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revision 1.1217 by jmc, Fri Jan 15 00:59:33 2010 UTC revision 1.1456 by heimbach, Thu Jun 16 22:50:41 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 adjoint monitor:
8     - Add adjoint monitor output for packages exf, seaice
9    o pkg/seaice:
10     - re-order diags inits so that they appear in order in available_diagnostics.log
11     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
12       area/heff/hsnow preceeding thermodynamic growth/melt.
13     - modified diag: SIdA; output actual effect, as the description states.
14     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
15     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
16       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
17        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
18     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
19     - added diagnostics for seaice genereic tracers (SItr*).
20     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
21     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
22    o pkg/diagnostics:
23      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
24      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
25        (was _RL, now integer) with option = 0 to retrieve all levels.
26      - add pieces of code to compute velocity potential at each level (new diagnostics
27        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
28        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
29    o model/src (rStar):
30      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
31        affect solution only if z* with full pressure in EOS;
32        update output of test-exp global_ocean.90x40x15.
33    o pkg/seaice:
34      - introduce siEps=1e-5 parameter
35      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
36      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
37      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
38        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
39        as well as ice cover age and ridging index (attached to AREA).
40        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
41        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
42        Up to SItrMaxNum=3 tracers can be used simultaneously.
43    o pkg/salt_plume:
44      -introduce SPsalFRAC run time parameter that sets the fraction of the
45       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
46       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
47    o model debug options:
48      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
49        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
50      - Refine debug-msg printing selection (3 new levels):
51        debugMode  : controls printing of debug messages (sequence of S/R calls).
52        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
53         debLevZero =  0 ; /* level of disabled aux. msg printing */
54         debLevA =  1 ; /* level of minimum  aux. msg printing */
55         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
56         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
57         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
58         debLevE =  5 ; /* level of extensive debug printing */
59        New debugLevel default: with default debugMode value (=F),
60          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
61          and if debugMode=T, default debugLevel = 4 (debLevD).
62        Relation with previous settings:
63         debLevB (=2) corresponds to former debLevA (=1)
64         debLevD (=4) corresponds to former debLevB (=2)
65        Note:
66         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
67         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
68            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
69      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
70        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
71    o pkg/obcs:
72      - change OBCSfixTopo default from True to False (should not change the results);
73        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
74    o pkg/thsice:
75      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
76        2nd layer seaice sublimation (unlikely to happen)
77      - use Interior mask for OBCS in thsice_advection.F (similar to what is
78        done in gad_advection & seaice_advection).
79    o adjoint:
80      bug fix spotted by Gael Forget:
81      seaice_advection and thsice_advection still had
82      legacy CPP options to avoid CS corner updates for adjoint
83    o pkg/seaice:
84      => Change some of the defaults (2011/05/29):
85         - change SEAICEuseFluxForm default (from False to True)
86         - change DIFF1 default (from 0.004 m/s to 0. m/s)
87         And print warnings if DIFF1 is not set in data.seaice and centered
88          avection scheme is used without any diffusion.
89      also:
90      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
91      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
92      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
93        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
94        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
95      update results of test exp.:
96         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
97             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
98             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
99         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
100         seaice_obcs: output (SEAICEuseFluxForm=T)
101      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
102          for standard fwd & AD lab_sea tests (to keep the same output).
103    o pkg/seaice/seaice_growth.F:
104      - use Ian Fenty's capping formulas for actual ice
105      thickness thoughout EVOLUTION branch.
106      - put treatment pathological case #2) in CPP brackets
107      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
108      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
109    o pkg/seaice:
110      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
111      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
112      also pass fac as a param, which can be 1. (to update the tendency
113      field) or the time step (to update the field itself).
114      - seaice_advdiff.F: for multidim, call seaice_diffusion with
115      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
116      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
117      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
118      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
119    o pkg/seaice:
120      diffusion with centered advection scheme (diffus.F & advect.F):
121      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
122        to just compute the laplacian of input-field.
123      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
124      - fix flux-form version in diffus.F to conserve tracer.
125      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
126       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
127    
128    checkpoint62y (2011/05/26)
129    o pkg/seaice:
130     - seaice_growth.F : in EVOLUTION branch, always include
131       a_QSWbyATM_cover in qnet (as it should be).
132     - verification/global_ocean.cs32x15 : update results accordingly
133       (output.seaice.txt output_adm.seaice.txt).
134    o pkg/seaice + obcs:
135     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
136       equivalent of assuming no tracer gradient outside the OB region.
137       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
138     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
139       after changes above);
140     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
141       only at OB location (instead of over a band of OLx width).
142    o pkg/seaice:
143     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
144       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
145    o pkg/obcs:
146      - split header file "OBCS.h" into 4 separated files:
147        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
148       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
149         (contain no conditional statement which depends on OBCS options).
150      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
151        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
152    o ctrl, cost, grdchk & autodiff pkgs:
153      - make options file more standard (like other {PKG}_OPTIONS.h file but
154        with AD_CONFIG.h); clean-up some of the included header files.
