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revision 1.1242 by heimbach, Wed Mar 24 21:56:45 2010 UTC revision 1.1465 by gforget, Mon Jun 27 16:00:08 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      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
9       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
10      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
11       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
12      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
13      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
14    o verification 1D_ocean_ice_column:
15       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
16       update results
17    o pkg/diagnostics:
18     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
19       which are not filled-up but computed from other diags ; In this case, the mate
20       diag points to the primary (filled-up) diag to used for post processing.
21     - Update Velocity-potential computation using post-processed diag framework.
22     ==> Change the ordering of fields and time-periods in MDS output file
23       when using periodic averaging: now writes one time record with the full set
24       of fields for this time period, then the next time reccord (it used to be
25       one field with the full set of time records then the next field).
26         Note: this is now similar to NetCDF (MNC) output file. <==
27     - Extend the use of "missing_value" setting from data.diagnostics for the case
28       of counter-diagnostics (where fraction-weight is zero). This applies both to
29       MNC and MDS output files.
30    
31    checkpoint62z (2011/06/21)
32    o adjoint monitor:
33     - Add adjoint monitor output for packages exf, seaice
34       and update relevant testreport output
35    o pkg/seaice:
36     - re-order diags inits so that they appear in order in available_diagnostics.log
37     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
38       area/heff/hsnow preceeding thermodynamic growth/melt.
39     - modified diag: SIdA; output actual effect, as the description states.
40     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
41     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
42       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
43        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
44     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
45     - added diagnostics for seaice generic tracers (SItr*).
46     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
47     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
48     I. Fenty: 18-Jun-2011:
49     Minor changes to seaice package:
50     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
51        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
52       - Differentiated "regularization variables" from "floor variables"
53        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
54        * hiceMin became SEAICE_hice_reg (old hiceMin)
55          (with _reg meaning regularization variable)
56       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
57        so as to ensure energy conservation when going between phases
58      - A22 was not used anywhere
59     2) Changed regularization procedure for heffActual and hsnowActual to ensure
60        well-boundedness and smooth adjoint in seaice_growth.F
61     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
62        because the old regularization always set heffActual >= 0.05 cm
63     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
64        on AREA when HEFF > 0.
65      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
66        requiring that DISABLE_AREA_FLOOR *not* be defined
67     Affected verifications:
68      - 1D_ocean_ice_column (output.txt output_adm.txt)
69      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
70    o pkg/diagnostics:
71      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
72      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
73        (was _RL, now integer) with option = 0 to retrieve all levels.
74      - add pieces of code to compute velocity potential at each level (new diagnostics
75        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
76        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
77      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
78        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
79        and in diagnostics_fract_fill.F (do not need a valid pointer for the
80        diagnostics counter-mate); check that definition of counter-diagnostic
81        includes a valid counter-mate (in diagnostics_set_levels.F).
82    o model/src (rStar):
83      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
84        affect solution only if z* with full pressure in EOS;
85        update output of test-exp global_ocean.90x40x15.
86    o pkg/seaice:
87      - introduce siEps=1e-5 parameter
88      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
89      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
90      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
91        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
92        as well as ice cover age and ridging index (attached to AREA).
93        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
94        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
95        Up to SItrMaxNum=3 tracers can be used simultaneously.
96    o pkg/salt_plume:
97      -introduce SPsalFRAC run time parameter that sets the fraction of the
98       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
99       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
100    o model debug options:
101      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
102        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
103      - Refine debug-msg printing selection (3 new levels):
104        debugMode  : controls printing of debug messages (sequence of S/R calls).
105        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
106         debLevZero =  0 ; /* level of disabled aux. msg printing */
107         debLevA =  1 ; /* level of minimum  aux. msg printing */
108         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
109         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
110         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
111         debLevE =  5 ; /* level of extensive debug printing */
112        New debugLevel default: with default debugMode value (=F),
113          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
114          and if debugMode=T, default debugLevel = 4 (debLevD).
115        Relation with previous settings:
116         debLevB (=2) corresponds to former debLevA (=1)
117         debLevD (=4) corresponds to former debLevB (=2)
118        Note:
119         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
120         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
121            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
122      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
123        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
124    o pkg/obcs:
125      - change OBCSfixTopo default from True to False (should not change the results);
126        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
127    o pkg/thsice:
128      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
129        2nd layer seaice sublimation (unlikely to happen)
130      - use Interior mask for OBCS in thsice_advection.F (similar to what is
131        done in gad_advection & seaice_advection).
132    o adjoint:
133      bug fix spotted by Gael Forget:
134      seaice_advection and thsice_advection still had
135      legacy CPP options to avoid CS corner updates for adjoint
136    o pkg/seaice:
137      => Change some of the defaults (2011/05/29):
138         - change SEAICEuseFluxForm default (from False to True)
139         - change DIFF1 default (from 0.004 m/s to 0. m/s)
140         And print warnings if DIFF1 is not set in data.seaice and centered
141          avection scheme is used without any diffusion.
142      also:
143      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
144      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
145      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
146        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
147        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
148      update results of test exp.:
149         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
150             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
151             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
152         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
153         seaice_obcs: output (SEAICEuseFluxForm=T)
154      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
155          for standard fwd & AD lab_sea tests (to keep the same output).
