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revision 1.1281 by jmc, Thu May 27 15:21:22 2010 UTC revision 1.1453 by jmc, Sun Jun 12 19:20:28 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/diagnostics:
8      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
9      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
10        (was _RL, now integer) with option = 0 to retrieve all levels.
11    o model/src (rStar):
12      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
13        affect solution only if z* with full pressure in EOS;
14        update output of test-exp global_ocean.90x40x15.
15    o pkg/seaice:
16      - introduce siEps=1e-5 parameter
17      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
18      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
19      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
20        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
21        as well as ice cover age and ridging index (attached to AREA).
22        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
23        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
24        Up to SItrMaxNum=3 tracers can be used simultaneously.
25    o pkg/salt_plume:
26      -introduce SPsalFRAC run time parameter that sets the fraction of the
27       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
28       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
29    o model debug options:
30      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
31        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
32      - Refine debug-msg printing selection (3 new levels):
33        debugMode  : controls printing of debug messages (sequence of S/R calls).
34        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
35         debLevZero =  0 ; /* level of disabled aux. msg printing */
36         debLevA =  1 ; /* level of minimum  aux. msg printing */
37         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
38         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
39         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
40         debLevE =  5 ; /* level of extensive debug printing */
41        New debugLevel default: with default debugMode value (=F),
42          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
43          and if debugMode=T, default debugLevel = 4 (debLevD).
44        Relation with previous settings:
45         debLevB (=2) corresponds to former debLevA (=1)
46         debLevD (=4) corresponds to former debLevB (=2)
47        Note:
48         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
49         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
50            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
51      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
52        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
53    o pkg/obcs:
54      - change OBCSfixTopo default from True to False (should not change the results);
55        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
56    o pkg/thsice:
57      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
58        2nd layer seaice sublimation (unlikely to happen)
59      - use Interior mask for OBCS in thsice_advection.F (similar to what is
60        done in gad_advection & seaice_advection).
61    o adjoint:
62      bug fix spotted by Gael Forget:
63      seaice_advection and thsice_advection still had
64      legacy CPP options to avoid CS corner updates for adjoint
65    o pkg/seaice:
66      => Change some of the defaults (2011/05/29):
67         - change SEAICEuseFluxForm default (from False to True)
68         - change DIFF1 default (from 0.004 m/s to 0. m/s)
69         And print warnings if DIFF1 is not set in data.seaice and centered
70          avection scheme is used without any diffusion.
71      also:
72      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
73      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
74      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
75        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
76        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
77      update results of test exp.:
78         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
79             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
80             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
81         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
82         seaice_obcs: output (SEAICEuseFluxForm=T)
83      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
84          for standard fwd & AD lab_sea tests (to keep the same output).
85    o pkg/seaice/seaice_growth.F:
86      - use Ian Fenty's capping formulas for actual ice
87      thickness thoughout EVOLUTION branch.
88      - put treatment pathological case #2) in CPP brackets
89      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
90      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
91    o pkg/seaice:
92      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
93      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
94      also pass fac as a param, which can be 1. (to update the tendency
95      field) or the time step (to update the field itself).
96      - seaice_advdiff.F: for multidim, call seaice_diffusion with
97      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
98      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
99      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
100      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
101    o pkg/seaice:
102      diffusion with centered advection scheme (diffus.F & advect.F):
103      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
104        to just compute the laplacian of input-field.
105      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
106      - fix flux-form version in diffus.F to conserve tracer.
107      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
108       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
109    
110    checkpoint62y (2011/05/26)
111    o pkg/seaice:
112     - seaice_growth.F : in EVOLUTION branch, always include
113       a_QSWbyATM_cover in qnet (as it should be).
114     - verification/global_ocean.cs32x15 : update results accordingly
115       (output.seaice.txt output_adm.seaice.txt).
116    o pkg/seaice + obcs:
117     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
118       equivalent of assuming no tracer gradient outside the OB region.
119       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
120     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
121       after changes above);
122     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
123       only at OB location (instead of over a band of OLx width).
124    o pkg/seaice:
125     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
126       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
127    o pkg/obcs:
128      - split header file "OBCS.h" into 4 separated files:
129        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
130       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
131         (contain no conditional statement which depends on OBCS options).
