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revision 1.1214 by jmc, Tue Jan 12 00:23:23 2010 UTC revision 1.1455 by gforget, Wed Jun 15 01:31:34 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8     - re-order diags inits so that they appear in order in available_diagnostics.log
9     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
10       area/heff/hsnow preceeding thermodynamic growth/melt.
11     - modified diag: SIdA; output actual effect, as the description states.
12     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
13     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
14       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
15        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
16     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
17     - added diagnostics for seaice genereic tracers (SItr*).
18     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
19     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
20    o pkg/diagnostics:
21      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
22      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
23        (was _RL, now integer) with option = 0 to retrieve all levels.
24      - add pieces of code to compute velocity potential at each level (new diagnostics
25        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
26        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
27    o model/src (rStar):
28      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
29        affect solution only if z* with full pressure in EOS;
30        update output of test-exp global_ocean.90x40x15.
31    o pkg/seaice:
32      - introduce siEps=1e-5 parameter
33      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
34      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
35      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
36        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
37        as well as ice cover age and ridging index (attached to AREA).
38        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
39        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
40        Up to SItrMaxNum=3 tracers can be used simultaneously.
41    o pkg/salt_plume:
42      -introduce SPsalFRAC run time parameter that sets the fraction of the
43       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
44       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
45    o model debug options:
46      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
47        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
48      - Refine debug-msg printing selection (3 new levels):
49        debugMode  : controls printing of debug messages (sequence of S/R calls).
50        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
51         debLevZero =  0 ; /* level of disabled aux. msg printing */
52         debLevA =  1 ; /* level of minimum  aux. msg printing */
53         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
54         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
55         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
56         debLevE =  5 ; /* level of extensive debug printing */
57        New debugLevel default: with default debugMode value (=F),
58          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
59          and if debugMode=T, default debugLevel = 4 (debLevD).
60        Relation with previous settings:
61         debLevB (=2) corresponds to former debLevA (=1)
62         debLevD (=4) corresponds to former debLevB (=2)
63        Note:
64         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
65         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
66            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
67      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
68        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
69    o pkg/obcs:
70      - change OBCSfixTopo default from True to False (should not change the results);
71        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
72    o pkg/thsice:
73      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
74        2nd layer seaice sublimation (unlikely to happen)
75      - use Interior mask for OBCS in thsice_advection.F (similar to what is
76        done in gad_advection & seaice_advection).
77    o adjoint:
78      bug fix spotted by Gael Forget:
79      seaice_advection and thsice_advection still had
80      legacy CPP options to avoid CS corner updates for adjoint
81    o pkg/seaice:
82      => Change some of the defaults (2011/05/29):
83         - change SEAICEuseFluxForm default (from False to True)
84         - change DIFF1 default (from 0.004 m/s to 0. m/s)
85         And print warnings if DIFF1 is not set in data.seaice and centered
86          avection scheme is used without any diffusion.
87      also:
88      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
89      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
90      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
91        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
92        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
93      update results of test exp.:
94         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
95             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
96             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
97         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
98         seaice_obcs: output (SEAICEuseFluxForm=T)
99      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
100          for standard fwd & AD lab_sea tests (to keep the same output).
101    o pkg/seaice/seaice_growth.F:
102      - use Ian Fenty's capping formulas for actual ice
103      thickness thoughout EVOLUTION branch.
104      - put treatment pathological case #2) in CPP brackets
105      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
106      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
107    o pkg/seaice:
108      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
109      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
110      also pass fac as a param, which can be 1. (to update the tendency
111      field) or the time step (to update the field itself).
112      - seaice_advdiff.F: for multidim, call seaice_diffusion with
113      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
114      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
115      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
116      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
117    o pkg/seaice:
118      diffusion with centered advection scheme (diffus.F & advect.F):
119      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
120        to just compute the laplacian of input-field.
121      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
122      - fix flux-form version in diffus.F to conserve tracer.
123      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
124       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
125    
126    checkpoint62y (2011/05/26)
127    o pkg/seaice:
128     - seaice_growth.F : in EVOLUTION branch, always include
129       a_QSWbyATM_cover in qnet (as it should be).
130     - verification/global_ocean.cs32x15 : update results accordingly
131       (output.seaice.txt output_adm.seaice.txt).
132    o pkg/seaice + obcs:
133     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
134       equivalent of assuming no tracer gradient outside the OB region.
135       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
136     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
137       after changes above);
138     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
139       only at OB location (instead of over a band of OLx width).
140    o pkg/seaice:
141     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
142       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
143    o pkg/obcs:
144      - split header file "OBCS.h" into 4 separated files:
145        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
146       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
147         (contain no conditional statement which depends on OBCS options).
148      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
149        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
150    o ctrl, cost, grdchk & autodiff pkgs:
151      - make options file more standard (like other {PKG}_OPTIONS.h file but
152        with AD_CONFIG.h); clean-up some of the included header files.
153    o pkg/obcs:
154      - do not mask tracer when applying OB (tracer == 0 could generate problems)
155      - apply tracer OB values to tracer field only at OB location (instead of
156        over a band of OLx width)
157      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
158      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
159        obcs_apply_tloc.F & obcs_apply_sloc.F
160    o obcs in model/src:
161      - call OBCS_APPLY_W only if NonHydrostatic.