156    o pkg/seaice/seaice_growth.F:
157      - use Ian Fenty's capping formulas for actual ice
158      thickness thoughout EVOLUTION branch.
159      - put treatment pathological case #2) in CPP brackets
160      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
161      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
162    o pkg/seaice:
163      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
164      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
165      also pass fac as a param, which can be 1. (to update the tendency
166      field) or the time step (to update the field itself).
167      - seaice_advdiff.F: for multidim, call seaice_diffusion with
168      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
169      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
170      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
171      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
172    o pkg/seaice:
173      diffusion with centered advection scheme (diffus.F & advect.F):
174      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
175        to just compute the laplacian of input-field.
176      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
177      - fix flux-form version in diffus.F to conserve tracer.
178      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
179       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
180    
181    checkpoint62y (2011/05/26)
182    o pkg/seaice:
183     - seaice_growth.F : in EVOLUTION branch, always include
184       a_QSWbyATM_cover in qnet (as it should be).
185     - verification/global_ocean.cs32x15 : update results accordingly
186       (output.seaice.txt output_adm.seaice.txt).
187    o pkg/seaice + obcs:
188     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
189       equivalent of assuming no tracer gradient outside the OB region.
190       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
191     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
192       after changes above);
193     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
194       only at OB location (instead of over a band of OLx width).
195    o pkg/seaice:
196     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
197       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
198    o pkg/obcs:
199      - split header file "OBCS.h" into 4 separated files:
200        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
201       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
202         (contain no conditional statement which depends on OBCS options).
203      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
204        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
205    o ctrl, cost, grdchk & autodiff pkgs:
206      - make options file more standard (like other {PKG}_OPTIONS.h file but
207        with AD_CONFIG.h); clean-up some of the included header files.
208    o pkg/obcs:
209      - do not mask tracer when applying OB (tracer == 0 could generate problems)
210      - apply tracer OB values to tracer field only at OB location (instead of
211        over a band of OLx width)
212      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
213      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
214        obcs_apply_tloc.F & obcs_apply_sloc.F
215    o obcs in model/src:
216      - call OBCS_APPLY_W only if NonHydrostatic.
217      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
218      - reset dEtaHdt and wVel to zero outside OB interior region ;
219      - leave tracer unchanged outside OB interior region: This has no effect
220        on the solution but just to prevent unrealistic tracer value outside OB.
221      - zero out velocity outside OB interior region: This has no effect on
222        the solution but just to prevent unrealistic velocity outside OB.
223    o obcs and non-lin free-surf:
224       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
225       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
226       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
227       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
228       update results of test-exp. exp4(nlfs).
229    o exp4 (nlfs) test-exp:
230       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
231       with NonLin-FreeSurf); update output.nlfs.txt
232    o obcs and 2d/3d solver norm:
233       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
234       and outside OB interior region (will allow to place OB further inside the
235       domain). Depending on the domain, can affects cg2d-Norm (previous
236       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
237       and cg3d-Norm (previous Norm was computed before canceling OB terms),
238       e.g. in tutorial_plume_on_slope.
239      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
240    o pkg rbcs:
241      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
242      - add capability to apply relaxation to horizontal velocity uVel & vVel.
243    o pkg/grdchk: add gradient check for control variable xx_shifwflx
244    o pkg/shelfice/shelfice_init_fixed.F
245      fix CPP-flag combinations
246    o pkg/seaice: Merge iceage code of Pierre Rampal
247      * update/change/correct ice age calculations
248      * add age updates for pathological cases
249      Probably needs more testing...
250    
251    checkpoint62x (2011/05/13)
252    o pkg/mom_vecinv:
253       high-order vorticity scheme: use interior masks (maskInW & S)
254       to zero-out (outside OB) gradient of vorticity.
255    o verification exp.:
256       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
257       hs94.128x64x5 and seaice_obcs ; update results.
258    o pkg/obcs:
259      fix bug in OBeta for YZ sections in obcs_exf_load.F
260    o pkg/ctrl, pkg/shelfice, and optim:
261      - add new control variable xx_shifwflx (fresh water flux underneath ice
262        shelves). This is almost as tedious as obcs-ctrl, because the
263        variables needs its own mask.
264      - add a cost function term that penalizes the deviation of xx_shifwflx
265        from the first guess (zero) in analogy to other control variables
266    o pkg/shelfice:
267      - start basic adjoint
268    o pkg/ctrl:
269      - remove extra 2D field "for good measure" when initializing in
270        ctrl_set_globfld_[xy/xz/yz].F
271      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
272      - improve error messages in ctrl_set_unpack_*
273    o OBC implementation in momentum:
274       use interior masks (maskInC,W & S) in momentum S/R:
275       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
276       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
277       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
278       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
279       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
280        (and also with Leith/Smagorinsky harmonic-viscosity).
281       Update output of experiment dome and exp4 (+nlfs).
282    o exp4 test-exp:
283      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
284        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
285        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
286        time-varying OB at Western-side for wVel (NonHyd); update output.
287      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
288        and biharmonic-viscosity ; also use prescribed time varying OB.
289    o pkg/obcs:
290      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
291    o model/src:
292      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
293      - initialise startTime & nIter0 with unlikely values: allows to set one
294        from the other without ambiguity.
295    o seaice_obcs test-exp.:
296      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
297    o pkg/obcs:
298      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
299        no longer needed with maskInC,W,S in pkg/generic_advdiff.