132      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
133        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
134    o ctrl, cost, grdchk & autodiff pkgs:
135      - make options file more standard (like other {PKG}_OPTIONS.h file but
136        with AD_CONFIG.h); clean-up some of the included header files.
137    o pkg/obcs:
138      - do not mask tracer when applying OB (tracer == 0 could generate problems)
139      - apply tracer OB values to tracer field only at OB location (instead of
140        over a band of OLx width)
141      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
142      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
143        obcs_apply_tloc.F & obcs_apply_sloc.F
144    o obcs in model/src:
145      - call OBCS_APPLY_W only if NonHydrostatic.
146      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
147      - reset dEtaHdt and wVel to zero outside OB interior region ;
148      - leave tracer unchanged outside OB interior region: This has no effect
149        on the solution but just to prevent unrealistic tracer value outside OB.
150      - zero out velocity outside OB interior region: This has no effect on
151        the solution but just to prevent unrealistic velocity outside OB.
152    o obcs and non-lin free-surf:
153       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
154       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
155       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
156       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
157       update results of test-exp. exp4(nlfs).
158    o exp4 (nlfs) test-exp:
159       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
160       with NonLin-FreeSurf); update output.nlfs.txt
161    o obcs and 2d/3d solver norm:
162       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
163       and outside OB interior region (will allow to place OB further inside the
164       domain). Depending on the domain, can affects cg2d-Norm (previous
165       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
166       and cg3d-Norm (previous Norm was computed before canceling OB terms),
167       e.g. in tutorial_plume_on_slope.
168      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
169    o pkg rbcs:
170      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
171      - add capability to apply relaxation to horizontal velocity uVel & vVel.
172    o pkg/grdchk: add gradient check for control variable xx_shifwflx
173    o pkg/shelfice/shelfice_init_fixed.F
174      fix CPP-flag combinations
175    o pkg/seaice: Merge iceage code of Pierre Rampal
176      * update/change/correct ice age calculations
177      * add age updates for pathological cases
178      Probably needs more testing...
179    
180    checkpoint62x (2011/05/13)
181    o pkg/mom_vecinv:
182       high-order vorticity scheme: use interior masks (maskInW & S)
183       to zero-out (outside OB) gradient of vorticity.
184    o verification exp.:
185       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
186       hs94.128x64x5 and seaice_obcs ; update results.
187    o pkg/obcs:
188      fix bug in OBeta for YZ sections in obcs_exf_load.F
189    o pkg/ctrl, pkg/shelfice, and optim:
190      - add new control variable xx_shifwflx (fresh water flux underneath ice
191        shelves). This is almost as tedious as obcs-ctrl, because the
192        variables needs its own mask.
193      - add a cost function term that penalizes the deviation of xx_shifwflx
194        from the first guess (zero) in analogy to other control variables
195    o pkg/shelfice:
196      - start basic adjoint
197    o pkg/ctrl:
198      - remove extra 2D field "for good measure" when initializing in
199        ctrl_set_globfld_[xy/xz/yz].F
200      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
201      - improve error messages in ctrl_set_unpack_*
202    o OBC implementation in momentum:
203       use interior masks (maskInC,W & S) in momentum S/R:
204       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
205       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
206       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
207       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
208       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
209        (and also with Leith/Smagorinsky harmonic-viscosity).
210       Update output of experiment dome and exp4 (+nlfs).
211    o exp4 test-exp:
212      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
213        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
214        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
215        time-varying OB at Western-side for wVel (NonHyd); update output.
216      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
217        and biharmonic-viscosity ; also use prescribed time varying OB.
218    o pkg/obcs:
219      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
220    o model/src:
221      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
222      - initialise startTime & nIter0 with unlikely values: allows to set one
223        from the other without ambiguity.
224    o seaice_obcs test-exp.:
225      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
226    o pkg/obcs:
227      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
228        no longer needed with maskInC,W,S in pkg/generic_advdiff.