162      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
163      - reset dEtaHdt and wVel to zero outside OB interior region ;
164      - leave tracer unchanged outside OB interior region: This has no effect
165        on the solution but just to prevent unrealistic tracer value outside OB.
166      - zero out velocity outside OB interior region: This has no effect on
167        the solution but just to prevent unrealistic velocity outside OB.
168    o obcs and non-lin free-surf:
169       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
170       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
171       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
172       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
173       update results of test-exp. exp4(nlfs).
174    o exp4 (nlfs) test-exp:
175       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
176       with NonLin-FreeSurf); update output.nlfs.txt
177    o obcs and 2d/3d solver norm:
178       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
179       and outside OB interior region (will allow to place OB further inside the
180       domain). Depending on the domain, can affects cg2d-Norm (previous
181       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
182       and cg3d-Norm (previous Norm was computed before canceling OB terms),
183       e.g. in tutorial_plume_on_slope.
184      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
185    o pkg rbcs:
186      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
187      - add capability to apply relaxation to horizontal velocity uVel & vVel.
188    o pkg/grdchk: add gradient check for control variable xx_shifwflx
189    o pkg/shelfice/shelfice_init_fixed.F
190      fix CPP-flag combinations
191    o pkg/seaice: Merge iceage code of Pierre Rampal
192      * update/change/correct ice age calculations
193      * add age updates for pathological cases
194      Probably needs more testing...
195    
196    checkpoint62x (2011/05/13)
197    o pkg/mom_vecinv:
198       high-order vorticity scheme: use interior masks (maskInW & S)
199       to zero-out (outside OB) gradient of vorticity.
200    o verification exp.:
201       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
202       hs94.128x64x5 and seaice_obcs ; update results.
203    o pkg/obcs:
204      fix bug in OBeta for YZ sections in obcs_exf_load.F
205    o pkg/ctrl, pkg/shelfice, and optim:
206      - add new control variable xx_shifwflx (fresh water flux underneath ice
207        shelves). This is almost as tedious as obcs-ctrl, because the
208        variables needs its own mask.
209      - add a cost function term that penalizes the deviation of xx_shifwflx
210        from the first guess (zero) in analogy to other control variables
211    o pkg/shelfice:
212      - start basic adjoint
213    o pkg/ctrl:
214      - remove extra 2D field "for good measure" when initializing in
215        ctrl_set_globfld_[xy/xz/yz].F
216      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
217      - improve error messages in ctrl_set_unpack_*
218    o OBC implementation in momentum:
219       use interior masks (maskInC,W & S) in momentum S/R:
220       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
221       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
222       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
223       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
224       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
225        (and also with Leith/Smagorinsky harmonic-viscosity).
226       Update output of experiment dome and exp4 (+nlfs).
227    o exp4 test-exp:
228      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
229        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
230        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
231        time-varying OB at Western-side for wVel (NonHyd); update output.
232      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
233        and biharmonic-viscosity ; also use prescribed time varying OB.
234    o pkg/obcs:
235      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
236    o model/src:
237      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
238      - initialise startTime & nIter0 with unlikely values: allows to set one
239        from the other without ambiguity.
240    o seaice_obcs test-exp.:
241      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
242    o pkg/obcs:
243      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
244        no longer needed with maskInC,W,S in pkg/generic_advdiff.
245    o pkg/seaice:
246      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
247        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
248      - fixed bug in the initialization of sea ice salinity variable HSALT
249        in seaice_init_varia.F  (removed dependence on ICE2WATR)
250    o fizhi-cs test exp.:
251       switch reference output convention for these 2 non-standard test-exp,
252        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
253          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
254       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
255    o model/inc:
256      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
257        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
258    o pkg/seaice:
259      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
260    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
261      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
262        and initial HSALT
263    
264    checkpoint62w (2011/04/26)
265    o pkg/mom_fluxform:
266      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
267      - use parameter "sideDragFactor" in no-slip BC side-drag part.
268      - update output of exp. global_ocean.90x40x15
269    o pkg/mom_vecinv:
270      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
271    o update seaice exp.:
272      use more consistent parameter values (remove "backward compatability only":
273       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
274      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
275       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
276    o update test-exp global_ocean.90x40x15:
277      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
278      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
279      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
280      o turn on zStar & viscA4 in standard set-up (dir input/)
281        and update output files: output.txt & output.dwnslp.txt
282    o new AD-test experiment: obcs_ctrl
283      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
284    o pkg/dic:
285      fix two bugs in handling water vapour pressure in carbonate chemistry
286      and air-sea fluxes. Found by Val Bennington and Galen McKinley
287      (add DIC Option = WATERVAP_BUG to recover old results)
288      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
289    o adding allowInteriorFreezing option to check for water below freezing point
290      at depth and bring the negative heat anomaly to the surface level
291    o pkgs _fields_load:
292      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
293      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
294        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
295        rbcs to get interpolation weights and time reccord number.
296      - fix multi-threading in aim_fields_load.F
297      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
298    o external_fields_load:
299      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
300       interpolation weights) to use in a periodic time-series ; do not divide by
301       time-step to convert to integer:
302       - this fixes case where externForcingPeriod is not multiple of time-step
303          (Thanks to Christopher L. Wolfe)
304       - this fixes case where externForcingPeriod is an odd multiple of time-step
305         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
306      store index of time-record which is currently loaded:
307       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
308       - needed for the adjoint but not yet used because of extensive recomputations;
309         (to be fixed soon)
310    
311    checkpoint62v (2011/04/02)
312    o verification/1D_ocean_ice_column added to test Ian Fenty's
313      pkg/seaice_growth.F modifications for improving sea ice code differentiability
314    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
315      (new velocity statistics after changing maskInW & maskInS definition)
316    o pkg/generic_advdiff with OBCS:
317      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
318      equivalent to assumption of no tracer gradient outside the OB region.
