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revision 1.1250 by jmc, Tue Apr 13 15:05:12 2010 UTC revision 1.1452 by jmc, Fri Jun 10 21:18:45 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 model/src (rStar):
8      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
9        affect solution only if z* with full pressure in EOS;
10        update output of test-exp global_ocean.90x40x15.
11    o pkg/seaice:
12      - introduce siEps=1e-5 parameter
13      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
14      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
15      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
16        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
17        as well as ice cover age and ridging index (attached to AREA).
18        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
19        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
20        Up to SItrMaxNum=3 tracers can be used simultaneously.
21    o pkg/salt_plume:
22      -introduce SPsalFRAC run time parameter that sets the fraction of the
23       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
24       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
25    o model debug options:
26      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
27        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
28      - Refine debug-msg printing selection (3 new levels):
29        debugMode  : controls printing of debug messages (sequence of S/R calls).
30        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
31         debLevZero =  0 ; /* level of disabled aux. msg printing */
32         debLevA =  1 ; /* level of minimum  aux. msg printing */
33         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
34         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
35         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
36         debLevE =  5 ; /* level of extensive debug printing */
37        New debugLevel default: with default debugMode value (=F),
38          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
39          and if debugMode=T, default debugLevel = 4 (debLevD).
40        Relation with previous settings:
41         debLevB (=2) corresponds to former debLevA (=1)
42         debLevD (=4) corresponds to former debLevB (=2)
43        Note:
44         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
45         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
46            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
47      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
48        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
49    o pkg/obcs:
50      - change OBCSfixTopo default from True to False (should not change the results);
51        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
52    o pkg/thsice:
53      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
54        2nd layer seaice sublimation (unlikely to happen)
55      - use Interior mask for OBCS in thsice_advection.F (similar to what is
56        done in gad_advection & seaice_advection).
57    o adjoint:
58      bug fix spotted by Gael Forget:
59      seaice_advection and thsice_advection still had
60      legacy CPP options to avoid CS corner updates for adjoint
61    o pkg/seaice:
62      => Change some of the defaults (2011/05/29):
63         - change SEAICEuseFluxForm default (from False to True)
64         - change DIFF1 default (from 0.004 m/s to 0. m/s)
65         And print warnings if DIFF1 is not set in data.seaice and centered
66          avection scheme is used without any diffusion.
67      also:
68      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
69      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
70      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
71        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
72        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
73      update results of test exp.:
74         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
75             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
76             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
77         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
78         seaice_obcs: output (SEAICEuseFluxForm=T)
79      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
80          for standard fwd & AD lab_sea tests (to keep the same output).
81    o pkg/seaice/seaice_growth.F:
82      - use Ian Fenty's capping formulas for actual ice
83      thickness thoughout EVOLUTION branch.
84      - put treatment pathological case #2) in CPP brackets
85      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
86      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
87    o pkg/seaice:
88      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
89      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
90      also pass fac as a param, which can be 1. (to update the tendency
91      field) or the time step (to update the field itself).
92      - seaice_advdiff.F: for multidim, call seaice_diffusion with
93      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
94      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
95      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
96      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
97    o pkg/seaice:
98      diffusion with centered advection scheme (diffus.F & advect.F):
99      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
100        to just compute the laplacian of input-field.
101      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
102      - fix flux-form version in diffus.F to conserve tracer.
103      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
104       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
105    
106    checkpoint62y (2011/05/26)
107    o pkg/seaice:
108     - seaice_growth.F : in EVOLUTION branch, always include
109       a_QSWbyATM_cover in qnet (as it should be).
110     - verification/global_ocean.cs32x15 : update results accordingly
111       (output.seaice.txt output_adm.seaice.txt).
112    o pkg/seaice + obcs:
113     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
114       equivalent of assuming no tracer gradient outside the OB region.
115       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
116     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
117       after changes above);
118     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
119       only at OB location (instead of over a band of OLx width).
120    o pkg/seaice:
121     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
122       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
123    o pkg/obcs:
124      - split header file "OBCS.h" into 4 separated files:
125        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
126       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
127         (contain no conditional statement which depends on OBCS options).
128      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
129        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
130    o ctrl, cost, grdchk & autodiff pkgs:
131      - make options file more standard (like other {PKG}_OPTIONS.h file but
132        with AD_CONFIG.h); clean-up some of the included header files.
133    o pkg/obcs:
134      - do not mask tracer when applying OB (tracer == 0 could generate problems)
135      - apply tracer OB values to tracer field only at OB location (instead of
136        over a band of OLx width)
137      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
138      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
139        obcs_apply_tloc.F & obcs_apply_sloc.F
140    o obcs in model/src:
141      - call OBCS_APPLY_W only if NonHydrostatic.