300    o pkg/seaice:
301      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
302        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
303      - fixed bug in the initialization of sea ice salinity variable HSALT
304        in seaice_init_varia.F  (removed dependence on ICE2WATR)
305    o fizhi-cs test exp.:
306       switch reference output convention for these 2 non-standard test-exp,
307        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
308          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
309       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
310    o model/inc:
311      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
312        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
313    o pkg/seaice:
314      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
315    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
316      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
317        and initial HSALT
318    
319    checkpoint62w (2011/04/26)
320    o pkg/mom_fluxform:
321      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
322      - use parameter "sideDragFactor" in no-slip BC side-drag part.
323      - update output of exp. global_ocean.90x40x15
324    o pkg/mom_vecinv:
325      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
326    o update seaice exp.:
327      use more consistent parameter values (remove "backward compatability only":
328       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
329      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
330       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
331    o update test-exp global_ocean.90x40x15:
332      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
333      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
334      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
335      o turn on zStar & viscA4 in standard set-up (dir input/)
336        and update output files: output.txt & output.dwnslp.txt
337    o new AD-test experiment: obcs_ctrl
338      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
339    o pkg/dic:
340      fix two bugs in handling water vapour pressure in carbonate chemistry
341      and air-sea fluxes. Found by Val Bennington and Galen McKinley
342      (add DIC Option = WATERVAP_BUG to recover old results)
343      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
344    o adding allowInteriorFreezing option to check for water below freezing point
345      at depth and bring the negative heat anomaly to the surface level
346    o pkgs _fields_load:
347      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
348      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
349        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
350        rbcs to get interpolation weights and time reccord number.
351      - fix multi-threading in aim_fields_load.F
352      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
353    o external_fields_load:
354      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
355       interpolation weights) to use in a periodic time-series ; do not divide by
356       time-step to convert to integer:
357       - this fixes case where externForcingPeriod is not multiple of time-step
358          (Thanks to Christopher L. Wolfe)
359       - this fixes case where externForcingPeriod is an odd multiple of time-step
360         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
361      store index of time-record which is currently loaded:
362       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
363       - needed for the adjoint but not yet used because of extensive recomputations;
364         (to be fixed soon)
365    
366    checkpoint62v (2011/04/02)
367    o verification/1D_ocean_ice_column added to test Ian Fenty's
368      pkg/seaice_growth.F modifications for improving sea ice code differentiability
369    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
370      (new velocity statistics after changing maskInW & maskInS definition)
371    o pkg/generic_advdiff with OBCS:
372      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
373      equivalent to assumption of no tracer gradient outside the OB region.
374      This will affect the results if using obcs+biharmonic diffusion.
375      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
376    o pkg/obcs:
377      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
378      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
379      in Interior region. No impact on solution but affects Velocity monitor stats.
380    o pkg/ptracers (adjoint)
381      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
382      tape file for each tracer
383    o model/inc/src and pkg/autodiff: add parameters that allow to turn
384      of parts of the adjoint code at run time. For now, there are only
385      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
386      parameters are set in data.pkg.
387      This is the lazy coward's version of doing this, but still useful for
388      debugging. In order to do it right, everything needs to be moved to
389      pkg/autodiff.
390    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
391      the end; this fixes the adjoint balancing code for open boundaries.
392    o pkg/ctrl:
393      - change behavior of xx_${varname}period to be analogous to exf-conventions:
394        xx_${varname}period =   0.,  means time-independent control part
395        xx_${varname}period = -12., means one-year-periodic monthly control part
396      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
397        clean up ctrl_init a little, remove unused variables
398      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
399      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
400    
401    checkpoint62u (2011/03/15)
402    o model/src:
403      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
404        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
405      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
406        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
407    o pkg/ctrl/obcs/ecco:
408      - remove obsolete, unused, and partially broken code:
409        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
410        ALLOW_CTRL_OBCS_BALANCE
411      - put a stop statement into ecco/cost_obcsvol.F, but also add
412        cost_obcsvol to ecco_ad_diff.list
413    o pkg/ecco: fix counting cost function contributions for obcs (code
414      by Matt M.) and diffkr for diagnostics
415    o pkg/ecco, pkg/ctrl, pkg/grdchk:
416      add cost penalty terms for initial uvel, vvel, eta controls
417      and I/O for prior error files
418    o pkg/mdsio:
419       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
420       (new argument) to check for tiled file in mdsioLocalDir : this fix the
421       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
422    o pkg/ctrl:
423     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
424       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
425       unused and superfluous variables
426     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
427    o pkg/ecco
428     - enable adjoint of Stevens OB
429    o pkg/ctrl/ecco/grdchk:
430      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
431        Fortunately, we do not have any tests for the numerous cpp-flagged
432        option of "obcs as control parameters" so we will never know
433        if this is an improvement (but at least now things compile).
434      - remove an obsolete initialization from ecco_cost_init_barfiles.F
435      - fix some problems within never used ifdefs to make the code compile
436    o pkg/obcs:
437     - Refine Interior mask definition to work with more complex OB (e.g.
438       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
439       read in Interior mask from file. Check if Interior mask is consistent
440       with OB list of indices.