319      This will affect the results if using obcs+biharmonic diffusion.
320      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
321    o pkg/obcs:
322      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
323      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
324      in Interior region. No impact on solution but affects Velocity monitor stats.
325    o pkg/ptracers (adjoint)
326      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
327      tape file for each tracer
328    o model/inc/src and pkg/autodiff: add parameters that allow to turn
329      of parts of the adjoint code at run time. For now, there are only
330      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
331      parameters are set in data.pkg.
332      This is the lazy coward's version of doing this, but still useful for
333      debugging. In order to do it right, everything needs to be moved to
334      pkg/autodiff.
335    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
336      the end; this fixes the adjoint balancing code for open boundaries.
337    o pkg/ctrl:
338      - change behavior of xx_${varname}period to be analogous to exf-conventions:
339        xx_${varname}period =   0.,  means time-independent control part
340        xx_${varname}period = -12., means one-year-periodic monthly control part
341      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
342        clean up ctrl_init a little, remove unused variables
343      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
344      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
345    
346    checkpoint62u (2011/03/15)
347    o model/src:
348      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
349        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
350      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
351        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
352    o pkg/ctrl/obcs/ecco:
353      - remove obsolete, unused, and partially broken code:
354        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
355        ALLOW_CTRL_OBCS_BALANCE
356      - put a stop statement into ecco/cost_obcsvol.F, but also add
357        cost_obcsvol to ecco_ad_diff.list
358    o pkg/ecco: fix counting cost function contributions for obcs (code
359      by Matt M.) and diffkr for diagnostics
360    o pkg/ecco, pkg/ctrl, pkg/grdchk:
361      add cost penalty terms for initial uvel, vvel, eta controls
362      and I/O for prior error files
363    o pkg/mdsio:
364       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
365       (new argument) to check for tiled file in mdsioLocalDir : this fix the
366       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
367    o pkg/ctrl:
368     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
369       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
370       unused and superfluous variables
371     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
372    o pkg/ecco
373     - enable adjoint of Stevens OB
374    o pkg/ctrl/ecco/grdchk:
375      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
376        Fortunately, we do not have any tests for the numerous cpp-flagged
377        option of "obcs as control parameters" so we will never know
378        if this is an improvement (but at least now things compile).
379      - remove an obsolete initialization from ecco_cost_init_barfiles.F
380      - fix some problems within never used ifdefs to make the code compile
381    o pkg/obcs:
382     - Refine Interior mask definition to work with more complex OB (e.g.
383       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
384       read in Interior mask from file. Check if Interior mask is consistent
385       with OB list of indices.
386    o pkg/seaice
387     - beginning code for a seaice tracer package,
388       but currently only used for seaice age: SEAICE_AGE
389       SEAICE_num = 4
390       iTracer = 1: area-weighted ice age
391               = 2: volume-weighted ice age
392               = 3, 4: template for one-year vs. multi-year ice
393       data.seaice has new namelist SEAICE_PARM03 for arrays related to
394       SEAICE_num
395    
396    checkpoint62t (2011/03/05)
397    o pkg/obcs:
398     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
399       then normal component. This ensures that the normal component is set
400       correctly even when it conficts with tangential setting from an other OB.
401       Affects results of test-experiment seaice_obcs: update the output.txt
402    o pkg/obcs:
403     - add code to monitor statistics of dynamical fields at OB.
404     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
405       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
406       - change default: balance the Net inflow through all OB (instead of balancing
407         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
408     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
409       to match Nortern OB inflow (OBCS_balanceFacN=0).
410    o pkg/seaice:
411     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
412    o pkg/seaice (seaice_growth v 1.113):
413     - reverting seaice_growth to v 1.111 in order to have code with exact bit
414       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
415       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
416       runtime flag SEAICEareaFormula is kept but is inactive
417    o model/src:
418     - add new param to scale curvilinear grid distance and area when using
419       a different sphere radius from the grid-files.
420     - test/check multi-threads EXCH applied to local variable (cg2d_x)
421    o adjoint:
422     - enable adjoint of Stevens OB
423     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
424       (a bit delicate because of potentially modified adj. common block structure;
425       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
426    
427    checkpoint62s (2011/02/15)
428    o pkg/seaice (seaice_growth v 1.112):
429     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
430       computing the ice cover tendency from effective thickness tendencies. Include
431       Ian Fenty's formula.
432     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
433       SEAICEareaFormula.
434     - simplify notations for the various d_HEFF/d_AREA terms.
435    o pkg/gmredi:
436     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
437       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
438       add a verification test-run (front_relax.bvp) to test GM_useBVP.
439    o pkg/seaice (seaice_growth v 1.111):
440     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
441     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
442       also melt ice.
443    o pkg/seaice:
444     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
445     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
446    o pkg/cheapaml:
447     - from Nico Wienders: New version of this package.
448    o pkg/flt:
449     - add CPP options to prevent floats to re-enter the opposite side of
450       a periodic domain (default: keep periodicity)
451    o pkg/gmredi:
452     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
453       (needed for multi-dim advection).