142      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
143      - reset dEtaHdt and wVel to zero outside OB interior region ;
144      - leave tracer unchanged outside OB interior region: This has no effect
145        on the solution but just to prevent unrealistic tracer value outside OB.
146      - zero out velocity outside OB interior region: This has no effect on
147        the solution but just to prevent unrealistic velocity outside OB.
148    o obcs and non-lin free-surf:
149       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
150       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
151       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
152       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
153       update results of test-exp. exp4(nlfs).
154    o exp4 (nlfs) test-exp:
155       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
156       with NonLin-FreeSurf); update output.nlfs.txt
157    o obcs and 2d/3d solver norm:
158       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
159       and outside OB interior region (will allow to place OB further inside the
160       domain). Depending on the domain, can affects cg2d-Norm (previous
161       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
162       and cg3d-Norm (previous Norm was computed before canceling OB terms),
163       e.g. in tutorial_plume_on_slope.
164      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
165    o pkg rbcs:
166      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
167      - add capability to apply relaxation to horizontal velocity uVel & vVel.
168    o pkg/grdchk: add gradient check for control variable xx_shifwflx
169    o pkg/shelfice/shelfice_init_fixed.F
170      fix CPP-flag combinations
171    o pkg/seaice: Merge iceage code of Pierre Rampal
172      * update/change/correct ice age calculations
173      * add age updates for pathological cases
174      Probably needs more testing...
175    
176    checkpoint62x (2011/05/13)
177    o pkg/mom_vecinv:
178       high-order vorticity scheme: use interior masks (maskInW & S)
179       to zero-out (outside OB) gradient of vorticity.
180    o verification exp.:
181       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
182       hs94.128x64x5 and seaice_obcs ; update results.
183    o pkg/obcs:
184      fix bug in OBeta for YZ sections in obcs_exf_load.F
185    o pkg/ctrl, pkg/shelfice, and optim:
186      - add new control variable xx_shifwflx (fresh water flux underneath ice
187        shelves). This is almost as tedious as obcs-ctrl, because the
188        variables needs its own mask.
189      - add a cost function term that penalizes the deviation of xx_shifwflx
190        from the first guess (zero) in analogy to other control variables
191    o pkg/shelfice:
192      - start basic adjoint
193    o pkg/ctrl:
194      - remove extra 2D field "for good measure" when initializing in
195        ctrl_set_globfld_[xy/xz/yz].F
196      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
197      - improve error messages in ctrl_set_unpack_*
198    o OBC implementation in momentum:
199       use interior masks (maskInC,W & S) in momentum S/R:
200       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
201       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
202       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
203       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
204       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
205        (and also with Leith/Smagorinsky harmonic-viscosity).
206       Update output of experiment dome and exp4 (+nlfs).
207    o exp4 test-exp:
208      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
209        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
210        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
211        time-varying OB at Western-side for wVel (NonHyd); update output.
212      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
213        and biharmonic-viscosity ; also use prescribed time varying OB.
214    o pkg/obcs:
215      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
216    o model/src:
217      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
218      - initialise startTime & nIter0 with unlikely values: allows to set one
219        from the other without ambiguity.
220    o seaice_obcs test-exp.:
221      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
222    o pkg/obcs:
223      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
224        no longer needed with maskInC,W,S in pkg/generic_advdiff.
225    o pkg/seaice:
226      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
227        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
228      - fixed bug in the initialization of sea ice salinity variable HSALT
229        in seaice_init_varia.F  (removed dependence on ICE2WATR)
230    o fizhi-cs test exp.:
231       switch reference output convention for these 2 non-standard test-exp,
232        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
233          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
234       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
235    o model/inc:
236      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
237        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
238    o pkg/seaice:
239      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
240    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
241      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
242        and initial HSALT
243    
244    checkpoint62w (2011/04/26)
245    o pkg/mom_fluxform:
246      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
247      - use parameter "sideDragFactor" in no-slip BC side-drag part.
248      - update output of exp. global_ocean.90x40x15
249    o pkg/mom_vecinv:
250      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
251    o update seaice exp.:
252      use more consistent parameter values (remove "backward compatability only":
253       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
254      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
255       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
256    o update test-exp global_ocean.90x40x15:
257      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
258      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
259      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
260      o turn on zStar & viscA4 in standard set-up (dir input/)
261        and update output files: output.txt & output.dwnslp.txt
262    o new AD-test experiment: obcs_ctrl
263      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
264    o pkg/dic:
265      fix two bugs in handling water vapour pressure in carbonate chemistry
266      and air-sea fluxes. Found by Val Bennington and Galen McKinley
267      (add DIC Option = WATERVAP_BUG to recover old results)
268      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
269    o adding allowInteriorFreezing option to check for water below freezing point
270      at depth and bring the negative heat anomaly to the surface level
271    o pkgs _fields_load:
272      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
273      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
274        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
275        rbcs to get interpolation weights and time reccord number.