229    o pkg/seaice:
230      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
231        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
232      - fixed bug in the initialization of sea ice salinity variable HSALT
233        in seaice_init_varia.F  (removed dependence on ICE2WATR)
234    o fizhi-cs test exp.:
235       switch reference output convention for these 2 non-standard test-exp,
236        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
237          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
238       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
239    o model/inc:
240      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
241        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
242    o pkg/seaice:
243      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
244    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
245      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
246        and initial HSALT
247    
248    checkpoint62w (2011/04/26)
249    o pkg/mom_fluxform:
250      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
251      - use parameter "sideDragFactor" in no-slip BC side-drag part.
252      - update output of exp. global_ocean.90x40x15
253    o pkg/mom_vecinv:
254      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
255    o update seaice exp.:
256      use more consistent parameter values (remove "backward compatability only":
257       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
258      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
259       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
260    o update test-exp global_ocean.90x40x15:
261      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
262      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
263      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
264      o turn on zStar & viscA4 in standard set-up (dir input/)
265        and update output files: output.txt & output.dwnslp.txt
266    o new AD-test experiment: obcs_ctrl
267      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
268    o pkg/dic:
269      fix two bugs in handling water vapour pressure in carbonate chemistry
270      and air-sea fluxes. Found by Val Bennington and Galen McKinley
271      (add DIC Option = WATERVAP_BUG to recover old results)
272      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
273    o adding allowInteriorFreezing option to check for water below freezing point
274      at depth and bring the negative heat anomaly to the surface level
275    o pkgs _fields_load:
276      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
277      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
278        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
279        rbcs to get interpolation weights and time reccord number.
280      - fix multi-threading in aim_fields_load.F
281      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
282    o external_fields_load:
283      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
284       interpolation weights) to use in a periodic time-series ; do not divide by
285       time-step to convert to integer:
286       - this fixes case where externForcingPeriod is not multiple of time-step
287          (Thanks to Christopher L. Wolfe)
288       - this fixes case where externForcingPeriod is an odd multiple of time-step
289         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
290      store index of time-record which is currently loaded:
291       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
292       - needed for the adjoint but not yet used because of extensive recomputations;
293         (to be fixed soon)
294    
295    checkpoint62v (2011/04/02)
296    o verification/1D_ocean_ice_column added to test Ian Fenty's
297      pkg/seaice_growth.F modifications for improving sea ice code differentiability
298    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
299      (new velocity statistics after changing maskInW & maskInS definition)
300    o pkg/generic_advdiff with OBCS:
301      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
302      equivalent to assumption of no tracer gradient outside the OB region.
303      This will affect the results if using obcs+biharmonic diffusion.
304      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
305    o pkg/obcs:
306      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
307      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
308      in Interior region. No impact on solution but affects Velocity monitor stats.
309    o pkg/ptracers (adjoint)
310      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
311      tape file for each tracer
312    o model/inc/src and pkg/autodiff: add parameters that allow to turn
313      of parts of the adjoint code at run time. For now, there are only
314      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
315      parameters are set in data.pkg.
316      This is the lazy coward's version of doing this, but still useful for
317      debugging. In order to do it right, everything needs to be moved to
318      pkg/autodiff.
319    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
320      the end; this fixes the adjoint balancing code for open boundaries.
321    o pkg/ctrl:
322      - change behavior of xx_${varname}period to be analogous to exf-conventions:
323        xx_${varname}period =   0.,  means time-independent control part
324        xx_${varname}period = -12., means one-year-periodic monthly control part
325      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
326        clean up ctrl_init a little, remove unused variables
327      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
328      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
329    
330    checkpoint62u (2011/03/15)
331    o model/src:
332      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
333        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
334      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
335        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
336    o pkg/ctrl/obcs/ecco:
337      - remove obsolete, unused, and partially broken code:
338        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
339        ALLOW_CTRL_OBCS_BALANCE
340      - put a stop statement into ecco/cost_obcsvol.F, but also add
341        cost_obcsvol to ecco_ad_diff.list
342    o pkg/ecco: fix counting cost function contributions for obcs (code
343      by Matt M.) and diffkr for diagnostics
344    o pkg/ecco, pkg/ctrl, pkg/grdchk:
345      add cost penalty terms for initial uvel, vvel, eta controls
346      and I/O for prior error files
347    o pkg/mdsio:
348       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
349       (new argument) to check for tiled file in mdsioLocalDir : this fix the
350       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
351    o pkg/ctrl:
352     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
353       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
354       unused and superfluous variables
355     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
356    o pkg/ecco
357     - enable adjoint of Stevens OB
358    o pkg/ctrl/ecco/grdchk:
359      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
360        Fortunately, we do not have any tests for the numerous cpp-flagged
361        option of "obcs as control parameters" so we will never know
362        if this is an improvement (but at least now things compile).