454     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
455    o model/src:
456     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
457    o tutorial_tracer_adjsens
458     - extend to NLFS and replace maskC by hFacC
459       (change reference output accordingly)
460    
461    checkpoint62r (2011/01/24)
462    o testreport:
463     - add option -deloutp (-do) to remove output file after successful run
464     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
465       extract exact list of procs from this file ; adjust COMMAND by
466       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
467    o pkg/ecco: replace old ineffective way of penalizing deviations from
468      first guess (of obcs) with code by Matt Mazloff
469    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
470      exf/cal
471      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
472        and handle case of obcs?period == 0
473        Not affected by these changes: There is still an inconsistency in
474        the computation of start/endrec for the obcs variables for ALLOW_CAL
475        defined (see comment by Menemenlis, 7-Mar-2003)
476      - make S/R ctrl_get_gen_rec return something meaningful even if
477        ALLOW_CAL is not defined
478      - ctrl_getobcs?: simplify code so that it does not need to use
479                       S/R exf_swapfields
480    o testreport:
481       allow to test MPI with different number of processors for each experiment:
482       create file "SIZE.h.mpi" in each build dir.
483       Note: update of "-command" argument not yet implemented.
484    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
485      alleviate the need for additional 3D tapes when using
486      the non-inear free surface in the adjoint. This is done
487      by adding an 'update' of hfacc etc. to their current
488      value at the beginning of forward_step.F.
489    o pkg/seaice
490      seaice_lsr: move stress-divergence computations out of outer pseudo-
491      timestepping loop
492    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
493      up, so that the calls of the ctrl_* subroutines are really at the end
494      of the routine.
495    o pkg/gmredi:
496      allow to specify a 2-D horizontal map and a 1-D vertical profil
497      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
498    o pkg/seaice:
499      move lsr iterations from seaice_dynsolver to seaice_lsr.
500    o pkg/seaice:
501      reduce memory footprint of seaice mutldim advection tapes,
502      by using a 2D tape independent of the generic_advdiff ones,
503      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
504    
505    checkpoint62q (2010/12/29)
506    o model/src:
507      - check horizontal grid-spacing for unset or zero/negative values.
508      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
509    o pkg/flt:
510      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
511      - precision of input and output files set according to readBinaryPrec
512        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
513      - initial float position from tiled file was not converted to index space
514        (looks like a bug): fixed to make it similar to initial pos. global file.
515    o global_ocean.cs32x15:
516       change SIZE.h of AD set-up to get same tiling as with MPI.
517       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
518    o model/src:
519       add flag to control printing of domain fields (bathymetry, hFac ...) in
520       ini_mask_etc (call to plot_fieds_xy*).
521    o pkg/thsice:
522       if useEXF, some forcing fields are not valid in overlap: fixed by computing
523       over the interior only + apply EXCH at the end (like with SEAICE advection).
524    o pkg/mdsio:
525      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
526        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
527      - change barrier call for safe multi-threads access to 3-D shared buffer.
528      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
529      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
530        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
531    o pkg/flt:
532      - add fourth-order Runge-Kutta integration
533      - add basic exch2 support (only 1 facet supported so far!)
534    o pkg/mdsio+rw:
535      new S/R to read local (or tile independent) vector (read counterpart of
536       mds_writevec_loc, and front-end write_glvec_rl/rs).
537    o global_ocean.cs32x15: additional input_ad.seaice experiment
538        that uses pkg/seaice rather than pkg/thsice.
539        (using multidim advection for seaice)
540    o towards more F95 syntax for array specification in namelist:
541      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
542        of all verification experiments.
543           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
544          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
545      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
546    o global_ocean.cs32x15: additional input.seaice experiment
547        that uses pkg/seaice rather than pkg/thsice.
548    
549    checkpoint62p (2010/12/17)
550    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
551        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
552    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
553        allow for use of multim. advection in seaice adjoint.
554    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
555      - first attempt to close budgets by taking into account the freshwater
556        flux implied by the sublimation of snow and ice. So far only the
557        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
558        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
559    o eesupp/src:
560      new S/R with new option (NML_EXTENDED_F77) to change array specification
561      from F95 standard to commonly accepted extended F77 form.
562      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
563      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
564      for less tolerant f77 compiler (e.g., pgf77, g77).
565    o globalFiles:
566      commented out in parameter file "data" since it's not safe with MPI
567      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
568      in this case); no longer commented out in restart test (tst_2+2).
569    o add adTapeDir to specify a special directory where adjoint tapes are
570      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
571      and cannot be used together with mdsioLocalDir.
572    o nesting pkgs:
573      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
574      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
575      - add parameter files + utils dir + output from short run on beagle.
576    o pkg/seaice:
577        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
578    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
579      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
580    
581    checkpoint62o (2010/11/25)
582    o pkg/exf:
583      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
584    o pkg/seaice:
585      - seaice_ocean_stress: split a loop for better vectorization of the
586        adjoint code
587      - seaice_growth.F: fix bug in conservation of freshwater connected to
588        capping of heff, put contribution into d_HEFFbyNEG
589      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
590        by something more sensible (parameters that are what their name implies)
591      - change some defaults, so that by default exf-parameters are used for
592        things like rhoAir, cpAir,latent/sensible heat parameters, in order
593        to reproduce the old results, many data.seaice now contain funny values
594        for cpAir and latent heat of sublimation
595    o packages_readparms.F: move exf_readparms up in line so that
596        exf-parameters are visible for other packages (e.g. seaice)
597    o debugMode & debugLevel=2:
598      - differentiate between debugMode & debugLevel=2:
599        debugMode: controls printing of debug messages (sequence of S/R calls).