276      - fix multi-threading in aim_fields_load.F
277      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
278    o external_fields_load:
279      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
280       interpolation weights) to use in a periodic time-series ; do not divide by
281       time-step to convert to integer:
282       - this fixes case where externForcingPeriod is not multiple of time-step
283          (Thanks to Christopher L. Wolfe)
284       - this fixes case where externForcingPeriod is an odd multiple of time-step
285         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
286      store index of time-record which is currently loaded:
287       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
288       - needed for the adjoint but not yet used because of extensive recomputations;
289         (to be fixed soon)
290    
291    checkpoint62v (2011/04/02)
292    o verification/1D_ocean_ice_column added to test Ian Fenty's
293      pkg/seaice_growth.F modifications for improving sea ice code differentiability
294    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
295      (new velocity statistics after changing maskInW & maskInS definition)
296    o pkg/generic_advdiff with OBCS:
297      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
298      equivalent to assumption of no tracer gradient outside the OB region.
299      This will affect the results if using obcs+biharmonic diffusion.
300      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
301    o pkg/obcs:
302      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
303      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
304      in Interior region. No impact on solution but affects Velocity monitor stats.
305    o pkg/ptracers (adjoint)
306      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
307      tape file for each tracer
308    o model/inc/src and pkg/autodiff: add parameters that allow to turn
309      of parts of the adjoint code at run time. For now, there are only
310      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
311      parameters are set in data.pkg.
312      This is the lazy coward's version of doing this, but still useful for
313      debugging. In order to do it right, everything needs to be moved to
314      pkg/autodiff.
315    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
316      the end; this fixes the adjoint balancing code for open boundaries.
317    o pkg/ctrl:
318      - change behavior of xx_${varname}period to be analogous to exf-conventions:
319        xx_${varname}period =   0.,  means time-independent control part
320        xx_${varname}period = -12., means one-year-periodic monthly control part
321      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
322        clean up ctrl_init a little, remove unused variables
323      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
324      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
325    
326    checkpoint62u (2011/03/15)
327    o model/src:
328      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
329        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
330      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
331        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
332    o pkg/ctrl/obcs/ecco:
333      - remove obsolete, unused, and partially broken code:
334        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
335        ALLOW_CTRL_OBCS_BALANCE
336      - put a stop statement into ecco/cost_obcsvol.F, but also add
337        cost_obcsvol to ecco_ad_diff.list
338    o pkg/ecco: fix counting cost function contributions for obcs (code
339      by Matt M.) and diffkr for diagnostics
340    o pkg/ecco, pkg/ctrl, pkg/grdchk:
341      add cost penalty terms for initial uvel, vvel, eta controls
342      and I/O for prior error files
343    o pkg/mdsio:
344       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
345       (new argument) to check for tiled file in mdsioLocalDir : this fix the
346       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
347    o pkg/ctrl:
348     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
349       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
350       unused and superfluous variables
351     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
352    o pkg/ecco
353     - enable adjoint of Stevens OB
354    o pkg/ctrl/ecco/grdchk:
355      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
356        Fortunately, we do not have any tests for the numerous cpp-flagged
357        option of "obcs as control parameters" so we will never know
358        if this is an improvement (but at least now things compile).
359      - remove an obsolete initialization from ecco_cost_init_barfiles.F
360      - fix some problems within never used ifdefs to make the code compile
361    o pkg/obcs:
362     - Refine Interior mask definition to work with more complex OB (e.g.
363       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
364       read in Interior mask from file. Check if Interior mask is consistent
365       with OB list of indices.
366    o pkg/seaice
367     - beginning code for a seaice tracer package,
368       but currently only used for seaice age: SEAICE_AGE
369       SEAICE_num = 4
370       iTracer = 1: area-weighted ice age
371               = 2: volume-weighted ice age
372               = 3, 4: template for one-year vs. multi-year ice
373       data.seaice has new namelist SEAICE_PARM03 for arrays related to
374       SEAICE_num
375    
376    checkpoint62t (2011/03/05)
377    o pkg/obcs:
378     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
379       then normal component. This ensures that the normal component is set
380       correctly even when it conficts with tangential setting from an other OB.
381       Affects results of test-experiment seaice_obcs: update the output.txt
382    o pkg/obcs:
383     - add code to monitor statistics of dynamical fields at OB.
384     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
385       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
386       - change default: balance the Net inflow through all OB (instead of balancing
387         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
388     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
389       to match Nortern OB inflow (OBCS_balanceFacN=0).
390    o pkg/seaice:
391     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
392    o pkg/seaice (seaice_growth v 1.113):
393     - reverting seaice_growth to v 1.111 in order to have code with exact bit
394       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
395       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
396       runtime flag SEAICEareaFormula is kept but is inactive
397    o model/src:
398     - add new param to scale curvilinear grid distance and area when using
399       a different sphere radius from the grid-files.