155    o pkg/obcs:
156      - do not mask tracer when applying OB (tracer == 0 could generate problems)
157      - apply tracer OB values to tracer field only at OB location (instead of
158        over a band of OLx width)
159      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
160      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
161        obcs_apply_tloc.F & obcs_apply_sloc.F
162    o obcs in model/src:
163      - call OBCS_APPLY_W only if NonHydrostatic.
164      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
165      - reset dEtaHdt and wVel to zero outside OB interior region ;
166      - leave tracer unchanged outside OB interior region: This has no effect
167        on the solution but just to prevent unrealistic tracer value outside OB.
168      - zero out velocity outside OB interior region: This has no effect on
169        the solution but just to prevent unrealistic velocity outside OB.
170    o obcs and non-lin free-surf:
171       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
172       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
173       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
174       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
175       update results of test-exp. exp4(nlfs).
176    o exp4 (nlfs) test-exp:
177       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
178       with NonLin-FreeSurf); update output.nlfs.txt
179    o obcs and 2d/3d solver norm:
180       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
181       and outside OB interior region (will allow to place OB further inside the
182       domain). Depending on the domain, can affects cg2d-Norm (previous
183       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
184       and cg3d-Norm (previous Norm was computed before canceling OB terms),
185       e.g. in tutorial_plume_on_slope.
186      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
187    o pkg rbcs:
188      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
189      - add capability to apply relaxation to horizontal velocity uVel & vVel.
190    o pkg/grdchk: add gradient check for control variable xx_shifwflx
191    o pkg/shelfice/shelfice_init_fixed.F
192      fix CPP-flag combinations
193    o pkg/seaice: Merge iceage code of Pierre Rampal
194      * update/change/correct ice age calculations
195      * add age updates for pathological cases
196      Probably needs more testing...
197    
198    checkpoint62x (2011/05/13)
199    o pkg/mom_vecinv:
200       high-order vorticity scheme: use interior masks (maskInW & S)
201       to zero-out (outside OB) gradient of vorticity.
202    o verification exp.:
203       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
204       hs94.128x64x5 and seaice_obcs ; update results.
205    o pkg/obcs:
206      fix bug in OBeta for YZ sections in obcs_exf_load.F
207    o pkg/ctrl, pkg/shelfice, and optim:
208      - add new control variable xx_shifwflx (fresh water flux underneath ice
209        shelves). This is almost as tedious as obcs-ctrl, because the
210        variables needs its own mask.
211      - add a cost function term that penalizes the deviation of xx_shifwflx
212        from the first guess (zero) in analogy to other control variables
213    o pkg/shelfice:
214      - start basic adjoint
215    o pkg/ctrl:
216      - remove extra 2D field "for good measure" when initializing in
217        ctrl_set_globfld_[xy/xz/yz].F
218      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
219      - improve error messages in ctrl_set_unpack_*
220    o OBC implementation in momentum:
221       use interior masks (maskInC,W & S) in momentum S/R:
222       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
223       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
224       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
225       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
226       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
227        (and also with Leith/Smagorinsky harmonic-viscosity).
228       Update output of experiment dome and exp4 (+nlfs).
229    o exp4 test-exp:
230      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
231        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
232        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
233        time-varying OB at Western-side for wVel (NonHyd); update output.
234      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
235        and biharmonic-viscosity ; also use prescribed time varying OB.
236    o pkg/obcs:
237      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
238    o model/src:
239      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
240      - initialise startTime & nIter0 with unlikely values: allows to set one
241        from the other without ambiguity.
242    o seaice_obcs test-exp.:
243      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
244    o pkg/obcs:
245      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
246        no longer needed with maskInC,W,S in pkg/generic_advdiff.
247    o pkg/seaice:
248      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
249        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
250      - fixed bug in the initialization of sea ice salinity variable HSALT
251        in seaice_init_varia.F  (removed dependence on ICE2WATR)
252    o fizhi-cs test exp.:
253       switch reference output convention for these 2 non-standard test-exp,
254        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
255          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
256       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
257    o model/inc:
258      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
259        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
260    o pkg/seaice:
261      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
262    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
263      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
264        and initial HSALT
265    
266    checkpoint62w (2011/04/26)
267    o pkg/mom_fluxform:
268      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
269      - use parameter "sideDragFactor" in no-slip BC side-drag part.
270      - update output of exp. global_ocean.90x40x15
271    o pkg/mom_vecinv:
272      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
273    o update seaice exp.:
274      use more consistent parameter values (remove "backward compatability only":
275       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
276      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
277       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
278    o update test-exp global_ocean.90x40x15:
279      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
280      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
281      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
282      o turn on zStar & viscA4 in standard set-up (dir input/)
283        and update output files: output.txt & output.dwnslp.txt
284    o new AD-test experiment: obcs_ctrl
285      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
286    o pkg/dic:
287      fix two bugs in handling water vapour pressure in carbonate chemistry
288      and air-sea fluxes. Found by Val Bennington and Galen McKinley
289      (add DIC Option = WATERVAP_BUG to recover old results)
290      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
291    o adding allowInteriorFreezing option to check for water below freezing point
292      at depth and bring the negative heat anomaly to the surface level
293    o pkgs _fields_load:
294      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
295      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
296        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
297        rbcs to get interpolation weights and time reccord number.