600        debugLevel: controls printing of algorithm intermediate results and stats.
601      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
602        => allows to print debug-stats without all sequence of call messages.
603      - switch control of debug print from debugLevel to debugMode in many S/R.
604    o pkg/obcs (obcs-sponge):
605        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
606        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
607    o pkg/generic_advdiff:
608      - record overlap minimum size for each advection scheme;
609      - refine criteria on overlap minimum size;
610      - check and stop (in gad_check) if overlap size is too small.
611    o pkg/obcs:
612      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
613        once, in ptracers_implicit.F)
614      - with seaice: remove test on empty file name in obcs_apply_seaice (always
615        apply OB values when tile has OB)
616    o model/src, coriolis setting:
617      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
618        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
619        files (selectCoriMap=3) with any grid.
620      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
621    o pkg/seaice/seaice_growth.F:
622        a few cosmetic changes that reduce the number of lines of code
623    o pkg/obcs: add boundary conditions following Stevens (1990)
624      - the code follows old MOM/NAOSIM code
625      - so far it is only implemented for the eastern and western boundaries
626        and NOT for pTracers
627    o pkg/rbcs:
628      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
629        beginning of the first rbcs forcing period.
630      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
631        offline package, i.e., one file per time, labeled by iteration number;
632        deltaTrbcs sets the timestep with which the data was generated;
633        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
634      - rbcsForcingCycle=0 makes forcing non-cyclic.
635      - make arithmetic safe for negative times and odd forcing periods.
636    
637    checkpoint62n (2010/11/09)
638    o pkg/seaice:
639        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
640    o pkg/obcs:
641       New S/R to copy tracer value from the OB location to narrow band region
642        (width = same as overlap) beyond the OB: preserve OB value (needed for
643        high-order scheme) which were overwritten by EXCH call if in overlap
644        region. Applied to theta, salt, ptracer and advected seaice variables.
645       With seaice: use maskInC in similar way as in gad_advection.F,
646        in seaice_advection.F and advect.F.
647       Update output of experiment seaice_obcs and change exp4 to test OBCS with
648        4th order Adv.Scheme. for pasive salt and ptracer.
649    o tools/genmake2:
650      - when looking for an optfile (not specified), only search for Fortran compiler
651        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
652      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
653        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
654      - set default for CPP to "cpp -traditional -P" (was the case without specifying
655        an optfile, but otherwise default was just "cpp".
656      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
657      - when "CC" is not set in the optfile, look for possible C compiler
658        (instead of just setting CC=cc)
659      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
660        => add a ".F" to ".o" rule for source files with no "#include" (such as
661           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
662      - move gfortran before g77 in list of possible Fortran compiler (consistent
663        with reference compiler switch from g77 to gfortran)
664    o pkg/seaice:
665      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
666        seaice_check that stops the model, when the CPP flag is used.
667      o seaice_growth.F: make capping of ice volume conserving by returning the
668        capped ice as freshwater to EmPmR. This does not change the verification
669        experiments but will change runs where the capping is acutally active
670    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
671      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
672         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
673         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
674    o tools/genmake2:
675      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
676      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
677      - clean previous genmake log files before anything else.
678      - change Makefile to remove testreport log files (*.tr_log) and genmake log
679        files only with "CLEAN" target (instead of "Clean");
680    o pkg/generic_advdiff:
681      Change OBCS in multiDim advection (gad_advection.F):
682       Use maskInC to prevent intermediate update of tracer-field in OB regions,
683       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
684       which were applying future time-step OB values.
685      This way, all explicit calculations use current-time-step OB values
686       (simpler and more consistent).
687      Affects results when set-up uses time-varying OBC and multi-dim advection;
688       update output of experiment seaice_obcs.
689    o pkg/seaice:
690      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
691       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
692         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
693      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
694       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
695       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
696    o pkg aim (2010/10/26):
697      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
698        formulation with obliquity, eccentricity, ... as run-time parameters,
699      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
700        upward shortwave radition at the surface (all-sky and clear-sky).
701    o pkg/obcs:
702      - writing sections with globalFiles=T does not work: switch to tiled-files
703        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
704      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
705      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
706    
707    checkpoint62m (2010/10/21)
708    o pkg/seaice: vectorize seaice_solve4temp.F
709      - move iterations loops outside of i/j-loops
710      - requires 2D arrays for TB and effConduct
711      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
712        modified in this routine
713      - a little bit of clean up, adjusting indentation, etc.
714      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
715        performance and '**TWO' by '**2' (because TWO is a float),
716        replaced ONE, ZERO
717    o eesupp/src:
718       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
719    o pkg/seaice/seaice_growth.F
720      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
721      merging process. The merged routine has two branches, and one activates the 'evolution'
722      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
723      In summary, here is what the '10/10 revision' did consist of
724        part 1: seaice_growth.F revisions 1.71 to 1.75
725          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
726            The emphasis here was on improving readability (e.g. by trying to use meaningful
727            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
728        part 1.5:
729          - revising the lab_sea experiment to make it a more useful (i.e. stable
730            and representative of an actual model run). This was done by generating a
731            (winter) pickup to start from, switching back the main experiment dynamic
732            solver from evp to lsr, having one of the experiments use the free drift solution.