441    o pkg/seaice
442     - beginning code for a seaice tracer package,
443       but currently only used for seaice age: SEAICE_AGE
444       SEAICE_num = 4
445       iTracer = 1: area-weighted ice age
446               = 2: volume-weighted ice age
447               = 3, 4: template for one-year vs. multi-year ice
448       data.seaice has new namelist SEAICE_PARM03 for arrays related to
449       SEAICE_num
450    
451    checkpoint62t (2011/03/05)
452    o pkg/obcs:
453     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
454       then normal component. This ensures that the normal component is set
455       correctly even when it conficts with tangential setting from an other OB.
456       Affects results of test-experiment seaice_obcs: update the output.txt
457    o pkg/obcs:
458     - add code to monitor statistics of dynamical fields at OB.
459     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
460       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
461       - change default: balance the Net inflow through all OB (instead of balancing
462         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
463     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
464       to match Nortern OB inflow (OBCS_balanceFacN=0).
465    o pkg/seaice:
466     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
467    o pkg/seaice (seaice_growth v 1.113):
468     - reverting seaice_growth to v 1.111 in order to have code with exact bit
469       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
470       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
471       runtime flag SEAICEareaFormula is kept but is inactive
472    o model/src:
473     - add new param to scale curvilinear grid distance and area when using
474       a different sphere radius from the grid-files.
475     - test/check multi-threads EXCH applied to local variable (cg2d_x)
476    o adjoint:
477     - enable adjoint of Stevens OB
478     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
479       (a bit delicate because of potentially modified adj. common block structure;
480       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
481    
482    checkpoint62s (2011/02/15)
483    o pkg/seaice (seaice_growth v 1.112):
484     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
485       computing the ice cover tendency from effective thickness tendencies. Include
486       Ian Fenty's formula.
487     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
488       SEAICEareaFormula.
489     - simplify notations for the various d_HEFF/d_AREA terms.
490    o pkg/gmredi:
491     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
492       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
493       add a verification test-run (front_relax.bvp) to test GM_useBVP.
494    o pkg/seaice (seaice_growth v 1.111):
495     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
496     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
497       also melt ice.
498    o pkg/seaice:
499     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
500     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
501    o pkg/cheapaml:
502     - from Nico Wienders: New version of this package.
503    o pkg/flt:
504     - add CPP options to prevent floats to re-enter the opposite side of
505       a periodic domain (default: keep periodicity)
506    o pkg/gmredi:
507     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
508       (needed for multi-dim advection).
509     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
510    o model/src:
511     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
512    o tutorial_tracer_adjsens
513     - extend to NLFS and replace maskC by hFacC
514       (change reference output accordingly)
515    
516    checkpoint62r (2011/01/24)
517    o testreport:
518     - add option -deloutp (-do) to remove output file after successful run
519     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
520       extract exact list of procs from this file ; adjust COMMAND by
521       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
522    o pkg/ecco: replace old ineffective way of penalizing deviations from
523      first guess (of obcs) with code by Matt Mazloff
524    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
525      exf/cal
526      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
527        and handle case of obcs?period == 0
528        Not affected by these changes: There is still an inconsistency in
529        the computation of start/endrec for the obcs variables for ALLOW_CAL
530        defined (see comment by Menemenlis, 7-Mar-2003)
531      - make S/R ctrl_get_gen_rec return something meaningful even if
532        ALLOW_CAL is not defined
533      - ctrl_getobcs?: simplify code so that it does not need to use
534                       S/R exf_swapfields
535    o testreport:
536       allow to test MPI with different number of processors for each experiment:
537       create file "SIZE.h.mpi" in each build dir.
538       Note: update of "-command" argument not yet implemented.
539    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
540      alleviate the need for additional 3D tapes when using
541      the non-inear free surface in the adjoint. This is done
542      by adding an 'update' of hfacc etc. to their current
543      value at the beginning of forward_step.F.
544    o pkg/seaice
545      seaice_lsr: move stress-divergence computations out of outer pseudo-
546      timestepping loop
547    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
548      up, so that the calls of the ctrl_* subroutines are really at the end
549      of the routine.
550    o pkg/gmredi:
551      allow to specify a 2-D horizontal map and a 1-D vertical profil
552      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
553    o pkg/seaice:
554      move lsr iterations from seaice_dynsolver to seaice_lsr.
555    o pkg/seaice:
556      reduce memory footprint of seaice mutldim advection tapes,
557      by using a 2D tape independent of the generic_advdiff ones,
558      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
559    
560    checkpoint62q (2010/12/29)
561    o model/src:
562      - check horizontal grid-spacing for unset or zero/negative values.
563      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
564    o pkg/flt:
565      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
566      - precision of input and output files set according to readBinaryPrec
567        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
568      - initial float position from tiled file was not converted to index space
569        (looks like a bug): fixed to make it similar to initial pos. global file.
570    o global_ocean.cs32x15:
571       change SIZE.h of AD set-up to get same tiling as with MPI.
572       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
573    o model/src:
574       add flag to control printing of domain fields (bathymetry, hFac ...) in
575       ini_mask_etc (call to plot_fieds_xy*).
576    o pkg/thsice:
577       if useEXF, some forcing fields are not valid in overlap: fixed by computing
578       over the interior only + apply EXCH at the end (like with SEAICE advection).
579    o pkg/mdsio:
580      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
581        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
582      - change barrier call for safe multi-threads access to 3-D shared buffer.