298      - fix multi-threading in aim_fields_load.F
299      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
300    o external_fields_load:
301      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
302       interpolation weights) to use in a periodic time-series ; do not divide by
303       time-step to convert to integer:
304       - this fixes case where externForcingPeriod is not multiple of time-step
305          (Thanks to Christopher L. Wolfe)
306       - this fixes case where externForcingPeriod is an odd multiple of time-step
307         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
308      store index of time-record which is currently loaded:
309       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
310       - needed for the adjoint but not yet used because of extensive recomputations;
311         (to be fixed soon)
312    
313    checkpoint62v (2011/04/02)
314    o verification/1D_ocean_ice_column added to test Ian Fenty's
315      pkg/seaice_growth.F modifications for improving sea ice code differentiability
316    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
317      (new velocity statistics after changing maskInW & maskInS definition)
318    o pkg/generic_advdiff with OBCS:
319      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
320      equivalent to assumption of no tracer gradient outside the OB region.
321      This will affect the results if using obcs+biharmonic diffusion.
322      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
323    o pkg/obcs:
324      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
325      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
326      in Interior region. No impact on solution but affects Velocity monitor stats.
327    o pkg/ptracers (adjoint)
328      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
329      tape file for each tracer
330    o model/inc/src and pkg/autodiff: add parameters that allow to turn
331      of parts of the adjoint code at run time. For now, there are only
332      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
333      parameters are set in data.pkg.
334      This is the lazy coward's version of doing this, but still useful for
335      debugging. In order to do it right, everything needs to be moved to
336      pkg/autodiff.
337    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
338      the end; this fixes the adjoint balancing code for open boundaries.
339    o pkg/ctrl:
340      - change behavior of xx_${varname}period to be analogous to exf-conventions:
341        xx_${varname}period =   0.,  means time-independent control part
342        xx_${varname}period = -12., means one-year-periodic monthly control part
343      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
344        clean up ctrl_init a little, remove unused variables
345      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
346      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
347    
348    checkpoint62u (2011/03/15)
349    o model/src:
350      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
351        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
352      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
353        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
354    o pkg/ctrl/obcs/ecco:
355      - remove obsolete, unused, and partially broken code:
356        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
357        ALLOW_CTRL_OBCS_BALANCE
358      - put a stop statement into ecco/cost_obcsvol.F, but also add
359        cost_obcsvol to ecco_ad_diff.list
360    o pkg/ecco: fix counting cost function contributions for obcs (code
361      by Matt M.) and diffkr for diagnostics
362    o pkg/ecco, pkg/ctrl, pkg/grdchk:
363      add cost penalty terms for initial uvel, vvel, eta controls
364      and I/O for prior error files
365    o pkg/mdsio:
366       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
367       (new argument) to check for tiled file in mdsioLocalDir : this fix the
368       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
369    o pkg/ctrl:
370     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
371       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
372       unused and superfluous variables
373     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
374    o pkg/ecco
375     - enable adjoint of Stevens OB
376    o pkg/ctrl/ecco/grdchk:
377      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
378        Fortunately, we do not have any tests for the numerous cpp-flagged
379        option of "obcs as control parameters" so we will never know
380        if this is an improvement (but at least now things compile).
381      - remove an obsolete initialization from ecco_cost_init_barfiles.F
382      - fix some problems within never used ifdefs to make the code compile
383    o pkg/obcs:
384     - Refine Interior mask definition to work with more complex OB (e.g.
385       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
386       read in Interior mask from file. Check if Interior mask is consistent
387       with OB list of indices.
388    o pkg/seaice
389     - beginning code for a seaice tracer package,
390       but currently only used for seaice age: SEAICE_AGE
391       SEAICE_num = 4
392       iTracer = 1: area-weighted ice age
393               = 2: volume-weighted ice age
394               = 3, 4: template for one-year vs. multi-year ice
395       data.seaice has new namelist SEAICE_PARM03 for arrays related to
396       SEAICE_num
397    
398    checkpoint62t (2011/03/05)
399    o pkg/obcs:
400     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
401       then normal component. This ensures that the normal component is set
402       correctly even when it conficts with tangential setting from an other OB.
403       Affects results of test-experiment seaice_obcs: update the output.txt
404    o pkg/obcs:
405     - add code to monitor statistics of dynamical fields at OB.
406     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
407       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
408       - change default: balance the Net inflow through all OB (instead of balancing
409         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
410     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
411       to match Nortern OB inflow (OBCS_balanceFacN=0).
412    o pkg/seaice:
413     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
414    o pkg/seaice (seaice_growth v 1.113):
415     - reverting seaice_growth to v 1.111 in order to have code with exact bit
416       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
417       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
418       runtime flag SEAICEareaFormula is kept but is inactive
419    o model/src:
420     - add new param to scale curvilinear grid distance and area when using
421       a different sphere radius from the grid-files.