400     - test/check multi-threads EXCH applied to local variable (cg2d_x)
401    o adjoint:
402     - enable adjoint of Stevens OB
403     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
404       (a bit delicate because of potentially modified adj. common block structure;
405       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
406    
407    checkpoint62s (2011/02/15)
408    o pkg/seaice (seaice_growth v 1.112):
409     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
410       computing the ice cover tendency from effective thickness tendencies. Include
411       Ian Fenty's formula.
412     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
413       SEAICEareaFormula.
414     - simplify notations for the various d_HEFF/d_AREA terms.
415    o pkg/gmredi:
416     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
417       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
418       add a verification test-run (front_relax.bvp) to test GM_useBVP.
419    o pkg/seaice (seaice_growth v 1.111):
420     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
421     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
422       also melt ice.
423    o pkg/seaice:
424     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
425     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
426    o pkg/cheapaml:
427     - from Nico Wienders: New version of this package.
428    o pkg/flt:
429     - add CPP options to prevent floats to re-enter the opposite side of
430       a periodic domain (default: keep periodicity)
431    o pkg/gmredi:
432     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
433       (needed for multi-dim advection).
434     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
435    o model/src:
436     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
437    o tutorial_tracer_adjsens
438     - extend to NLFS and replace maskC by hFacC
439       (change reference output accordingly)
440    
441    checkpoint62r (2011/01/24)
442    o testreport:
443     - add option -deloutp (-do) to remove output file after successful run
444     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
445       extract exact list of procs from this file ; adjust COMMAND by
446       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
447    o pkg/ecco: replace old ineffective way of penalizing deviations from
448      first guess (of obcs) with code by Matt Mazloff
449    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
450      exf/cal
451      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
452        and handle case of obcs?period == 0
453        Not affected by these changes: There is still an inconsistency in
454        the computation of start/endrec for the obcs variables for ALLOW_CAL
455        defined (see comment by Menemenlis, 7-Mar-2003)
456      - make S/R ctrl_get_gen_rec return something meaningful even if
457        ALLOW_CAL is not defined
458      - ctrl_getobcs?: simplify code so that it does not need to use
459                       S/R exf_swapfields
460    o testreport:
461       allow to test MPI with different number of processors for each experiment:
462       create file "SIZE.h.mpi" in each build dir.
463       Note: update of "-command" argument not yet implemented.
464    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
465      alleviate the need for additional 3D tapes when using
466      the non-inear free surface in the adjoint. This is done
467      by adding an 'update' of hfacc etc. to their current
468      value at the beginning of forward_step.F.
469    o pkg/seaice
470      seaice_lsr: move stress-divergence computations out of outer pseudo-
471      timestepping loop
472    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
473      up, so that the calls of the ctrl_* subroutines are really at the end
474      of the routine.
475    o pkg/gmredi:
476      allow to specify a 2-D horizontal map and a 1-D vertical profil
477      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
478    o pkg/seaice:
479      move lsr iterations from seaice_dynsolver to seaice_lsr.
480    o pkg/seaice:
481      reduce memory footprint of seaice mutldim advection tapes,
482      by using a 2D tape independent of the generic_advdiff ones,
483      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
484    
485    checkpoint62q (2010/12/29)
486    o model/src:
487      - check horizontal grid-spacing for unset or zero/negative values.
488      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
489    o pkg/flt:
490      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
491      - precision of input and output files set according to readBinaryPrec
492        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
493      - initial float position from tiled file was not converted to index space
494        (looks like a bug): fixed to make it similar to initial pos. global file.
495    o global_ocean.cs32x15:
496       change SIZE.h of AD set-up to get same tiling as with MPI.
497       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
498    o model/src:
499       add flag to control printing of domain fields (bathymetry, hFac ...) in
500       ini_mask_etc (call to plot_fieds_xy*).
501    o pkg/thsice:
502       if useEXF, some forcing fields are not valid in overlap: fixed by computing
503       over the interior only + apply EXCH at the end (like with SEAICE advection).
504    o pkg/mdsio:
505      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
506        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
507      - change barrier call for safe multi-threads access to 3-D shared buffer.
508      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
509      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
510        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
511    o pkg/flt:
512      - add fourth-order Runge-Kutta integration
513      - add basic exch2 support (only 1 facet supported so far!)
514    o pkg/mdsio+rw:
515      new S/R to read local (or tile independent) vector (read counterpart of
516       mds_writevec_loc, and front-end write_glvec_rl/rs).
517    o global_ocean.cs32x15: additional input_ad.seaice experiment
518        that uses pkg/seaice rather than pkg/thsice.