583      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
584      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
585        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
586    o pkg/flt:
587      - add fourth-order Runge-Kutta integration
588      - add basic exch2 support (only 1 facet supported so far!)
589    o pkg/mdsio+rw:
590      new S/R to read local (or tile independent) vector (read counterpart of
591       mds_writevec_loc, and front-end write_glvec_rl/rs).
592    o global_ocean.cs32x15: additional input_ad.seaice experiment
593        that uses pkg/seaice rather than pkg/thsice.
594        (using multidim advection for seaice)
595    o towards more F95 syntax for array specification in namelist:
596      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
597        of all verification experiments.
598           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
599          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
600      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
601    o global_ocean.cs32x15: additional input.seaice experiment
602        that uses pkg/seaice rather than pkg/thsice.
603    
604    checkpoint62p (2010/12/17)
605    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
606        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
607    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
608        allow for use of multim. advection in seaice adjoint.
609    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
610      - first attempt to close budgets by taking into account the freshwater
611        flux implied by the sublimation of snow and ice. So far only the
612        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
613        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
614    o eesupp/src:
615      new S/R with new option (NML_EXTENDED_F77) to change array specification
616      from F95 standard to commonly accepted extended F77 form.
617      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
618      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
619      for less tolerant f77 compiler (e.g., pgf77, g77).
620    o globalFiles:
621      commented out in parameter file "data" since it's not safe with MPI
622      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
623      in this case); no longer commented out in restart test (tst_2+2).
624    o add adTapeDir to specify a special directory where adjoint tapes are
625      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
626      and cannot be used together with mdsioLocalDir.
627    o nesting pkgs:
628      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
629      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
630      - add parameter files + utils dir + output from short run on beagle.
631    o pkg/seaice:
632        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
633    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
634      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
635    
636    checkpoint62o (2010/11/25)
637    o pkg/exf:
638      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
639    o pkg/seaice:
640      - seaice_ocean_stress: split a loop for better vectorization of the
641        adjoint code
642      - seaice_growth.F: fix bug in conservation of freshwater connected to
643        capping of heff, put contribution into d_HEFFbyNEG
644      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
645        by something more sensible (parameters that are what their name implies)
646      - change some defaults, so that by default exf-parameters are used for
647        things like rhoAir, cpAir,latent/sensible heat parameters, in order
648        to reproduce the old results, many data.seaice now contain funny values
649        for cpAir and latent heat of sublimation
650    o packages_readparms.F: move exf_readparms up in line so that
651        exf-parameters are visible for other packages (e.g. seaice)
652    o debugMode & debugLevel=2:
653      - differentiate between debugMode & debugLevel=2:
654        debugMode: controls printing of debug messages (sequence of S/R calls).
655        debugLevel: controls printing of algorithm intermediate results and stats.
656      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
657        => allows to print debug-stats without all sequence of call messages.
658      - switch control of debug print from debugLevel to debugMode in many S/R.
659    o pkg/obcs (obcs-sponge):
660        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
661        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
662    o pkg/generic_advdiff:
663      - record overlap minimum size for each advection scheme;
664      - refine criteria on overlap minimum size;
665      - check and stop (in gad_check) if overlap size is too small.
666    o pkg/obcs:
667      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
668        once, in ptracers_implicit.F)
669      - with seaice: remove test on empty file name in obcs_apply_seaice (always
670        apply OB values when tile has OB)
671    o model/src, coriolis setting:
672      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
673        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
674        files (selectCoriMap=3) with any grid.
675      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
676    o pkg/seaice/seaice_growth.F:
677        a few cosmetic changes that reduce the number of lines of code
678    o pkg/obcs: add boundary conditions following Stevens (1990)
679      - the code follows old MOM/NAOSIM code
680      - so far it is only implemented for the eastern and western boundaries
681        and NOT for pTracers
682    o pkg/rbcs:
683      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
684        beginning of the first rbcs forcing period.
685      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
686        offline package, i.e., one file per time, labeled by iteration number;
687        deltaTrbcs sets the timestep with which the data was generated;
688        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
689      - rbcsForcingCycle=0 makes forcing non-cyclic.
690      - make arithmetic safe for negative times and odd forcing periods.
691    
692    checkpoint62n (2010/11/09)
693    o pkg/seaice:
694        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
695    o pkg/obcs:
696       New S/R to copy tracer value from the OB location to narrow band region
697        (width = same as overlap) beyond the OB: preserve OB value (needed for
698        high-order scheme) which were overwritten by EXCH call if in overlap
699        region. Applied to theta, salt, ptracer and advected seaice variables.
700       With seaice: use maskInC in similar way as in gad_advection.F,
701        in seaice_advection.F and advect.F.
702       Update output of experiment seaice_obcs and change exp4 to test OBCS with
703        4th order Adv.Scheme. for pasive salt and ptracer.
704    o tools/genmake2:
705      - when looking for an optfile (not specified), only search for Fortran compiler
706        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
707      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
708        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
709      - set default for CPP to "cpp -traditional -P" (was the case without specifying
710        an optfile, but otherwise default was just "cpp".