422     - test/check multi-threads EXCH applied to local variable (cg2d_x)
423    o adjoint:
424     - enable adjoint of Stevens OB
425     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
426       (a bit delicate because of potentially modified adj. common block structure;
427       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
428    
429    checkpoint62s (2011/02/15)
430    o pkg/seaice (seaice_growth v 1.112):
431     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
432       computing the ice cover tendency from effective thickness tendencies. Include
433       Ian Fenty's formula.
434     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
435       SEAICEareaFormula.
436     - simplify notations for the various d_HEFF/d_AREA terms.
437    o pkg/gmredi:
438     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
439       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
440       add a verification test-run (front_relax.bvp) to test GM_useBVP.
441    o pkg/seaice (seaice_growth v 1.111):
442     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
443     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
444       also melt ice.
445    o pkg/seaice:
446     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
447     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
448    o pkg/cheapaml:
449     - from Nico Wienders: New version of this package.
450    o pkg/flt:
451     - add CPP options to prevent floats to re-enter the opposite side of
452       a periodic domain (default: keep periodicity)
453    o pkg/gmredi:
454     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
455       (needed for multi-dim advection).
456     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
457    o model/src:
458     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
459    o tutorial_tracer_adjsens
460     - extend to NLFS and replace maskC by hFacC
461       (change reference output accordingly)
462    
463    checkpoint62r (2011/01/24)
464    o testreport:
465     - add option -deloutp (-do) to remove output file after successful run
466     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
467       extract exact list of procs from this file ; adjust COMMAND by
468       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
469    o pkg/ecco: replace old ineffective way of penalizing deviations from
470      first guess (of obcs) with code by Matt Mazloff
471    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
472      exf/cal
473      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
474        and handle case of obcs?period == 0
475        Not affected by these changes: There is still an inconsistency in
476        the computation of start/endrec for the obcs variables for ALLOW_CAL
477        defined (see comment by Menemenlis, 7-Mar-2003)
478      - make S/R ctrl_get_gen_rec return something meaningful even if
479        ALLOW_CAL is not defined
480      - ctrl_getobcs?: simplify code so that it does not need to use
481                       S/R exf_swapfields
482    o testreport:
483       allow to test MPI with different number of processors for each experiment:
484       create file "SIZE.h.mpi" in each build dir.
485       Note: update of "-command" argument not yet implemented.
486    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
487      alleviate the need for additional 3D tapes when using
488      the non-inear free surface in the adjoint. This is done
489      by adding an 'update' of hfacc etc. to their current
490      value at the beginning of forward_step.F.
491    o pkg/seaice
492      seaice_lsr: move stress-divergence computations out of outer pseudo-
493      timestepping loop
494    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
495      up, so that the calls of the ctrl_* subroutines are really at the end
496      of the routine.
497    o pkg/gmredi:
498      allow to specify a 2-D horizontal map and a 1-D vertical profil
499      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
500    o pkg/seaice:
501      move lsr iterations from seaice_dynsolver to seaice_lsr.
502    o pkg/seaice:
503      reduce memory footprint of seaice mutldim advection tapes,
504      by using a 2D tape independent of the generic_advdiff ones,
505      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
506    
507    checkpoint62q (2010/12/29)
508    o model/src:
509      - check horizontal grid-spacing for unset or zero/negative values.
510      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
511    o pkg/flt:
512      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
513      - precision of input and output files set according to readBinaryPrec
514        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
515      - initial float position from tiled file was not converted to index space
516        (looks like a bug): fixed to make it similar to initial pos. global file.
517    o global_ocean.cs32x15:
518       change SIZE.h of AD set-up to get same tiling as with MPI.
519       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
520    o model/src:
521       add flag to control printing of domain fields (bathymetry, hFac ...) in
522       ini_mask_etc (call to plot_fieds_xy*).
523    o pkg/thsice:
524       if useEXF, some forcing fields are not valid in overlap: fixed by computing
525       over the interior only + apply EXCH at the end (like with SEAICE advection).
526    o pkg/mdsio:
527      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
528        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
529      - change barrier call for safe multi-threads access to 3-D shared buffer.
530      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
531      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
532        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
533    o pkg/flt:
534      - add fourth-order Runge-Kutta integration
535      - add basic exch2 support (only 1 facet supported so far!)
536    o pkg/mdsio+rw:
537      new S/R to read local (or tile independent) vector (read counterpart of
538       mds_writevec_loc, and front-end write_glvec_rl/rs).
539    o global_ocean.cs32x15: additional input_ad.seaice experiment
540        that uses pkg/seaice rather than pkg/thsice.
541        (using multidim advection for seaice)
542    o towards more F95 syntax for array specification in namelist:
543      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
544        of all verification experiments.
545           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
546          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
547      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
548    o global_ocean.cs32x15: additional input.seaice experiment
549        that uses pkg/seaice rather than pkg/thsice.
550    
551    checkpoint62p (2010/12/17)
552    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
553        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
554    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
555        allow for use of multim. advection in seaice adjoint.
556    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
557      - first attempt to close budgets by taking into account the freshwater
558        flux implied by the sublimation of snow and ice. So far only the
559        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
560        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
561    o eesupp/src:
562      new S/R with new option (NML_EXTENDED_F77) to change array specification
563      from F95 standard to commonly accepted extended F77 form.