363      - remove an obsolete initialization from ecco_cost_init_barfiles.F
364      - fix some problems within never used ifdefs to make the code compile
365    o pkg/obcs:
366     - Refine Interior mask definition to work with more complex OB (e.g.
367       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
368       read in Interior mask from file. Check if Interior mask is consistent
369       with OB list of indices.
370    o pkg/seaice
371     - beginning code for a seaice tracer package,
372       but currently only used for seaice age: SEAICE_AGE
373       SEAICE_num = 4
374       iTracer = 1: area-weighted ice age
375               = 2: volume-weighted ice age
376               = 3, 4: template for one-year vs. multi-year ice
377       data.seaice has new namelist SEAICE_PARM03 for arrays related to
378       SEAICE_num
379    
380    checkpoint62t (2011/03/05)
381    o pkg/obcs:
382     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
383       then normal component. This ensures that the normal component is set
384       correctly even when it conficts with tangential setting from an other OB.
385       Affects results of test-experiment seaice_obcs: update the output.txt
386    o pkg/obcs:
387     - add code to monitor statistics of dynamical fields at OB.
388     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
389       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
390       - change default: balance the Net inflow through all OB (instead of balancing
391         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
392     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
393       to match Nortern OB inflow (OBCS_balanceFacN=0).
394    o pkg/seaice:
395     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
396    o pkg/seaice (seaice_growth v 1.113):
397     - reverting seaice_growth to v 1.111 in order to have code with exact bit
398       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
399       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
400       runtime flag SEAICEareaFormula is kept but is inactive
401    o model/src:
402     - add new param to scale curvilinear grid distance and area when using
403       a different sphere radius from the grid-files.
404     - test/check multi-threads EXCH applied to local variable (cg2d_x)
405    o adjoint:
406     - enable adjoint of Stevens OB
407     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
408       (a bit delicate because of potentially modified adj. common block structure;
409       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
410    
411    checkpoint62s (2011/02/15)
412    o pkg/seaice (seaice_growth v 1.112):
413     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
414       computing the ice cover tendency from effective thickness tendencies. Include
415       Ian Fenty's formula.
416     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
417       SEAICEareaFormula.
418     - simplify notations for the various d_HEFF/d_AREA terms.
419    o pkg/gmredi:
420     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
421       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
422       add a verification test-run (front_relax.bvp) to test GM_useBVP.
423    o pkg/seaice (seaice_growth v 1.111):
424     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
425     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
426       also melt ice.
427    o pkg/seaice:
428     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
429     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
430    o pkg/cheapaml:
431     - from Nico Wienders: New version of this package.
432    o pkg/flt:
433     - add CPP options to prevent floats to re-enter the opposite side of
434       a periodic domain (default: keep periodicity)
435    o pkg/gmredi:
436     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
437       (needed for multi-dim advection).
438     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
439    o model/src:
440     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
441    o tutorial_tracer_adjsens
442     - extend to NLFS and replace maskC by hFacC
443       (change reference output accordingly)
444    
445    checkpoint62r (2011/01/24)
446    o testreport:
447     - add option -deloutp (-do) to remove output file after successful run
448     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
449       extract exact list of procs from this file ; adjust COMMAND by
450       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
451    o pkg/ecco: replace old ineffective way of penalizing deviations from
452      first guess (of obcs) with code by Matt Mazloff
453    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
454      exf/cal
455      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
456        and handle case of obcs?period == 0
457        Not affected by these changes: There is still an inconsistency in
458        the computation of start/endrec for the obcs variables for ALLOW_CAL
459        defined (see comment by Menemenlis, 7-Mar-2003)
460      - make S/R ctrl_get_gen_rec return something meaningful even if
461        ALLOW_CAL is not defined
462      - ctrl_getobcs?: simplify code so that it does not need to use
463                       S/R exf_swapfields
464    o testreport:
465       allow to test MPI with different number of processors for each experiment:
466       create file "SIZE.h.mpi" in each build dir.