519        (using multidim advection for seaice)
520    o towards more F95 syntax for array specification in namelist:
521      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
522        of all verification experiments.
523           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
524          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
525      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
526    o global_ocean.cs32x15: additional input.seaice experiment
527        that uses pkg/seaice rather than pkg/thsice.
528    
529    checkpoint62p (2010/12/17)
530    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
531        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
532    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
533        allow for use of multim. advection in seaice adjoint.
534    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
535      - first attempt to close budgets by taking into account the freshwater
536        flux implied by the sublimation of snow and ice. So far only the
537        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
538        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
539    o eesupp/src:
540      new S/R with new option (NML_EXTENDED_F77) to change array specification
541      from F95 standard to commonly accepted extended F77 form.
542      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
543      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
544      for less tolerant f77 compiler (e.g., pgf77, g77).
545    o globalFiles:
546      commented out in parameter file "data" since it's not safe with MPI
547      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
548      in this case); no longer commented out in restart test (tst_2+2).
549    o add adTapeDir to specify a special directory where adjoint tapes are
550      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
551      and cannot be used together with mdsioLocalDir.
552    o nesting pkgs:
553      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
554      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
555      - add parameter files + utils dir + output from short run on beagle.
556    o pkg/seaice:
557        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
558    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
559      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
560    
561    checkpoint62o (2010/11/25)
562    o pkg/exf:
563      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
564    o pkg/seaice:
565      - seaice_ocean_stress: split a loop for better vectorization of the
566        adjoint code
567      - seaice_growth.F: fix bug in conservation of freshwater connected to
568        capping of heff, put contribution into d_HEFFbyNEG
569      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
570        by something more sensible (parameters that are what their name implies)
571      - change some defaults, so that by default exf-parameters are used for
572        things like rhoAir, cpAir,latent/sensible heat parameters, in order
573        to reproduce the old results, many data.seaice now contain funny values
574        for cpAir and latent heat of sublimation
575    o packages_readparms.F: move exf_readparms up in line so that
576        exf-parameters are visible for other packages (e.g. seaice)
577    o debugMode & debugLevel=2:
578      - differentiate between debugMode & debugLevel=2:
579        debugMode: controls printing of debug messages (sequence of S/R calls).
580        debugLevel: controls printing of algorithm intermediate results and stats.
581      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
582        => allows to print debug-stats without all sequence of call messages.
583      - switch control of debug print from debugLevel to debugMode in many S/R.
584    o pkg/obcs (obcs-sponge):
585        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
586        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
587    o pkg/generic_advdiff:
588      - record overlap minimum size for each advection scheme;
589      - refine criteria on overlap minimum size;
590      - check and stop (in gad_check) if overlap size is too small.
591    o pkg/obcs:
592      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
593        once, in ptracers_implicit.F)
594      - with seaice: remove test on empty file name in obcs_apply_seaice (always
595        apply OB values when tile has OB)
596    o model/src, coriolis setting:
597      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
598        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
599        files (selectCoriMap=3) with any grid.
600      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
601    o pkg/seaice/seaice_growth.F:
602        a few cosmetic changes that reduce the number of lines of code
603    o pkg/obcs: add boundary conditions following Stevens (1990)
604      - the code follows old MOM/NAOSIM code
605      - so far it is only implemented for the eastern and western boundaries
606        and NOT for pTracers
607    o pkg/rbcs:
608      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
609        beginning of the first rbcs forcing period.
610      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
611        offline package, i.e., one file per time, labeled by iteration number;
612        deltaTrbcs sets the timestep with which the data was generated;
613        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
614      - rbcsForcingCycle=0 makes forcing non-cyclic.
615      - make arithmetic safe for negative times and odd forcing periods.
616    
617    checkpoint62n (2010/11/09)
618    o pkg/seaice:
619        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
620    o pkg/obcs:
621       New S/R to copy tracer value from the OB location to narrow band region
622        (width = same as overlap) beyond the OB: preserve OB value (needed for
623        high-order scheme) which were overwritten by EXCH call if in overlap
624        region. Applied to theta, salt, ptracer and advected seaice variables.
625       With seaice: use maskInC in similar way as in gad_advection.F,
626        in seaice_advection.F and advect.F.
627       Update output of experiment seaice_obcs and change exp4 to test OBCS with
628        4th order Adv.Scheme. for pasive salt and ptracer.
629    o tools/genmake2:
630      - when looking for an optfile (not specified), only search for Fortran compiler
631        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
632      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
633        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
634      - set default for CPP to "cpp -traditional -P" (was the case without specifying
635        an optfile, but otherwise default was just "cpp".
636      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
637      - when "CC" is not set in the optfile, look for possible C compiler
638        (instead of just setting CC=cc)
639      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
640        => add a ".F" to ".o" rule for source files with no "#include" (such as
641           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
642      - move gfortran before g77 in list of possible Fortran compiler (consistent
643        with reference compiler switch from g77 to gfortran)
644    o pkg/seaice:
645      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
646        seaice_check that stops the model, when the CPP flag is used.