564      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
565      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
566      for less tolerant f77 compiler (e.g., pgf77, g77).
567    o globalFiles:
568      commented out in parameter file "data" since it's not safe with MPI
569      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
570      in this case); no longer commented out in restart test (tst_2+2).
571    o add adTapeDir to specify a special directory where adjoint tapes are
572      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
573      and cannot be used together with mdsioLocalDir.
574    o nesting pkgs:
575      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
576      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
577      - add parameter files + utils dir + output from short run on beagle.
578    o pkg/seaice:
579        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
580    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
581      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
582    
583    checkpoint62o (2010/11/25)
584    o pkg/exf:
585      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
586    o pkg/seaice:
587      - seaice_ocean_stress: split a loop for better vectorization of the
588        adjoint code
589      - seaice_growth.F: fix bug in conservation of freshwater connected to
590        capping of heff, put contribution into d_HEFFbyNEG
591      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
592        by something more sensible (parameters that are what their name implies)
593      - change some defaults, so that by default exf-parameters are used for
594        things like rhoAir, cpAir,latent/sensible heat parameters, in order
595        to reproduce the old results, many data.seaice now contain funny values
596        for cpAir and latent heat of sublimation
597    o packages_readparms.F: move exf_readparms up in line so that
598        exf-parameters are visible for other packages (e.g. seaice)
599    o debugMode & debugLevel=2:
600      - differentiate between debugMode & debugLevel=2:
601        debugMode: controls printing of debug messages (sequence of S/R calls).
602        debugLevel: controls printing of algorithm intermediate results and stats.
603      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
604        => allows to print debug-stats without all sequence of call messages.
605      - switch control of debug print from debugLevel to debugMode in many S/R.
606    o pkg/obcs (obcs-sponge):
607        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
608        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
609    o pkg/generic_advdiff:
610      - record overlap minimum size for each advection scheme;
611      - refine criteria on overlap minimum size;
612      - check and stop (in gad_check) if overlap size is too small.
613    o pkg/obcs:
614      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
615        once, in ptracers_implicit.F)
616      - with seaice: remove test on empty file name in obcs_apply_seaice (always
617        apply OB values when tile has OB)
618    o model/src, coriolis setting:
619      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
620        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
621        files (selectCoriMap=3) with any grid.
622      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
623    o pkg/seaice/seaice_growth.F:
624        a few cosmetic changes that reduce the number of lines of code
625    o pkg/obcs: add boundary conditions following Stevens (1990)
626      - the code follows old MOM/NAOSIM code
627      - so far it is only implemented for the eastern and western boundaries
628        and NOT for pTracers
629    o pkg/rbcs:
630      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
631        beginning of the first rbcs forcing period.
632      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
633        offline package, i.e., one file per time, labeled by iteration number;
634        deltaTrbcs sets the timestep with which the data was generated;
635        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
636      - rbcsForcingCycle=0 makes forcing non-cyclic.
637      - make arithmetic safe for negative times and odd forcing periods.
638    
639    checkpoint62n (2010/11/09)
640    o pkg/seaice:
641        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
642    o pkg/obcs:
643       New S/R to copy tracer value from the OB location to narrow band region
644        (width = same as overlap) beyond the OB: preserve OB value (needed for
645        high-order scheme) which were overwritten by EXCH call if in overlap
646        region. Applied to theta, salt, ptracer and advected seaice variables.
647       With seaice: use maskInC in similar way as in gad_advection.F,
648        in seaice_advection.F and advect.F.
649       Update output of experiment seaice_obcs and change exp4 to test OBCS with
650        4th order Adv.Scheme. for pasive salt and ptracer.
651    o tools/genmake2:
652      - when looking for an optfile (not specified), only search for Fortran compiler
653        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
654      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
655        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
656      - set default for CPP to "cpp -traditional -P" (was the case without specifying
657        an optfile, but otherwise default was just "cpp".
658      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
659      - when "CC" is not set in the optfile, look for possible C compiler
660        (instead of just setting CC=cc)
661      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
662        => add a ".F" to ".o" rule for source files with no "#include" (such as
663           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
664      - move gfortran before g77 in list of possible Fortran compiler (consistent
665        with reference compiler switch from g77 to gfortran)
666    o pkg/seaice:
667      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
668        seaice_check that stops the model, when the CPP flag is used.
669      o seaice_growth.F: make capping of ice volume conserving by returning the
670        capped ice as freshwater to EmPmR. This does not change the verification
671        experiments but will change runs where the capping is acutally active
672    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
673      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
674         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
675         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
676    o tools/genmake2:
677      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
678      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
679      - clean previous genmake log files before anything else.
680      - change Makefile to remove testreport log files (*.tr_log) and genmake log
681        files only with "CLEAN" target (instead of "Clean");
682    o pkg/generic_advdiff:
683      Change OBCS in multiDim advection (gad_advection.F):
684       Use maskInC to prevent intermediate update of tracer-field in OB regions,
685       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
686       which were applying future time-step OB values.
687      This way, all explicit calculations use current-time-step OB values
688       (simpler and more consistent).