467       Note: update of "-command" argument not yet implemented.
468    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
469      alleviate the need for additional 3D tapes when using
470      the non-inear free surface in the adjoint. This is done
471      by adding an 'update' of hfacc etc. to their current
472      value at the beginning of forward_step.F.
473    o pkg/seaice
474      seaice_lsr: move stress-divergence computations out of outer pseudo-
475      timestepping loop
476    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
477      up, so that the calls of the ctrl_* subroutines are really at the end
478      of the routine.
479    o pkg/gmredi:
480      allow to specify a 2-D horizontal map and a 1-D vertical profil
481      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
482    o pkg/seaice:
483      move lsr iterations from seaice_dynsolver to seaice_lsr.
484    o pkg/seaice:
485      reduce memory footprint of seaice mutldim advection tapes,
486      by using a 2D tape independent of the generic_advdiff ones,
487      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
488    
489    checkpoint62q (2010/12/29)
490    o model/src:
491      - check horizontal grid-spacing for unset or zero/negative values.
492      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
493    o pkg/flt:
494      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
495      - precision of input and output files set according to readBinaryPrec
496        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
497      - initial float position from tiled file was not converted to index space
498        (looks like a bug): fixed to make it similar to initial pos. global file.
499    o global_ocean.cs32x15:
500       change SIZE.h of AD set-up to get same tiling as with MPI.
501       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
502    o model/src:
503       add flag to control printing of domain fields (bathymetry, hFac ...) in
504       ini_mask_etc (call to plot_fieds_xy*).
505    o pkg/thsice:
506       if useEXF, some forcing fields are not valid in overlap: fixed by computing
507       over the interior only + apply EXCH at the end (like with SEAICE advection).
508    o pkg/mdsio:
509      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
510        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
511      - change barrier call for safe multi-threads access to 3-D shared buffer.
512      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
513      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
514        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
515    o pkg/flt:
516      - add fourth-order Runge-Kutta integration
517      - add basic exch2 support (only 1 facet supported so far!)
518    o pkg/mdsio+rw:
519      new S/R to read local (or tile independent) vector (read counterpart of
520       mds_writevec_loc, and front-end write_glvec_rl/rs).
521    o global_ocean.cs32x15: additional input_ad.seaice experiment
522        that uses pkg/seaice rather than pkg/thsice.
523        (using multidim advection for seaice)
524    o towards more F95 syntax for array specification in namelist:
525      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
526        of all verification experiments.
527           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
528          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
529      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
530    o global_ocean.cs32x15: additional input.seaice experiment
531        that uses pkg/seaice rather than pkg/thsice.
532    
533    checkpoint62p (2010/12/17)
534    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
535        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
536    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
537        allow for use of multim. advection in seaice adjoint.
538    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
539      - first attempt to close budgets by taking into account the freshwater
540        flux implied by the sublimation of snow and ice. So far only the
541        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
542        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
543    o eesupp/src:
544      new S/R with new option (NML_EXTENDED_F77) to change array specification
545      from F95 standard to commonly accepted extended F77 form.
546      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
547      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
548      for less tolerant f77 compiler (e.g., pgf77, g77).
549    o globalFiles:
550      commented out in parameter file "data" since it's not safe with MPI
551      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
552      in this case); no longer commented out in restart test (tst_2+2).
553    o add adTapeDir to specify a special directory where adjoint tapes are
554      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
555      and cannot be used together with mdsioLocalDir.
556    o nesting pkgs:
557      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
558      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
559      - add parameter files + utils dir + output from short run on beagle.
560    o pkg/seaice:
561        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
562    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
563      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
564    
565    checkpoint62o (2010/11/25)
566    o pkg/exf:
567      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
568    o pkg/seaice:
569      - seaice_ocean_stress: split a loop for better vectorization of the
570        adjoint code
571      - seaice_growth.F: fix bug in conservation of freshwater connected to
572        capping of heff, put contribution into d_HEFFbyNEG
573      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
574        by something more sensible (parameters that are what their name implies)
575      - change some defaults, so that by default exf-parameters are used for
576        things like rhoAir, cpAir,latent/sensible heat parameters, in order
577        to reproduce the old results, many data.seaice now contain funny values
578        for cpAir and latent heat of sublimation
579    o packages_readparms.F: move exf_readparms up in line so that
580        exf-parameters are visible for other packages (e.g. seaice)
581    o debugMode & debugLevel=2:
582      - differentiate between debugMode & debugLevel=2:
583        debugMode: controls printing of debug messages (sequence of S/R calls).