647      o seaice_growth.F: make capping of ice volume conserving by returning the
648        capped ice as freshwater to EmPmR. This does not change the verification
649        experiments but will change runs where the capping is acutally active
650    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
651      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
652         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
653         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
654    o tools/genmake2:
655      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
656      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
657      - clean previous genmake log files before anything else.
658      - change Makefile to remove testreport log files (*.tr_log) and genmake log
659        files only with "CLEAN" target (instead of "Clean");
660    o pkg/generic_advdiff:
661      Change OBCS in multiDim advection (gad_advection.F):
662       Use maskInC to prevent intermediate update of tracer-field in OB regions,
663       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
664       which were applying future time-step OB values.
665      This way, all explicit calculations use current-time-step OB values
666       (simpler and more consistent).
667      Affects results when set-up uses time-varying OBC and multi-dim advection;
668       update output of experiment seaice_obcs.
669    o pkg/seaice:
670      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
671       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
672         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
673      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
674       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
675       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
676    o pkg aim (2010/10/26):
677      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
678        formulation with obliquity, eccentricity, ... as run-time parameters,
679      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
680        upward shortwave radition at the surface (all-sky and clear-sky).
681    o pkg/obcs:
682      - writing sections with globalFiles=T does not work: switch to tiled-files
683        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
684      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
685      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
686    
687    checkpoint62m (2010/10/21)
688    o pkg/seaice: vectorize seaice_solve4temp.F
689      - move iterations loops outside of i/j-loops
690      - requires 2D arrays for TB and effConduct
691      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
692        modified in this routine
693      - a little bit of clean up, adjusting indentation, etc.
694      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
695        performance and '**TWO' by '**2' (because TWO is a float),
696        replaced ONE, ZERO
697    o eesupp/src:
698       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
699    o pkg/seaice/seaice_growth.F
700      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
701      merging process. The merged routine has two branches, and one activates the 'evolution'
702      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
703      In summary, here is what the '10/10 revision' did consist of
704        part 1: seaice_growth.F revisions 1.71 to 1.75
705          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
706            The emphasis here was on improving readability (e.g. by trying to use meaningful
707            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
708        part 1.5:
709          - revising the lab_sea experiment to make it a more useful (i.e. stable
710            and representative of an actual model run). This was done by generating a
711            (winter) pickup to start from, switching back the main experiment dynamic
712            solver from evp to lsr, having one of the experiments use the free drift solution.
713        part 2: seaice_growth.F revisions 1.76 to 1.85
714          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
715          - Sorting out the various fields units and sign (set early on and reset at the end)
716            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
717            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
718          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
719            and simplifying logical expressions to further improve readibility.
720        part 3: seaice_growth.F revisions 1.86 to 1.89
721          - Re-organize the blocks of code more logically.
722          - Merging the '_if.F' pieces that add something new.
723    o pkg/thsice:
724      - vectorize thsice_solve4temp and thsice_get_exf.
725        Problem: thsice_solve4temp has an unvectorizable statement that
726        might also be problematic for TAF
727      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
728        does not change the verifcation experiment, but will change all
729        experiments that have this flag undefined (not tested in verification);
730        a little reorganization to save a few 2D fields and recomputations
731      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
732      - 2nd step:  fix some store dirs
733        o seems to work somewhat, i.e. using ifort but not g77
734        o likely cause are incomplete init. or recomputation
735        o start verification/global_ocean.cs32x15/input_ad.thsice
736    o pkg/obcs: add support for exch2
737      - the position of the boundary and prescribed values are specified using
738        a global domain with exch2 facets stacked
739        - in x for N,S boundaries (like W2_mapIO=-1)
740        - in y for E,W boundaries (so E,W boundaries do not overlap)
741    o pkg/mdsio: add support for writing global sections with exch2
742        file layout is as for obcs described above:
743        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
744        - for y-z sections, facets are stacked in y
745    o pkg/thsice:
746       - change a few routines for better vectorization: thsice_albedo.F,
747         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
748         not affected, but in particular the latter routine has changed
749         dramatically (not necessarily easier to read now).
750       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
751       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
752    o verification/lab_sea:
753      - overhaul of the forward model experiments. The main motivation
754        for this revision is that lab_sea has proven quite fragile (when
755        changing the sea-ice code, and switching platforms) to a point
756        when failures were very hard to attribute to specific code problems.
757      - the suspected reason for this fragility is noise amplification by evp so,
758        to start with, we decided to replace evp with lsr in the main experiment.
759      - the input.lsr experiment thus became obsolete and was removed.