733        part 2: seaice_growth.F revisions 1.76 to 1.85
734          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
735          - Sorting out the various fields units and sign (set early on and reset at the end)
736            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
737            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
738          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
739            and simplifying logical expressions to further improve readibility.
740        part 3: seaice_growth.F revisions 1.86 to 1.89
741          - Re-organize the blocks of code more logically.
742          - Merging the '_if.F' pieces that add something new.
743    o pkg/thsice:
744      - vectorize thsice_solve4temp and thsice_get_exf.
745        Problem: thsice_solve4temp has an unvectorizable statement that
746        might also be problematic for TAF
747      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
748        does not change the verifcation experiment, but will change all
749        experiments that have this flag undefined (not tested in verification);
750        a little reorganization to save a few 2D fields and recomputations
751      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
752      - 2nd step:  fix some store dirs
753        o seems to work somewhat, i.e. using ifort but not g77
754        o likely cause are incomplete init. or recomputation
755        o start verification/global_ocean.cs32x15/input_ad.thsice
756    o pkg/obcs: add support for exch2
757      - the position of the boundary and prescribed values are specified using
758        a global domain with exch2 facets stacked
759        - in x for N,S boundaries (like W2_mapIO=-1)
760        - in y for E,W boundaries (so E,W boundaries do not overlap)
761    o pkg/mdsio: add support for writing global sections with exch2
762        file layout is as for obcs described above:
763        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
764        - for y-z sections, facets are stacked in y
765    o pkg/thsice:
766       - change a few routines for better vectorization: thsice_albedo.F,
767         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
768         not affected, but in particular the latter routine has changed
769         dramatically (not necessarily easier to read now).
770       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
771       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
772    o verification/lab_sea:
773      - overhaul of the forward model experiments. The main motivation
774        for this revision is that lab_sea has proven quite fragile (when
775        changing the sea-ice code, and switching platforms) to a point
776        when failures were very hard to attribute to specific code problems.
777      - the suspected reason for this fragility is noise amplification by evp so,
778        to start with, we decided to replace evp with lsr in the main experiment.
779      - the input.lsr experiment thus became obsolete and was removed.
780      - it was replaced with the input.fd experiment that uses an
781        analytical "free drift" solution as the ice velocity field.
782      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
783        will hopefully allow us to discriminate problems due to dynamic solvers
784        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
785        us to test additional options, along with the salt plume package.
786      - Finally a pickup was generated (at the end of a one year run) to
787        make the tests more representative of an actual model run. Previously
788        the tests starting point was a 1m thickness of ice everywhere.
789    o pkg/seaice:
790      - introducing S\R seaice_freedrift.F that compute the
791        analytical solution to an approximate ice momentum
792        equation (i.e. the simple stress/coriolis balance).
793      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
794        of the free drift velocity field, and enable its use.
795        To actually use the free drift solution as the model ice
796        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
797    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
798    
799    checkpoint62l (2010/10/04)
800    o pkg/seaice:
801      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
802      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
803       version (with USE_ORIGINAL_SBI undef);
804    o add hooks for new packages OASIS, the package will follow
805      (hooks exclude the seaice pkg for now)
806    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
807      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
808      rather than mdsio_readvector.F/mdsio_writevector.F, within
809      adread_adwrite.F to read/write adjoint-related tapes to disk.
810    o eesupp and pkg/mdsio: ALLOW_WHIO
811      Option to write/read 2D fields to files including tiles halos.
812      The main purpose is for adjoint related "tape I/O".
813      The secondary purpose is for debugging phases.
814      A word on those rather specifically intended purposes.
815      The code was meant to be stripped down to the bare minimum.
816      Typically, there is a unique and basic mapping to the global
817      buffer (tile by tile, then proc by proc, then level by level), and
818      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
819      meant to generate user friendly outputs of various shapes and forms.
820      Rather it is intended, for the knowledgeabale developers,
821      to be largely independent of the many mdsio options, to allow
822      outputs of tiles+halos in debugging phases and in adjoint runs,
823      and to allow some flexibility in tuning (adoint) I/O depending on each
824      file system behavior. With regard to tuning, most of the potential knobs
825      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
826      to specify directories, to specify the typical size of I/O calls, etc.)
827      are not yet included, and will be added if they prove useful.
828    o pkg/seaice:
829       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
830    o pkg/seaice:
831       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
832       code (seaice_budget_ice_if.F) which enable to recover old standard
833       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
834       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
835    o model/src (rStar):
836       use simple average (not area weighted) of rStarFac at U,V point when using
837       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
838       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
839    
840    checkpoint62k (2010/09/17)
841    o adjoint
842       * changed verification/global_ocean.cs32x15 ; adjoint now tests
843         Adams-Bashforth 3 + NLFS + RSTAR
844       * some more modifs required for ECCO-GODAE v4
845    o pkg/seaice
846       add SEAICE_AGE_VOL option to use volume instead of area for
847       integrating SEAICE_AGE
848    o model/src:
849       first check-in of sigma & hybrid-sigma coordinate code ; also includes
850       non-linear free-surface parts ; but pressure-gradient not yet coded.