584        debugLevel: controls printing of algorithm intermediate results and stats.
585      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
586        => allows to print debug-stats without all sequence of call messages.
587      - switch control of debug print from debugLevel to debugMode in many S/R.
588    o pkg/obcs (obcs-sponge):
589        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
590        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
591    o pkg/generic_advdiff:
592      - record overlap minimum size for each advection scheme;
593      - refine criteria on overlap minimum size;
594      - check and stop (in gad_check) if overlap size is too small.
595    o pkg/obcs:
596      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
597        once, in ptracers_implicit.F)
598      - with seaice: remove test on empty file name in obcs_apply_seaice (always
599        apply OB values when tile has OB)
600    o model/src, coriolis setting:
601      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
602        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
603        files (selectCoriMap=3) with any grid.
604      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
605    o pkg/seaice/seaice_growth.F:
606        a few cosmetic changes that reduce the number of lines of code
607    o pkg/obcs: add boundary conditions following Stevens (1990)
608      - the code follows old MOM/NAOSIM code
609      - so far it is only implemented for the eastern and western boundaries
610        and NOT for pTracers
611    o pkg/rbcs:
612      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
613        beginning of the first rbcs forcing period.
614      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
615        offline package, i.e., one file per time, labeled by iteration number;
616        deltaTrbcs sets the timestep with which the data was generated;
617        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
618      - rbcsForcingCycle=0 makes forcing non-cyclic.
619      - make arithmetic safe for negative times and odd forcing periods.
620    
621    checkpoint62n (2010/11/09)
622    o pkg/seaice:
623        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
624    o pkg/obcs:
625       New S/R to copy tracer value from the OB location to narrow band region
626        (width = same as overlap) beyond the OB: preserve OB value (needed for
627        high-order scheme) which were overwritten by EXCH call if in overlap
628        region. Applied to theta, salt, ptracer and advected seaice variables.
629       With seaice: use maskInC in similar way as in gad_advection.F,
630        in seaice_advection.F and advect.F.
631       Update output of experiment seaice_obcs and change exp4 to test OBCS with
632        4th order Adv.Scheme. for pasive salt and ptracer.
633    o tools/genmake2:
634      - when looking for an optfile (not specified), only search for Fortran compiler
635        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
636      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
637        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
638      - set default for CPP to "cpp -traditional -P" (was the case without specifying
639        an optfile, but otherwise default was just "cpp".
640      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
641      - when "CC" is not set in the optfile, look for possible C compiler
642        (instead of just setting CC=cc)
643      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
644        => add a ".F" to ".o" rule for source files with no "#include" (such as
645           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
646      - move gfortran before g77 in list of possible Fortran compiler (consistent
647        with reference compiler switch from g77 to gfortran)
648    o pkg/seaice:
649      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
650        seaice_check that stops the model, when the CPP flag is used.
651      o seaice_growth.F: make capping of ice volume conserving by returning the
652        capped ice as freshwater to EmPmR. This does not change the verification
653        experiments but will change runs where the capping is acutally active
654    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
655      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
656         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
657         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
658    o tools/genmake2:
659      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
660      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
661      - clean previous genmake log files before anything else.
662      - change Makefile to remove testreport log files (*.tr_log) and genmake log
663        files only with "CLEAN" target (instead of "Clean");
664    o pkg/generic_advdiff:
665      Change OBCS in multiDim advection (gad_advection.F):
666       Use maskInC to prevent intermediate update of tracer-field in OB regions,
667       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
668       which were applying future time-step OB values.
669      This way, all explicit calculations use current-time-step OB values
670       (simpler and more consistent).
671      Affects results when set-up uses time-varying OBC and multi-dim advection;
672       update output of experiment seaice_obcs.