689      Affects results when set-up uses time-varying OBC and multi-dim advection;
690       update output of experiment seaice_obcs.
691    o pkg/seaice:
692      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
693       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
694         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
695      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
696       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
697       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
698    o pkg aim (2010/10/26):
699      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
700        formulation with obliquity, eccentricity, ... as run-time parameters,
701      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
702        upward shortwave radition at the surface (all-sky and clear-sky).
703    o pkg/obcs:
704      - writing sections with globalFiles=T does not work: switch to tiled-files
705        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
706      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
707      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
708    
709    checkpoint62m (2010/10/21)
710    o pkg/seaice: vectorize seaice_solve4temp.F
711      - move iterations loops outside of i/j-loops
712      - requires 2D arrays for TB and effConduct
713      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
714        modified in this routine
715      - a little bit of clean up, adjusting indentation, etc.
716      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
717        performance and '**TWO' by '**2' (because TWO is a float),
718        replaced ONE, ZERO
719    o eesupp/src:
720       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
721    o pkg/seaice/seaice_growth.F
722      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
723      merging process. The merged routine has two branches, and one activates the 'evolution'
724      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
725      In summary, here is what the '10/10 revision' did consist of
726        part 1: seaice_growth.F revisions 1.71 to 1.75
727          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
728            The emphasis here was on improving readability (e.g. by trying to use meaningful
729            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
730        part 1.5:
731          - revising the lab_sea experiment to make it a more useful (i.e. stable
732            and representative of an actual model run). This was done by generating a
733            (winter) pickup to start from, switching back the main experiment dynamic
734            solver from evp to lsr, having one of the experiments use the free drift solution.
735        part 2: seaice_growth.F revisions 1.76 to 1.85
736          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
737          - Sorting out the various fields units and sign (set early on and reset at the end)
738            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
739            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
740          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
741            and simplifying logical expressions to further improve readibility.
742        part 3: seaice_growth.F revisions 1.86 to 1.89
743          - Re-organize the blocks of code more logically.
744          - Merging the '_if.F' pieces that add something new.
745    o pkg/thsice:
746      - vectorize thsice_solve4temp and thsice_get_exf.
747        Problem: thsice_solve4temp has an unvectorizable statement that
748        might also be problematic for TAF
749      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
750        does not change the verifcation experiment, but will change all
751        experiments that have this flag undefined (not tested in verification);
752        a little reorganization to save a few 2D fields and recomputations
753      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
754      - 2nd step:  fix some store dirs
755        o seems to work somewhat, i.e. using ifort but not g77
756        o likely cause are incomplete init. or recomputation
757        o start verification/global_ocean.cs32x15/input_ad.thsice
758    o pkg/obcs: add support for exch2
759      - the position of the boundary and prescribed values are specified using
760        a global domain with exch2 facets stacked
761        - in x for N,S boundaries (like W2_mapIO=-1)
762        - in y for E,W boundaries (so E,W boundaries do not overlap)
763    o pkg/mdsio: add support for writing global sections with exch2
764        file layout is as for obcs described above:
765        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
766        - for y-z sections, facets are stacked in y
767    o pkg/thsice:
768       - change a few routines for better vectorization: thsice_albedo.F,
769         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
770         not affected, but in particular the latter routine has changed
771         dramatically (not necessarily easier to read now).
772       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
773       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
774    o verification/lab_sea:
775      - overhaul of the forward model experiments. The main motivation
776        for this revision is that lab_sea has proven quite fragile (when
777        changing the sea-ice code, and switching platforms) to a point
778        when failures were very hard to attribute to specific code problems.
779      - the suspected reason for this fragility is noise amplification by evp so,
780        to start with, we decided to replace evp with lsr in the main experiment.
781      - the input.lsr experiment thus became obsolete and was removed.
782      - it was replaced with the input.fd experiment that uses an
783        analytical "free drift" solution as the ice velocity field.
784      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
785        will hopefully allow us to discriminate problems due to dynamic solvers
786        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
787        us to test additional options, along with the salt plume package.
788      - Finally a pickup was generated (at the end of a one year run) to
789        make the tests more representative of an actual model run. Previously
790        the tests starting point was a 1m thickness of ice everywhere.
791    o pkg/seaice:
792      - introducing S\R seaice_freedrift.F that compute the
793        analytical solution to an approximate ice momentum
794        equation (i.e. the simple stress/coriolis balance).
795      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
796        of the free drift velocity field, and enable its use.
797        To actually use the free drift solution as the model ice
798        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
799    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
800    
801    checkpoint62l (2010/10/04)
802    o pkg/seaice:
803      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
804      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
805       version (with USE_ORIGINAL_SBI undef);
806    o add hooks for new packages OASIS, the package will follow
807      (hooks exclude the seaice pkg for now)
808    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
809      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
810      rather than mdsio_readvector.F/mdsio_writevector.F, within
811      adread_adwrite.F to read/write adjoint-related tapes to disk.
