716      - change some defaults, so that by default exf-parameters are used for
717        things like rhoAir, cpAir,latent/sensible heat parameters, in order
718        to reproduce the old results, many data.seaice now contain funny values
719        for cpAir and latent heat of sublimation
720    o packages_readparms.F: move exf_readparms up in line so that
721        exf-parameters are visible for other packages (e.g. seaice)
722    o debugMode & debugLevel=2:
723      - differentiate between debugMode & debugLevel=2:
724        debugMode: controls printing of debug messages (sequence of S/R calls).
725        debugLevel: controls printing of algorithm intermediate results and stats.
726      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
727        => allows to print debug-stats without all sequence of call messages.
728      - switch control of debug print from debugLevel to debugMode in many S/R.
729    o pkg/obcs (obcs-sponge):
730        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
731        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
732    o pkg/generic_advdiff:
733      - record overlap minimum size for each advection scheme;
734      - refine criteria on overlap minimum size;
735      - check and stop (in gad_check) if overlap size is too small.
736    o pkg/obcs:
737      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
738        once, in ptracers_implicit.F)
739      - with seaice: remove test on empty file name in obcs_apply_seaice (always
740        apply OB values when tile has OB)
741    o model/src, coriolis setting:
742      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
743        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
744        files (selectCoriMap=3) with any grid.
745      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
746    o pkg/seaice/seaice_growth.F:
747        a few cosmetic changes that reduce the number of lines of code
748    o pkg/obcs: add boundary conditions following Stevens (1990)
749      - the code follows old MOM/NAOSIM code
750      - so far it is only implemented for the eastern and western boundaries
751        and NOT for pTracers
752    o pkg/rbcs:
753      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
754        beginning of the first rbcs forcing period.
755      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
756        offline package, i.e., one file per time, labeled by iteration number;
757        deltaTrbcs sets the timestep with which the data was generated;
758        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
759      - rbcsForcingCycle=0 makes forcing non-cyclic.
760      - make arithmetic safe for negative times and odd forcing periods.
761    
762    checkpoint62n (2010/11/09)
763    o pkg/seaice:
764        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
765    o pkg/obcs:
766       New S/R to copy tracer value from the OB location to narrow band region
767        (width = same as overlap) beyond the OB: preserve OB value (needed for
768        high-order scheme) which were overwritten by EXCH call if in overlap
769        region. Applied to theta, salt, ptracer and advected seaice variables.
770       With seaice: use maskInC in similar way as in gad_advection.F,
771        in seaice_advection.F and advect.F.
772       Update output of experiment seaice_obcs and change exp4 to test OBCS with
773        4th order Adv.Scheme. for pasive salt and ptracer.
774    o tools/genmake2:
775      - when looking for an optfile (not specified), only search for Fortran compiler
776        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
777      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
778        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
779      - set default for CPP to "cpp -traditional -P" (was the case without specifying
780        an optfile, but otherwise default was just "cpp".
781      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
782      - when "CC" is not set in the optfile, look for possible C compiler
783        (instead of just setting CC=cc)
784      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
785        => add a ".F" to ".o" rule for source files with no "#include" (such as
786           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
787      - move gfortran before g77 in list of possible Fortran compiler (consistent
788        with reference compiler switch from g77 to gfortran)
789    o pkg/seaice:
790      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
791        seaice_check that stops the model, when the CPP flag is used.
792      o seaice_growth.F: make capping of ice volume conserving by returning the
793        capped ice as freshwater to EmPmR. This does not change the verification
794        experiments but will change runs where the capping is acutally active
795    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
796      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
797         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
798         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
799    o tools/genmake2:
800      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
801      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
802      - clean previous genmake log files before anything else.
803      - change Makefile to remove testreport log files (*.tr_log) and genmake log
804        files only with "CLEAN" target (instead of "Clean");
805    o pkg/generic_advdiff:
806      Change OBCS in multiDim advection (gad_advection.F):
807       Use maskInC to prevent intermediate update of tracer-field in OB regions,
808       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
809       which were applying future time-step OB values.
810      This way, all explicit calculations use current-time-step OB values
811       (simpler and more consistent).