851    o pkg/ptracers:
852       option for ptracer to convert Salt Relax into additional EmP.
853        tested in exp. global_ocean.90x40x15.dwnslp (update output)
854    
855    checkpoint62j (2010/08/25)
856    o pkg/ggl90:
857       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
858    o pkg/dic: car_flux.F, phos_flux.F
859      - reduce number of exp-calls in order to improve performance
860      - clean up a little (replace fields by their macros, etc., fix
861        typo in CPP-flag)
862    o pkg/ggl90: minor changes
863      - GGL90diffKrS was removed --> always use GGL90diffKr
864      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
865      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
866        (commented out for now)
867      - change in max/min operations to ensure that smoothing is ok
868      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
869      - always use diffKrNrT as background profile (i.e. never use diffKr field)
870    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
871    o pkg/dic:
872      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
873        vectorization
874      - small bug fix in insol for the unlikely case of a cartesian grid
875      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
876        + now vectorize, which also removes adjoint recomputations;
877        + replace integer maksp1 by _RL maskp1
878        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
879    
880    checkpoint62i (2010/07/21)
881    o pkg/flt:
882      - with OBCS: stop floats which enter the OB region
883    o model/src:
884      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
885        for implicit vertical advection.
886    o pkg/seaice:
887     - account for melting in seaice age evolution.
888     - remove double counting of seaice ridging effect on seaice age.
889    
890    checkpoint62h (2010/06/18)
891    o pkg/exch2:
892     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
893    o tools/genmake2
894      - remove "-pdefault" option: redundant with the use of "packages.conf";
895      - remove file pkg/pkg_default : set the default as a pkg group
896        ("default_pkg_list") defined in pkg/pkg_groups;
897      - fix for case pkg/pkg_depend is missing (was hanging before);
898      - add option "-pgroups" to specify a different pkg_groups than the default.
899    o verification/adjustment.cs-32x32x1:
900       add a "minimal" set-up test (code_min & input_min) which only compiles
901       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
902    o tools/genmake2
903      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
904      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
905    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
906      files are nearly the same anyway.
907      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
908       - redefinition of tau(i,i) (by a factor of ustar)
909       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
910       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
911       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
912       - replace
913         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
914         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
915         by
916         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
917         (changes results)
918       -> exf_bulkformulae v1.22,
919          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
920          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
921                    output.txt 1.63
922           offline_exf_seaice: output.seaicetd.txt 1.7
923           seaice_obcs: output.txt 1.10)
924      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
925       -> exf_bulkformulae v1.23,
926          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
927          and global_ocean.cs32x15.icedyn (only 11 matching digits)
928      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
929    o adjoint of exch-1:
930     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
931       (note: was already like this when using EXCH-2) and remove flow dir
932       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
933     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
934     - update pkg/exch2 diff list.
935    
936    checkpoint62g (2010/05/19)
937    o eesupp/src (exch-1):
938     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
939       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
940       (renamed to exch1_*rx_cube.F).
941     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
942       to call new exch1 S/R ; update Makefile and .cvsignore.
943     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
944       exch2_xy_rx later)
945      Note: after updating your code, need to run "make clean" in eesupp/src
946    o test experiment bottom_ctrl_5x5:
947       new output_adm.txt with fewer grdchk & less monitor output.
948    o model/src:
949      remove the call to ini_cori in initialise_varia.F (just keep the usual one
950       in initialise_fixed.F). More consistent with coriolis & horizontal grid
951       beeing treated in the same way (ini_grid is not called a 2nd time).
952    o pkg/exf:
953      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
954      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
955      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
956      - cosmetic changes to exf_bulkformulae.F to make it look more like
957        exf_bulk_largeyeager04.F
958    o eesupp/src (exch-1):
959      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
960      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
961        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
962        (even without using MPI).
963      - Message mode: move RecvAck setting (indicator of buffer being ready)
964        from send_put to recv_get S/R (was useless before, but not sure if
965        it's much more useful now);
966      - Switch the order of sync: MPI-proc 1rst and then threads;
967      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
968      - fix AD code for communication mode ='get' (but not used).
969    o model/src:
970      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
971      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
972    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
973    o pkg/ctrl: require a specific set of control variables and exf-flags for
974      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
975    o model/src:
976     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
977       1rst forward sweep, to avoid over-writing output files during recomputations
978       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
979     b) 2nd version:
980      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
981      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
982         writePickupAtEnd) + seaice & ptracers output;
983      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
984    o model/src:
985      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
986    o pkg/exch2:
987      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
988      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
989    o pkg/autodiff & exch2:
990      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
991      (for now, only if ALLOW_EXCH2 is defined).
992    o pkg/autodiff:
993      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
994        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
995       + clean-up comments (_RS is not always real*4)
996      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
997      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
998        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
999    o testreport (AD-tests):
1000      no longer link files from dir "../input" (1rst link files from
1001      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1002    
1003    checkpoint62f (2010/04/29)
1004    o model/src/the_main_loop.F:
1005      adjust store directives for seaice evp and multicategory according to
1006      pkg/ecco/the_main_loop.F
1007    o adjoint:
1008      global_sum_ad was incomplete (noted many times by many people ;)
1009      nice description by Jean U. as follows:
1010      * allreduce(var) in global_sum.F can be interpreted as
1011        reduce(sum) followed by broadcast of sum.