812    o eesupp and pkg/mdsio: ALLOW_WHIO
813      Option to write/read 2D fields to files including tiles halos.
814      The main purpose is for adjoint related "tape I/O".
815      The secondary purpose is for debugging phases.
816      A word on those rather specifically intended purposes.
817      The code was meant to be stripped down to the bare minimum.
818      Typically, there is a unique and basic mapping to the global
819      buffer (tile by tile, then proc by proc, then level by level), and
820      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
821      meant to generate user friendly outputs of various shapes and forms.
822      Rather it is intended, for the knowledgeabale developers,
823      to be largely independent of the many mdsio options, to allow
824      outputs of tiles+halos in debugging phases and in adjoint runs,
825      and to allow some flexibility in tuning (adoint) I/O depending on each
826      file system behavior. With regard to tuning, most of the potential knobs
827      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
828      to specify directories, to specify the typical size of I/O calls, etc.)
829      are not yet included, and will be added if they prove useful.
830    o pkg/seaice:
831       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
832    o pkg/seaice:
833       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
834       code (seaice_budget_ice_if.F) which enable to recover old standard
835       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
836       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
837    o model/src (rStar):
838       use simple average (not area weighted) of rStarFac at U,V point when using
839       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
840       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
841    
842    checkpoint62k (2010/09/17)
843    o adjoint
844       * changed verification/global_ocean.cs32x15 ; adjoint now tests
845         Adams-Bashforth 3 + NLFS + RSTAR
846       * some more modifs required for ECCO-GODAE v4
847    o pkg/seaice
848       add SEAICE_AGE_VOL option to use volume instead of area for
849       integrating SEAICE_AGE
850    o model/src:
851       first check-in of sigma & hybrid-sigma coordinate code ; also includes
852       non-linear free-surface parts ; but pressure-gradient not yet coded.
853    o pkg/ptracers:
854       option for ptracer to convert Salt Relax into additional EmP.
855        tested in exp. global_ocean.90x40x15.dwnslp (update output)
856    
857    checkpoint62j (2010/08/25)
858    o pkg/ggl90:
859       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
860    o pkg/dic: car_flux.F, phos_flux.F
861      - reduce number of exp-calls in order to improve performance
862      - clean up a little (replace fields by their macros, etc., fix
863        typo in CPP-flag)
864    o pkg/ggl90: minor changes
865      - GGL90diffKrS was removed --> always use GGL90diffKr
866      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
867      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
868        (commented out for now)
869      - change in max/min operations to ensure that smoothing is ok
870      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
871      - always use diffKrNrT as background profile (i.e. never use diffKr field)
872    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
873    o pkg/dic:
874      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
875        vectorization
876      - small bug fix in insol for the unlikely case of a cartesian grid
877      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
878        + now vectorize, which also removes adjoint recomputations;
879        + replace integer maksp1 by _RL maskp1
880        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
881    
882    checkpoint62i (2010/07/21)
883    o pkg/flt:
884      - with OBCS: stop floats which enter the OB region
885    o model/src:
886      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
887        for implicit vertical advection.
888    o pkg/seaice:
889     - account for melting in seaice age evolution.
890     - remove double counting of seaice ridging effect on seaice age.
891    
892    checkpoint62h (2010/06/18)
893    o pkg/exch2:
894     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
895    o tools/genmake2
896      - remove "-pdefault" option: redundant with the use of "packages.conf";
897      - remove file pkg/pkg_default : set the default as a pkg group
898        ("default_pkg_list") defined in pkg/pkg_groups;
899      - fix for case pkg/pkg_depend is missing (was hanging before);
900      - add option "-pgroups" to specify a different pkg_groups than the default.
901    o verification/adjustment.cs-32x32x1:
902       add a "minimal" set-up test (code_min & input_min) which only compiles
903       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
904    o tools/genmake2
905      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
906      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
907    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
908      files are nearly the same anyway.
909      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
910       - redefinition of tau(i,i) (by a factor of ustar)
911       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
912       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
913       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
914       - replace
915         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
916         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
917         by
918         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
919         (changes results)
920       -> exf_bulkformulae v1.22,
921          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
922          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
923                    output.txt 1.63
924           offline_exf_seaice: output.seaicetd.txt 1.7
925           seaice_obcs: output.txt 1.10)
926      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
927       -> exf_bulkformulae v1.23,
928          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
929          and global_ocean.cs32x15.icedyn (only 11 matching digits)
930      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
931    o adjoint of exch-1:
932     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
933       (note: was already like this when using EXCH-2) and remove flow dir
934       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
935     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
936     - update pkg/exch2 diff list.
937    
938    checkpoint62g (2010/05/19)
939    o eesupp/src (exch-1):
940     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
941       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
942       (renamed to exch1_*rx_cube.F).
943     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
944       to call new exch1 S/R ; update Makefile and .cvsignore.
945     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
946       exch2_xy_rx later)
947      Note: after updating your code, need to run "make clean" in eesupp/src
948    o test experiment bottom_ctrl_5x5:
949       new output_adm.txt with fewer grdchk & less monitor output.
950    o model/src:
951      remove the call to ini_cori in initialise_varia.F (just keep the usual one
952       in initialise_fixed.F). More consistent with coriolis & horizontal grid
953       beeing treated in the same way (ini_grid is not called a 2nd time).