760      - it was replaced with the input.fd experiment that uses an
761        analytical "free drift" solution as the ice velocity field.
762      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
763        will hopefully allow us to discriminate problems due to dynamic solvers
764        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
765        us to test additional options, along with the salt plume package.
766      - Finally a pickup was generated (at the end of a one year run) to
767        make the tests more representative of an actual model run. Previously
768        the tests starting point was a 1m thickness of ice everywhere.
769    o pkg/seaice:
770      - introducing S\R seaice_freedrift.F that compute the
771        analytical solution to an approximate ice momentum
772        equation (i.e. the simple stress/coriolis balance).
773      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
774        of the free drift velocity field, and enable its use.
775        To actually use the free drift solution as the model ice
776        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
777    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
778    
779    checkpoint62l (2010/10/04)
780    o pkg/seaice:
781      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
782      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
783       version (with USE_ORIGINAL_SBI undef);
784    o add hooks for new packages OASIS, the package will follow
785      (hooks exclude the seaice pkg for now)
786    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
787      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
788      rather than mdsio_readvector.F/mdsio_writevector.F, within
789      adread_adwrite.F to read/write adjoint-related tapes to disk.
790    o eesupp and pkg/mdsio: ALLOW_WHIO
791      Option to write/read 2D fields to files including tiles halos.
792      The main purpose is for adjoint related "tape I/O".
793      The secondary purpose is for debugging phases.
794      A word on those rather specifically intended purposes.
795      The code was meant to be stripped down to the bare minimum.
796      Typically, there is a unique and basic mapping to the global
797      buffer (tile by tile, then proc by proc, then level by level), and
798      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
799      meant to generate user friendly outputs of various shapes and forms.
800      Rather it is intended, for the knowledgeabale developers,
801      to be largely independent of the many mdsio options, to allow
802      outputs of tiles+halos in debugging phases and in adjoint runs,
803      and to allow some flexibility in tuning (adoint) I/O depending on each
804      file system behavior. With regard to tuning, most of the potential knobs
805      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
806      to specify directories, to specify the typical size of I/O calls, etc.)
807      are not yet included, and will be added if they prove useful.
808    o pkg/seaice:
809       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
810    o pkg/seaice:
811       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
812       code (seaice_budget_ice_if.F) which enable to recover old standard
813       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
814       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
815    o model/src (rStar):
816       use simple average (not area weighted) of rStarFac at U,V point when using
817       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
818       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
819    
820    checkpoint62k (2010/09/17)
821    o adjoint
822       * changed verification/global_ocean.cs32x15 ; adjoint now tests
823         Adams-Bashforth 3 + NLFS + RSTAR
824       * some more modifs required for ECCO-GODAE v4
825    o pkg/seaice
826       add SEAICE_AGE_VOL option to use volume instead of area for
827       integrating SEAICE_AGE
828    o model/src:
829       first check-in of sigma & hybrid-sigma coordinate code ; also includes
830       non-linear free-surface parts ; but pressure-gradient not yet coded.
831    o pkg/ptracers:
832       option for ptracer to convert Salt Relax into additional EmP.
833        tested in exp. global_ocean.90x40x15.dwnslp (update output)
834    
835    checkpoint62j (2010/08/25)
836    o pkg/ggl90:
837       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
838    o pkg/dic: car_flux.F, phos_flux.F
839      - reduce number of exp-calls in order to improve performance
840      - clean up a little (replace fields by their macros, etc., fix
841        typo in CPP-flag)
842    o pkg/ggl90: minor changes
843      - GGL90diffKrS was removed --> always use GGL90diffKr
844      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
845      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
846        (commented out for now)
847      - change in max/min operations to ensure that smoothing is ok
848      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
849      - always use diffKrNrT as background profile (i.e. never use diffKr field)
850    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
851    o pkg/dic:
852      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
853        vectorization
854      - small bug fix in insol for the unlikely case of a cartesian grid
855      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
856        + now vectorize, which also removes adjoint recomputations;
857        + replace integer maksp1 by _RL maskp1
858        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
859    
860    checkpoint62i (2010/07/21)
861    o pkg/flt:
862      - with OBCS: stop floats which enter the OB region
863    o model/src:
864      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
865        for implicit vertical advection.
866    o pkg/seaice:
867     - account for melting in seaice age evolution.
868     - remove double counting of seaice ridging effect on seaice age.
869    
870    checkpoint62h (2010/06/18)
871    o pkg/exch2:
872     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
873    o tools/genmake2
874      - remove "-pdefault" option: redundant with the use of "packages.conf";
875      - remove file pkg/pkg_default : set the default as a pkg group
876        ("default_pkg_list") defined in pkg/pkg_groups;
877      - fix for case pkg/pkg_depend is missing (was hanging before);
878      - add option "-pgroups" to specify a different pkg_groups than the default.