812      Affects results when set-up uses time-varying OBC and multi-dim advection;
813       update output of experiment seaice_obcs.
814    o pkg/seaice:
815      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
816       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
817         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
818      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
819       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
820       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
821    o pkg aim (2010/10/26):
822      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
823        formulation with obliquity, eccentricity, ... as run-time parameters,
824      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
825        upward shortwave radition at the surface (all-sky and clear-sky).
826    o pkg/obcs:
827      - writing sections with globalFiles=T does not work: switch to tiled-files
828        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
829      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
830      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
831    
832    checkpoint62m (2010/10/21)
833    o pkg/seaice: vectorize seaice_solve4temp.F
834      - move iterations loops outside of i/j-loops
835      - requires 2D arrays for TB and effConduct
836      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
837        modified in this routine
838      - a little bit of clean up, adjusting indentation, etc.
839      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
840        performance and '**TWO' by '**2' (because TWO is a float),
841        replaced ONE, ZERO
842    o eesupp/src:
843       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
844    o pkg/seaice/seaice_growth.F
845      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
846      merging process. The merged routine has two branches, and one activates the 'evolution'
847      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
848      In summary, here is what the '10/10 revision' did consist of
849        part 1: seaice_growth.F revisions 1.71 to 1.75
850          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
851            The emphasis here was on improving readability (e.g. by trying to use meaningful
852            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
853        part 1.5:
854          - revising the lab_sea experiment to make it a more useful (i.e. stable
855            and representative of an actual model run). This was done by generating a
856            (winter) pickup to start from, switching back the main experiment dynamic
857            solver from evp to lsr, having one of the experiments use the free drift solution.
858        part 2: seaice_growth.F revisions 1.76 to 1.85
859          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
860          - Sorting out the various fields units and sign (set early on and reset at the end)
861            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
862            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
863          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
864            and simplifying logical expressions to further improve readibility.
865        part 3: seaice_growth.F revisions 1.86 to 1.89
866          - Re-organize the blocks of code more logically.
867          - Merging the '_if.F' pieces that add something new.
868    o pkg/thsice:
869      - vectorize thsice_solve4temp and thsice_get_exf.
870        Problem: thsice_solve4temp has an unvectorizable statement that
871        might also be problematic for TAF
872      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
873        does not change the verifcation experiment, but will change all
874        experiments that have this flag undefined (not tested in verification);
875        a little reorganization to save a few 2D fields and recomputations
876      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
877      - 2nd step:  fix some store dirs
878        o seems to work somewhat, i.e. using ifort but not g77
879        o likely cause are incomplete init. or recomputation
880        o start verification/global_ocean.cs32x15/input_ad.thsice
881    o pkg/obcs: add support for exch2
882      - the position of the boundary and prescribed values are specified using
883        a global domain with exch2 facets stacked
884        - in x for N,S boundaries (like W2_mapIO=-1)
885        - in y for E,W boundaries (so E,W boundaries do not overlap)
886    o pkg/mdsio: add support for writing global sections with exch2
887        file layout is as for obcs described above:
888        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
889        - for y-z sections, facets are stacked in y
890    o pkg/thsice:
891       - change a few routines for better vectorization: thsice_albedo.F,
892         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
893         not affected, but in particular the latter routine has changed
894         dramatically (not necessarily easier to read now).
895       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
896       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
897    o verification/lab_sea:
898      - overhaul of the forward model experiments. The main motivation
899        for this revision is that lab_sea has proven quite fragile (when
900        changing the sea-ice code, and switching platforms) to a point
901        when failures were very hard to attribute to specific code problems.
902      - the suspected reason for this fragility is noise amplification by evp so,
903        to start with, we decided to replace evp with lsr in the main experiment.
904      - the input.lsr experiment thus became obsolete and was removed.
905      - it was replaced with the input.fd experiment that uses an
906        analytical "free drift" solution as the ice velocity field.
907      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
908        will hopefully allow us to discriminate problems due to dynamic solvers
909        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
910        us to test additional options, along with the salt plume package.
911      - Finally a pickup was generated (at the end of a one year run) to
912        make the tests more representative of an actual model run. Previously
913        the tests starting point was a 1m thickness of ice everywhere.