1012      * The adjoint of that is
1013        sum(adjoint) followed by broadcast(summed adjoint value)
1014        or in other words, allreduce(sum, adjoint vars)
1015      We were missing the sum(adjoint)!
1016      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1017      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1018      The fix should produce 16-digit accuracy between
1019      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1020      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1021      We'll probably change this yet again shortly
1022    o eesupp/src:
1023      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1024    o pkg/icefront
1025      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1026        specification of addmass array based on a 2D field, which is added
1027        at bottommost wet level at each horizontal location.
1028    o model/src:
1029     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1030     layout; (not always compatible with delX,delY setting; commented out for now).
1031    o pkg/exch2:
1032     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1033     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1034    
1035    checkpoint62e (2010/04/15)
1036    o pkg/obcs:
1037      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1038    o pkg/dic:
1039      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1040        (note: not presently tested in any forward verification exp.)
1041       update tutorial_global_oce_biogeo AD output file.
1042    o pkg/exf:
1043      - account for the variation of albedo as a function of zenith angle
1044        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1045    o build_options:
1046     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1047    o pkg/dic:
1048      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1049      - use binary pickup file for restart;
1050      - initialise atmos-CO2 box from dic_pCO2 parameter;
1051      - fix multi-threaded.
1052    o pkg/rbcs:
1053     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1054       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1055     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1056       and update output.txt
1057    o pkg/kpp:
1058     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1059     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1060       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1061       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1062     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1063       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1064    o pkg/offline:
1065      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1066      (bug was added in version 1.10 on 2007-08-23).
1067    o pkg/offline:
1068      - no need to specify periodicExternalForcing, etc ... to use offline pack
1069      - offline input files no longer just single prec --> parameter offlineLoadPrec
1070    o verification/lab_sea:
1071      change AD test to multi-tile setup and update all 4 AD output.
1072      NOTE: while cost function values remain very similar,
1073      gradients are very different, although gradient checks are self-consistent
1074      Should try to get to the bottom of this (cost function summation order?)
1075    o pkg/dic:
1076      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1077      a weakness of TAF that drops part of double precision in log10 derivative.
1078      <= changes removed since problem has been fixed in current TAF version 1.9.71
1079      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1080    o pkg/ecco:
1081      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1082      update all 4 lab_sea AD output.
1083    
1084    checkpoint62d (2010/03/22)
1085    o build_options:
1086      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1087    o remove unbalanced quote (single or double) in commented line of source code
1088      (may cause some warning with some preprocessor/makedepend versions).
1089    o pkg/seaice:
1090      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1091       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1092    o testreport:
1093      add option '-runonly' (short: '-ro') to just do the run part (without make).
1094    o eesupp: remove JAM communication code (obsolete).
1095    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1096      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1097      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1098      (update also the output).
1099    
1100    checkpoint62c (2010/03/02)
1101    o tools/build_options :
1102       move (some) old optfiles from build_options/ to build_options/unsupported/
1103    o model/src and pkg/exf
1104       surface relaxation -- separating data and data.exf options
1105       The point is to ensure that we specify the surface relaxation
1106       either in data or in data.exf (but not half and half) and to
1107       avoid an accidental relaxation to 0 (which happened if a time
1108       scale was specified but the file name was left empty)
1109    o model/src model/inc and pkg/mom_common
1110       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1111       => addition to the viscosity field as computed by others schemes
1112    o tools/build_options:
1113      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1114        but keep the former optfile for few weeks for smooth transition
1115    o pkg/ecco
1116      - allow user defined cost function contributions
1117         CPP: ALLOW_USERCOST_CONTRIBUTION
1118         USAGE: compute contributions in cost_usercost_all.F
1119      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1120          the two options are complementary.
1121    o pkg/smooth
1122      - migration from contrib to the main repository
1123    
1124    checkpoint62b (2010/01/26)
1125    o pkg/monitor:
1126      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1127        (in case someone forgot to update customized pieces of code)
1128    o nonHydrostatic:
1129      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1130      - add a simple 2-D experiment (short_surf_wave) to test it.
1131    o pkg/icefront:
1132       adding the shell of, and the hooks to, a new package that
1133       will model melting and freezing of vertical glacier ice fronts
1134    o momentum:
1135      add diagnostics of momentum tendency from Hydrostatic pressure gradient
1136       (without surf.pressure term: would need a 2nd filling since implicit term).
1137    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1138      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1139      cannot deal with the former
1140    o cleaning:
1141      - remove all (except OpenAD) old TLM output from results_ad dirs.
1142      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1143      - comment out maskH definition (replaced by maskInC)
1144    o pkg/monitor:
1145      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1146        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1147    
1148    checkpoint62a (2010/01/15)
1149    o model/src:
1150      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1151    o pkg/diagnostics:
1152      - add optional level number diagnostics (i.e., level number to be define
1153        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1154      - strictly check for valid parser-code(10) ;
1155      - check if adding diag to the list from the right place.
1156    o pkg/longstep:
1157      - change parameters and fix tracer conservation with rstar/nonlinear free surface
1158    o diagnostics:
1159     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1160       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1161  o pkg/diagnostics:  o pkg/diagnostics:
1162   - Add option for writing vertical integral (sum of selected levels) of an output   - Add option for writing vertical integral (sum of selected levels) of an output
1163      field instead of writing output field levels. Activate this option on a per      field instead of writing output field levels. Activate this option on a per
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