711      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
712      - when "CC" is not set in the optfile, look for possible C compiler
713        (instead of just setting CC=cc)
714      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
715        => add a ".F" to ".o" rule for source files with no "#include" (such as
716           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
717      - move gfortran before g77 in list of possible Fortran compiler (consistent
718        with reference compiler switch from g77 to gfortran)
719    o pkg/seaice:
720      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
721        seaice_check that stops the model, when the CPP flag is used.
722      o seaice_growth.F: make capping of ice volume conserving by returning the
723        capped ice as freshwater to EmPmR. This does not change the verification
724        experiments but will change runs where the capping is acutally active
725    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
726      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
727         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
728         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
729    o tools/genmake2:
730      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
731      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
732      - clean previous genmake log files before anything else.
733      - change Makefile to remove testreport log files (*.tr_log) and genmake log
734        files only with "CLEAN" target (instead of "Clean");
735    o pkg/generic_advdiff:
736      Change OBCS in multiDim advection (gad_advection.F):
737       Use maskInC to prevent intermediate update of tracer-field in OB regions,
738       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
739       which were applying future time-step OB values.
740      This way, all explicit calculations use current-time-step OB values
741       (simpler and more consistent).
742      Affects results when set-up uses time-varying OBC and multi-dim advection;
743       update output of experiment seaice_obcs.
744    o pkg/seaice:
745      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
746       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
747         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
748      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
749       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
750       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
751    o pkg aim (2010/10/26):
752      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
753        formulation with obliquity, eccentricity, ... as run-time parameters,
754      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
755        upward shortwave radition at the surface (all-sky and clear-sky).
756    o pkg/obcs:
757      - writing sections with globalFiles=T does not work: switch to tiled-files
758        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
759      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
760      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
761    
762    checkpoint62m (2010/10/21)
763    o pkg/seaice: vectorize seaice_solve4temp.F
764      - move iterations loops outside of i/j-loops
765      - requires 2D arrays for TB and effConduct
766      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
767        modified in this routine
768      - a little bit of clean up, adjusting indentation, etc.
769      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
770        performance and '**TWO' by '**2' (because TWO is a float),
771        replaced ONE, ZERO
772    o eesupp/src:
773       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
774    o pkg/seaice/seaice_growth.F
775      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
776      merging process. The merged routine has two branches, and one activates the 'evolution'
777      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
778      In summary, here is what the '10/10 revision' did consist of
779        part 1: seaice_growth.F revisions 1.71 to 1.75
780          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
781            The emphasis here was on improving readability (e.g. by trying to use meaningful
782            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
783        part 1.5:
784          - revising the lab_sea experiment to make it a more useful (i.e. stable
785            and representative of an actual model run). This was done by generating a
786            (winter) pickup to start from, switching back the main experiment dynamic
787            solver from evp to lsr, having one of the experiments use the free drift solution.
788        part 2: seaice_growth.F revisions 1.76 to 1.85
789          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
790          - Sorting out the various fields units and sign (set early on and reset at the end)
791            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
792            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
793          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
794            and simplifying logical expressions to further improve readibility.
795        part 3: seaice_growth.F revisions 1.86 to 1.89
796          - Re-organize the blocks of code more logically.
797          - Merging the '_if.F' pieces that add something new.
798    o pkg/thsice:
799      - vectorize thsice_solve4temp and thsice_get_exf.
800        Problem: thsice_solve4temp has an unvectorizable statement that
801        might also be problematic for TAF
802      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
803        does not change the verifcation experiment, but will change all
804        experiments that have this flag undefined (not tested in verification);
805        a little reorganization to save a few 2D fields and recomputations
806      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
807      - 2nd step:  fix some store dirs
808        o seems to work somewhat, i.e. using ifort but not g77
809        o likely cause are incomplete init. or recomputation
810        o start verification/global_ocean.cs32x15/input_ad.thsice
811    o pkg/obcs: add support for exch2
812      - the position of the boundary and prescribed values are specified using
813        a global domain with exch2 facets stacked
814        - in x for N,S boundaries (like W2_mapIO=-1)
815        - in y for E,W boundaries (so E,W boundaries do not overlap)
816    o pkg/mdsio: add support for writing global sections with exch2
817        file layout is as for obcs described above:
818        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
819        - for y-z sections, facets are stacked in y
820    o pkg/thsice:
821       - change a few routines for better vectorization: thsice_albedo.F,
822         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
823         not affected, but in particular the latter routine has changed
824         dramatically (not necessarily easier to read now).
825       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
826       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
827    o verification/lab_sea:
828      - overhaul of the forward model experiments. The main motivation
829        for this revision is that lab_sea has proven quite fragile (when
830        changing the sea-ice code, and switching platforms) to a point
831        when failures were very hard to attribute to specific code problems.
832      - the suspected reason for this fragility is noise amplification by evp so,
833        to start with, we decided to replace evp with lsr in the main experiment.
834      - the input.lsr experiment thus became obsolete and was removed.
835      - it was replaced with the input.fd experiment that uses an
836        analytical "free drift" solution as the ice velocity field.
837      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
838        will hopefully allow us to discriminate problems due to dynamic solvers
839        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
840        us to test additional options, along with the salt plume package.
841      - Finally a pickup was generated (at the end of a one year run) to
842        make the tests more representative of an actual model run. Previously
843        the tests starting point was a 1m thickness of ice everywhere.
844    o pkg/seaice:
845      - introducing S\R seaice_freedrift.F that compute the
846        analytical solution to an approximate ice momentum
847        equation (i.e. the simple stress/coriolis balance).