914    o pkg/seaice:
915      - introducing S\R seaice_freedrift.F that compute the
916        analytical solution to an approximate ice momentum
917        equation (i.e. the simple stress/coriolis balance).
918      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
919        of the free drift velocity field, and enable its use.
920        To actually use the free drift solution as the model ice
921        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
922    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
923    
924    checkpoint62l (2010/10/04)
925    o pkg/seaice:
926      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
927      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
928       version (with USE_ORIGINAL_SBI undef);
929    o add hooks for new packages OASIS, the package will follow
930      (hooks exclude the seaice pkg for now)
931    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
932      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
933      rather than mdsio_readvector.F/mdsio_writevector.F, within
934      adread_adwrite.F to read/write adjoint-related tapes to disk.
935    o eesupp and pkg/mdsio: ALLOW_WHIO
936      Option to write/read 2D fields to files including tiles halos.
937      The main purpose is for adjoint related "tape I/O".
938      The secondary purpose is for debugging phases.
939      A word on those rather specifically intended purposes.
940      The code was meant to be stripped down to the bare minimum.
941      Typically, there is a unique and basic mapping to the global
942      buffer (tile by tile, then proc by proc, then level by level), and
943      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
944      meant to generate user friendly outputs of various shapes and forms.
945      Rather it is intended, for the knowledgeabale developers,
946      to be largely independent of the many mdsio options, to allow
947      outputs of tiles+halos in debugging phases and in adjoint runs,
948      and to allow some flexibility in tuning (adoint) I/O depending on each
949      file system behavior. With regard to tuning, most of the potential knobs
950      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
951      to specify directories, to specify the typical size of I/O calls, etc.)
952      are not yet included, and will be added if they prove useful.
953    o pkg/seaice:
954       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
955    o pkg/seaice:
956       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
957       code (seaice_budget_ice_if.F) which enable to recover old standard
958       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
959       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
960    o model/src (rStar):
961       use simple average (not area weighted) of rStarFac at U,V point when using
962       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
963       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
964    
965    checkpoint62k (2010/09/17)
966    o adjoint
967       * changed verification/global_ocean.cs32x15 ; adjoint now tests
968         Adams-Bashforth 3 + NLFS + RSTAR
969       * some more modifs required for ECCO-GODAE v4
970    o pkg/seaice
971       add SEAICE_AGE_VOL option to use volume instead of area for
972       integrating SEAICE_AGE
973    o model/src:
974       first check-in of sigma & hybrid-sigma coordinate code ; also includes
975       non-linear free-surface parts ; but pressure-gradient not yet coded.
976    o pkg/ptracers:
977       option for ptracer to convert Salt Relax into additional EmP.
978        tested in exp. global_ocean.90x40x15.dwnslp (update output)
979    
980    checkpoint62j (2010/08/25)
981    o pkg/ggl90:
982       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
983    o pkg/dic: car_flux.F, phos_flux.F
984      - reduce number of exp-calls in order to improve performance
985      - clean up a little (replace fields by their macros, etc., fix
986        typo in CPP-flag)
987  o pkg/ggl90: minor changes  o pkg/ggl90: minor changes
988    - GGL90diffKrS was removed --> always use GGL90diffKr    - GGL90diffKrS was removed --> always use GGL90diffKr
989    - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV    - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
990    - hack of mxlMaxFlag=2 --> ensure mixing between first and second level (commented out for now)    - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
991        (commented out for now)
992    - change in max/min operations to ensure that smoothing is ok    - change in max/min operations to ensure that smoothing is ok
993    - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)    - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
994    - always use diffKrNrT as background profile (i.e. never use diffKr field)    - always use diffKrNrT as background profile (i.e. never use diffKr field)
# Line 258  o tools/build_options: Line 1239  o tools/build_options:
1239      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1240  o pkg/ecco  o pkg/ecco
1241    - allow user defined cost function contributions    - allow user defined cost function contributions
1242          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1243          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1244    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1245        the two options are complementary.        the two options are complementary.
1246  o pkg/smooth  o pkg/smooth
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