673    o pkg/seaice:
674      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
675       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
676         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
677      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
678       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
679       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
680    o pkg aim (2010/10/26):
681      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
682        formulation with obliquity, eccentricity, ... as run-time parameters,
683      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
684        upward shortwave radition at the surface (all-sky and clear-sky).
685    o pkg/obcs:
686      - writing sections with globalFiles=T does not work: switch to tiled-files
687        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
688      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
689      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
690    
691    checkpoint62m (2010/10/21)
692    o pkg/seaice: vectorize seaice_solve4temp.F
693      - move iterations loops outside of i/j-loops
694      - requires 2D arrays for TB and effConduct
695      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
696        modified in this routine
697      - a little bit of clean up, adjusting indentation, etc.
698      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
699        performance and '**TWO' by '**2' (because TWO is a float),
700        replaced ONE, ZERO
701    o eesupp/src:
702       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
703    o pkg/seaice/seaice_growth.F
704      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
705      merging process. The merged routine has two branches, and one activates the 'evolution'
706      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
707      In summary, here is what the '10/10 revision' did consist of
708        part 1: seaice_growth.F revisions 1.71 to 1.75
709          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
710            The emphasis here was on improving readability (e.g. by trying to use meaningful
711            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
712        part 1.5:
713          - revising the lab_sea experiment to make it a more useful (i.e. stable
714            and representative of an actual model run). This was done by generating a
715            (winter) pickup to start from, switching back the main experiment dynamic
716            solver from evp to lsr, having one of the experiments use the free drift solution.
717        part 2: seaice_growth.F revisions 1.76 to 1.85
718          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
719          - Sorting out the various fields units and sign (set early on and reset at the end)
720            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
721            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
722          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
723            and simplifying logical expressions to further improve readibility.
724        part 3: seaice_growth.F revisions 1.86 to 1.89
725          - Re-organize the blocks of code more logically.
726          - Merging the '_if.F' pieces that add something new.
727    o pkg/thsice:
728      - vectorize thsice_solve4temp and thsice_get_exf.
729        Problem: thsice_solve4temp has an unvectorizable statement that
730        might also be problematic for TAF
731      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
732        does not change the verifcation experiment, but will change all
733        experiments that have this flag undefined (not tested in verification);
734        a little reorganization to save a few 2D fields and recomputations
735      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
736      - 2nd step:  fix some store dirs
737        o seems to work somewhat, i.e. using ifort but not g77
738        o likely cause are incomplete init. or recomputation
739        o start verification/global_ocean.cs32x15/input_ad.thsice
740    o pkg/obcs: add support for exch2
741      - the position of the boundary and prescribed values are specified using
742        a global domain with exch2 facets stacked
743        - in x for N,S boundaries (like W2_mapIO=-1)
744        - in y for E,W boundaries (so E,W boundaries do not overlap)
745    o pkg/mdsio: add support for writing global sections with exch2
746        file layout is as for obcs described above:
747        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
748        - for y-z sections, facets are stacked in y
749    o pkg/thsice:
750       - change a few routines for better vectorization: thsice_albedo.F,
751         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
752         not affected, but in particular the latter routine has changed
753         dramatically (not necessarily easier to read now).
754       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
755       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
756    o verification/lab_sea:
757      - overhaul of the forward model experiments. The main motivation
758        for this revision is that lab_sea has proven quite fragile (when
759        changing the sea-ice code, and switching platforms) to a point
760        when failures were very hard to attribute to specific code problems.
761      - the suspected reason for this fragility is noise amplification by evp so,
762        to start with, we decided to replace evp with lsr in the main experiment.
763      - the input.lsr experiment thus became obsolete and was removed.
764      - it was replaced with the input.fd experiment that uses an
765        analytical "free drift" solution as the ice velocity field.
766      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
767        will hopefully allow us to discriminate problems due to dynamic solvers
768        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
769        us to test additional options, along with the salt plume package.
770      - Finally a pickup was generated (at the end of a one year run) to
771        make the tests more representative of an actual model run. Previously
772        the tests starting point was a 1m thickness of ice everywhere.
773    o pkg/seaice:
774      - introducing S\R seaice_freedrift.F that compute the
775        analytical solution to an approximate ice momentum
776        equation (i.e. the simple stress/coriolis balance).
777      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
778        of the free drift velocity field, and enable its use.