848      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
849        of the free drift velocity field, and enable its use.
850        To actually use the free drift solution as the model ice
851        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
852    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
853    
854    checkpoint62l (2010/10/04)
855    o pkg/seaice:
856      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
857      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
858       version (with USE_ORIGINAL_SBI undef);
859    o add hooks for new packages OASIS, the package will follow
860      (hooks exclude the seaice pkg for now)
861    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
862      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
863      rather than mdsio_readvector.F/mdsio_writevector.F, within
864      adread_adwrite.F to read/write adjoint-related tapes to disk.
865    o eesupp and pkg/mdsio: ALLOW_WHIO
866      Option to write/read 2D fields to files including tiles halos.
867      The main purpose is for adjoint related "tape I/O".
868      The secondary purpose is for debugging phases.
869      A word on those rather specifically intended purposes.
870      The code was meant to be stripped down to the bare minimum.
871      Typically, there is a unique and basic mapping to the global
872      buffer (tile by tile, then proc by proc, then level by level), and
873      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
874      meant to generate user friendly outputs of various shapes and forms.
875      Rather it is intended, for the knowledgeabale developers,
876      to be largely independent of the many mdsio options, to allow
877      outputs of tiles+halos in debugging phases and in adjoint runs,
878      and to allow some flexibility in tuning (adoint) I/O depending on each
879      file system behavior. With regard to tuning, most of the potential knobs
880      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
881      to specify directories, to specify the typical size of I/O calls, etc.)
882      are not yet included, and will be added if they prove useful.
883    o pkg/seaice:
884       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
885    o pkg/seaice:
886       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
887       code (seaice_budget_ice_if.F) which enable to recover old standard
888       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
889       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
890    o model/src (rStar):
891       use simple average (not area weighted) of rStarFac at U,V point when using
892       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
893       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
894    
895    checkpoint62k (2010/09/17)
896    o adjoint
897       * changed verification/global_ocean.cs32x15 ; adjoint now tests
898         Adams-Bashforth 3 + NLFS + RSTAR
899       * some more modifs required for ECCO-GODAE v4
900    o pkg/seaice
901       add SEAICE_AGE_VOL option to use volume instead of area for
902       integrating SEAICE_AGE
903    o model/src:
904       first check-in of sigma & hybrid-sigma coordinate code ; also includes
905       non-linear free-surface parts ; but pressure-gradient not yet coded.
906    o pkg/ptracers:
907       option for ptracer to convert Salt Relax into additional EmP.
908        tested in exp. global_ocean.90x40x15.dwnslp (update output)
909    
910    checkpoint62j (2010/08/25)
911    o pkg/ggl90:
912       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
913    o pkg/dic: car_flux.F, phos_flux.F
914      - reduce number of exp-calls in order to improve performance
915      - clean up a little (replace fields by their macros, etc., fix
916        typo in CPP-flag)
917    o pkg/ggl90: minor changes
918      - GGL90diffKrS was removed --> always use GGL90diffKr
919      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
920      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
921        (commented out for now)
922      - change in max/min operations to ensure that smoothing is ok
923      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
924      - always use diffKrNrT as background profile (i.e. never use diffKr field)
925    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
926    o pkg/dic:
927      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
928        vectorization
929      - small bug fix in insol for the unlikely case of a cartesian grid
930      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
931        + now vectorize, which also removes adjoint recomputations;
932        + replace integer maksp1 by _RL maskp1
933        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
934    
935    checkpoint62i (2010/07/21)
936    o pkg/flt:
937      - with OBCS: stop floats which enter the OB region
938    o model/src:
939      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
940        for implicit vertical advection.
941    o pkg/seaice:
942     - account for melting in seaice age evolution.
943     - remove double counting of seaice ridging effect on seaice age.
944    
945    checkpoint62h (2010/06/18)
946    o pkg/exch2:
947     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
948    o tools/genmake2
949      - remove "-pdefault" option: redundant with the use of "packages.conf";
950      - remove file pkg/pkg_default : set the default as a pkg group
951        ("default_pkg_list") defined in pkg/pkg_groups;
952      - fix for case pkg/pkg_depend is missing (was hanging before);
953      - add option "-pgroups" to specify a different pkg_groups than the default.
954    o verification/adjustment.cs-32x32x1:
955       add a "minimal" set-up test (code_min & input_min) which only compiles
956       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
957    o tools/genmake2
958      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
959      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
960    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
961      files are nearly the same anyway.
962      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
963       - redefinition of tau(i,i) (by a factor of ustar)
964       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
965       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
966       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
967       - replace
968         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
969         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
970         by
971         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
972         (changes results)
973       -> exf_bulkformulae v1.22,
974          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
975          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
976                    output.txt 1.63
977           offline_exf_seaice: output.seaicetd.txt 1.7
978           seaice_obcs: output.txt 1.10)
979      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
980       -> exf_bulkformulae v1.23,
981          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
982          and global_ocean.cs32x15.icedyn (only 11 matching digits)
983      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
984    o adjoint of exch-1:
985     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
986       (note: was already like this when using EXCH-2) and remove flow dir
987       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
988     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
989     - update pkg/exch2 diff list.
990    
991    checkpoint62g (2010/05/19)
992    o eesupp/src (exch-1):
993     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
994       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
995       (renamed to exch1_*rx_cube.F).