879    o verification/adjustment.cs-32x32x1:
880       add a "minimal" set-up test (code_min & input_min) which only compiles
881       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
882    o tools/genmake2
883      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
884      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
885    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
886      files are nearly the same anyway.
887      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
888       - redefinition of tau(i,i) (by a factor of ustar)
889       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
890       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
891       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
892       - replace
893         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
894         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
895         by
896         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
897         (changes results)
898       -> exf_bulkformulae v1.22,
899          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
900          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
901                    output.txt 1.63
902           offline_exf_seaice: output.seaicetd.txt 1.7
903           seaice_obcs: output.txt 1.10)
904      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
905       -> exf_bulkformulae v1.23,
906          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
907          and global_ocean.cs32x15.icedyn (only 11 matching digits)
908      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
909    o adjoint of exch-1:
910     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
911       (note: was already like this when using EXCH-2) and remove flow dir
912       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
913     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
914     - update pkg/exch2 diff list.
915    
916    checkpoint62g (2010/05/19)
917    o eesupp/src (exch-1):
918     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
919       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
920       (renamed to exch1_*rx_cube.F).
921     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
922       to call new exch1 S/R ; update Makefile and .cvsignore.
923     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
924       exch2_xy_rx later)
925      Note: after updating your code, need to run "make clean" in eesupp/src
926    o test experiment bottom_ctrl_5x5:
927       new output_adm.txt with fewer grdchk & less monitor output.
928    o model/src:
929      remove the call to ini_cori in initialise_varia.F (just keep the usual one
930       in initialise_fixed.F). More consistent with coriolis & horizontal grid
931       beeing treated in the same way (ini_grid is not called a 2nd time).
932    o pkg/exf:
933      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
934      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
935      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
936      - cosmetic changes to exf_bulkformulae.F to make it look more like
937        exf_bulk_largeyeager04.F
938    o eesupp/src (exch-1):
939      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
940      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
941        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
942        (even without using MPI).
943      - Message mode: move RecvAck setting (indicator of buffer being ready)
944        from send_put to recv_get S/R (was useless before, but not sure if
945        it's much more useful now);
946      - Switch the order of sync: MPI-proc 1rst and then threads;
947      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
948      - fix AD code for communication mode ='get' (but not used).
949    o model/src:
950      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
951      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
952    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
953    o pkg/ctrl: require a specific set of control variables and exf-flags for
954      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
955    o model/src:
956     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
957       1rst forward sweep, to avoid over-writing output files during recomputations
958       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
959     b) 2nd version:
960      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
961      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
962         writePickupAtEnd) + seaice & ptracers output;
963      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
964    o model/src:
965      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
966    o pkg/exch2:
967      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
968      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
969    o pkg/autodiff & exch2:
970      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
971      (for now, only if ALLOW_EXCH2 is defined).
972    o pkg/autodiff:
973      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
974        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
975       + clean-up comments (_RS is not always real*4)
976      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
977      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
978        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
979    o testreport (AD-tests):
980      no longer link files from dir "../input" (1rst link files from
981      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
982    
983    checkpoint62f (2010/04/29)
984    o model/src/the_main_loop.F:
985      adjust store directives for seaice evp and multicategory according to
986      pkg/ecco/the_main_loop.F
987    o adjoint:
988      global_sum_ad was incomplete (noted many times by many people ;)
989      nice description by Jean U. as follows:
990      * allreduce(var) in global_sum.F can be interpreted as
991        reduce(sum) followed by broadcast of sum.
992      * The adjoint of that is
993        sum(adjoint) followed by broadcast(summed adjoint value)
994        or in other words, allreduce(sum, adjoint vars)
995      We were missing the sum(adjoint)!
996      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
997      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
998      The fix should produce 16-digit accuracy between
999      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1000      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1001      We'll probably change this yet again shortly
1002    o eesupp/src:
1003      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1004    o pkg/icefront
1005      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1006        specification of addmass array based on a 2D field, which is added
1007        at bottommost wet level at each horizontal location.
1008    o model/src:
1009     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1010     layout; (not always compatible with delX,delY setting; commented out for now).
1011    o pkg/exch2:
1012     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1013     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1014    
1015    checkpoint62e (2010/04/15)
1016    o pkg/obcs:
1017      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1018  o pkg/dic:  o pkg/dic:
1019    -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;    -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1020      (note: not presently tested in any forward verification exp.)      (note: not presently tested in any forward verification exp.)
# Line 83  o tools/build_options: Line 1094  o tools/build_options:
1094      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1095  o pkg/ecco  o pkg/ecco
1096    - allow user defined cost function contributions    - allow user defined cost function contributions
1097          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1098          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1099    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1100        the two options are complementary.        the two options are complementary.
1101  o pkg/smooth  o pkg/smooth
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