779        To actually use the free drift solution as the model ice
780        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
781    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
782    
783    checkpoint62l (2010/10/04)
784    o pkg/seaice:
785      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
786      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
787       version (with USE_ORIGINAL_SBI undef);
788    o add hooks for new packages OASIS, the package will follow
789      (hooks exclude the seaice pkg for now)
790    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
791      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
792      rather than mdsio_readvector.F/mdsio_writevector.F, within
793      adread_adwrite.F to read/write adjoint-related tapes to disk.
794    o eesupp and pkg/mdsio: ALLOW_WHIO
795      Option to write/read 2D fields to files including tiles halos.
796      The main purpose is for adjoint related "tape I/O".
797      The secondary purpose is for debugging phases.
798      A word on those rather specifically intended purposes.
799      The code was meant to be stripped down to the bare minimum.
800      Typically, there is a unique and basic mapping to the global
801      buffer (tile by tile, then proc by proc, then level by level), and
802      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
803      meant to generate user friendly outputs of various shapes and forms.
804      Rather it is intended, for the knowledgeabale developers,
805      to be largely independent of the many mdsio options, to allow
806      outputs of tiles+halos in debugging phases and in adjoint runs,
807      and to allow some flexibility in tuning (adoint) I/O depending on each
808      file system behavior. With regard to tuning, most of the potential knobs
809      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
810      to specify directories, to specify the typical size of I/O calls, etc.)
811      are not yet included, and will be added if they prove useful.
812    o pkg/seaice:
813       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
814    o pkg/seaice:
815       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
816       code (seaice_budget_ice_if.F) which enable to recover old standard
817       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
818       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
819    o model/src (rStar):
820       use simple average (not area weighted) of rStarFac at U,V point when using
821       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
822       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
823    
824    checkpoint62k (2010/09/17)
825    o adjoint
826       * changed verification/global_ocean.cs32x15 ; adjoint now tests
827         Adams-Bashforth 3 + NLFS + RSTAR
828       * some more modifs required for ECCO-GODAE v4
829    o pkg/seaice
830       add SEAICE_AGE_VOL option to use volume instead of area for
831       integrating SEAICE_AGE
832    o model/src:
833       first check-in of sigma & hybrid-sigma coordinate code ; also includes
834       non-linear free-surface parts ; but pressure-gradient not yet coded.
835    o pkg/ptracers:
836       option for ptracer to convert Salt Relax into additional EmP.
837        tested in exp. global_ocean.90x40x15.dwnslp (update output)
838    
839    checkpoint62j (2010/08/25)
840    o pkg/ggl90:
841       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
842    o pkg/dic: car_flux.F, phos_flux.F
843      - reduce number of exp-calls in order to improve performance
844      - clean up a little (replace fields by their macros, etc., fix
845        typo in CPP-flag)
846    o pkg/ggl90: minor changes
847      - GGL90diffKrS was removed --> always use GGL90diffKr
848      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
849      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
850        (commented out for now)
851      - change in max/min operations to ensure that smoothing is ok
852      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
853      - always use diffKrNrT as background profile (i.e. never use diffKr field)
854    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
855    o pkg/dic:
856      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
857        vectorization
858      - small bug fix in insol for the unlikely case of a cartesian grid
859      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
860        + now vectorize, which also removes adjoint recomputations;
861        + replace integer maksp1 by _RL maskp1
862        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
863    
864    checkpoint62i (2010/07/21)
865    o pkg/flt:
866      - with OBCS: stop floats which enter the OB region
867    o model/src:
868      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
869        for implicit vertical advection.
870    o pkg/seaice:
871     - account for melting in seaice age evolution.
872     - remove double counting of seaice ridging effect on seaice age.
873    
874    checkpoint62h (2010/06/18)
875  o pkg/exch2:  o pkg/exch2:
876   - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).   - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
877  o tools/genmake2  o tools/genmake2
# Line 230  o tools/build_options: Line 1098  o tools/build_options:
1098      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1099  o pkg/ecco  o pkg/ecco
1100    - allow user defined cost function contributions    - allow user defined cost function contributions
1101          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1102          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1103    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1104        the two options are complementary.        the two options are complementary.
1105  o pkg/smooth  o pkg/smooth
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