996     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
997       to call new exch1 S/R ; update Makefile and .cvsignore.
998     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
999       exch2_xy_rx later)
1000      Note: after updating your code, need to run "make clean" in eesupp/src
1001    o test experiment bottom_ctrl_5x5:
1002       new output_adm.txt with fewer grdchk & less monitor output.
1003    o model/src:
1004      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1005       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1006       beeing treated in the same way (ini_grid is not called a 2nd time).
1007    o pkg/exf:
1008      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1009      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1010      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1011      - cosmetic changes to exf_bulkformulae.F to make it look more like
1012        exf_bulk_largeyeager04.F
1013    o eesupp/src (exch-1):
1014      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1015      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1016        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1017        (even without using MPI).
1018      - Message mode: move RecvAck setting (indicator of buffer being ready)
1019        from send_put to recv_get S/R (was useless before, but not sure if
1020        it's much more useful now);
1021      - Switch the order of sync: MPI-proc 1rst and then threads;
1022      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1023      - fix AD code for communication mode ='get' (but not used).
1024    o model/src:
1025      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1026      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1027    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1028    o pkg/ctrl: require a specific set of control variables and exf-flags for
1029      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1030    o model/src:
1031     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1032       1rst forward sweep, to avoid over-writing output files during recomputations
1033       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1034     b) 2nd version:
1035      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1036      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1037         writePickupAtEnd) + seaice & ptracers output;
1038      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1039    o model/src:
1040      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1041    o pkg/exch2:
1042      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1043      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1044    o pkg/autodiff & exch2:
1045      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1046      (for now, only if ALLOW_EXCH2 is defined).
1047    o pkg/autodiff:
1048      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1049        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1050       + clean-up comments (_RS is not always real*4)
1051      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1052      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1053        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1054    o testreport (AD-tests):
1055      no longer link files from dir "../input" (1rst link files from
1056      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1057    
1058    checkpoint62f (2010/04/29)
1059    o model/src/the_main_loop.F:
1060      adjust store directives for seaice evp and multicategory according to
1061      pkg/ecco/the_main_loop.F
1062    o adjoint:
1063      global_sum_ad was incomplete (noted many times by many people ;)
1064      nice description by Jean U. as follows:
1065      * allreduce(var) in global_sum.F can be interpreted as
1066        reduce(sum) followed by broadcast of sum.
1067      * The adjoint of that is
1068        sum(adjoint) followed by broadcast(summed adjoint value)
1069        or in other words, allreduce(sum, adjoint vars)
1070      We were missing the sum(adjoint)!
1071      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1072      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1073      The fix should produce 16-digit accuracy between
1074      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1075      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1076      We'll probably change this yet again shortly
1077    o eesupp/src:
1078      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1079    o pkg/icefront
1080      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1081        specification of addmass array based on a 2D field, which is added
1082        at bottommost wet level at each horizontal location.
1083    o model/src:
1084     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1085     layout; (not always compatible with delX,delY setting; commented out for now).
1086    o pkg/exch2:
1087     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1088     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1089    
1090    checkpoint62e (2010/04/15)
1091    o pkg/obcs:
1092      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1093    o pkg/dic:
1094      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1095        (note: not presently tested in any forward verification exp.)
1096       update tutorial_global_oce_biogeo AD output file.
1097    o pkg/exf:
1098      - account for the variation of albedo as a function of zenith angle
1099        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1100    o build_options:
1101     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1102    o pkg/dic:
1103      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1104      - use binary pickup file for restart;
1105      - initialise atmos-CO2 box from dic_pCO2 parameter;
1106      - fix multi-threaded.
1107    o pkg/rbcs:
1108     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1109       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1110     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1111       and update output.txt
1112    o pkg/kpp:
1113     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1114     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1115       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1116       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1117     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1118       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1119    o pkg/offline:
1120      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1121      (bug was added in version 1.10 on 2007-08-23).
1122    o pkg/offline:
1123      - no need to specify periodicExternalForcing, etc ... to use offline pack
1124      - offline input files no longer just single prec --> parameter offlineLoadPrec
1125  o verification/lab_sea:  o verification/lab_sea:
1126    change to multi-tile setup.    change AD test to multi-tile setup and update all 4 AD output.
1127    NOTE: while cost function values remain very similar,    NOTE: while cost function values remain very similar,
1128    gradients are very different, although gradient checks are self-consistent    gradients are very different, although gradient checks are self-consistent
1129    Should try to get to the bottom of this (cost function summation order?)    Should try to get to the bottom of this (cost function summation order?)
1130  o pkg/dic:  o pkg/dic:
1131    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1132    a weakness of TAF that drops part of double precision in log10 derivative.    a weakness of TAF that drops part of double precision in log10 derivative.
1133      <= changes removed since problem has been fixed in current TAF version 1.9.71
1134    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1135  o pkg/ecco:  o pkg/ecco:
1136    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
# Line 50  o tools/build_options: Line 1169  o tools/build_options:
1169      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1170  o pkg/ecco  o pkg/ecco
1171    - allow user defined cost function contributions    - allow user defined cost function contributions
1172          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1173          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1174    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1175        the two options are complementary.        the two options are complementary.
1176  o pkg/smooth  o pkg/smooth
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