954    o pkg/exf:
955      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
956      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
957      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
958      - cosmetic changes to exf_bulkformulae.F to make it look more like
959        exf_bulk_largeyeager04.F
960    o eesupp/src (exch-1):
961      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
962      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
963        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
964        (even without using MPI).
965      - Message mode: move RecvAck setting (indicator of buffer being ready)
966        from send_put to recv_get S/R (was useless before, but not sure if
967        it's much more useful now);
968      - Switch the order of sync: MPI-proc 1rst and then threads;
969      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
970      - fix AD code for communication mode ='get' (but not used).
971    o model/src:
972      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
973      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
974    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
975    o pkg/ctrl: require a specific set of control variables and exf-flags for
976      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
977    o model/src:
978     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
979       1rst forward sweep, to avoid over-writing output files during recomputations
980       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
981     b) 2nd version:
982      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
983      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
984         writePickupAtEnd) + seaice & ptracers output;
985      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
986    o model/src:
987      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
988    o pkg/exch2:
989      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
990      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
991    o pkg/autodiff & exch2:
992      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
993      (for now, only if ALLOW_EXCH2 is defined).
994    o pkg/autodiff:
995      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
996        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
997       + clean-up comments (_RS is not always real*4)
998      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
999      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1000        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1001    o testreport (AD-tests):
1002      no longer link files from dir "../input" (1rst link files from
1003      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1004    
1005    checkpoint62f (2010/04/29)
1006    o model/src/the_main_loop.F:
1007      adjust store directives for seaice evp and multicategory according to
1008      pkg/ecco/the_main_loop.F
1009    o adjoint:
1010      global_sum_ad was incomplete (noted many times by many people ;)
1011      nice description by Jean U. as follows:
1012      * allreduce(var) in global_sum.F can be interpreted as
1013        reduce(sum) followed by broadcast of sum.
1014      * The adjoint of that is
1015        sum(adjoint) followed by broadcast(summed adjoint value)
1016        or in other words, allreduce(sum, adjoint vars)
1017      We were missing the sum(adjoint)!
1018      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1019      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1020      The fix should produce 16-digit accuracy between
1021      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1022      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1023      We'll probably change this yet again shortly
1024    o eesupp/src:
1025      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1026    o pkg/icefront
1027      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1028        specification of addmass array based on a 2D field, which is added
1029        at bottommost wet level at each horizontal location.
1030    o model/src:
1031     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1032     layout; (not always compatible with delX,delY setting; commented out for now).
1033    o pkg/exch2:
1034     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1035     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1036    
1037    checkpoint62e (2010/04/15)
1038    o pkg/obcs:
1039      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1040    o pkg/dic:
1041      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1042        (note: not presently tested in any forward verification exp.)
1043       update tutorial_global_oce_biogeo AD output file.
1044    o pkg/exf:
1045      - account for the variation of albedo as a function of zenith angle
1046        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1047    o build_options:
1048     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1049    o pkg/dic:
1050      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1051      - use binary pickup file for restart;
1052      - initialise atmos-CO2 box from dic_pCO2 parameter;
1053      - fix multi-threaded.
1054    o pkg/rbcs:
1055     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1056       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1057     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1058       and update output.txt
1059    o pkg/kpp:
1060     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1061     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1062       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1063       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1064     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1065       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1066    o pkg/offline:
1067      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1068      (bug was added in version 1.10 on 2007-08-23).
1069    o pkg/offline:
1070      - no need to specify periodicExternalForcing, etc ... to use offline pack
1071      - offline input files no longer just single prec --> parameter offlineLoadPrec
1072    o verification/lab_sea:
1073      change AD test to multi-tile setup and update all 4 AD output.
1074      NOTE: while cost function values remain very similar,
1075      gradients are very different, although gradient checks are self-consistent
1076      Should try to get to the bottom of this (cost function summation order?)
1077    o pkg/dic:
1078      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1079      a weakness of TAF that drops part of double precision in log10 derivative.
1080      <= changes removed since problem has been fixed in current TAF version 1.9.71
1081      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1082    o pkg/ecco:
1083      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1084      update all 4 lab_sea AD output.
1085    
1086    checkpoint62d (2010/03/22)
1087    o build_options:
1088      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1089    o remove unbalanced quote (single or double) in commented line of source code
1090      (may cause some warning with some preprocessor/makedepend versions).
1091    o pkg/seaice:
1092      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1093       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1094    o testreport:
1095      add option '-runonly' (short: '-ro') to just do the run part (without make).
1096    o eesupp: remove JAM communication code (obsolete).
1097    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1098      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1099      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1100      (update also the output).
1101    
1102    checkpoint62c (2010/03/02)
1103    o tools/build_options :
1104       move (some) old optfiles from build_options/ to build_options/unsupported/
1105    o model/src and pkg/exf
1106       surface relaxation -- separating data and data.exf options
1107       The point is to ensure that we specify the surface relaxation
1108       either in data or in data.exf (but not half and half) and to
1109       avoid an accidental relaxation to 0 (which happened if a time
1110       scale was specified but the file name was left empty)
1111    o model/src model/inc and pkg/mom_common
1112       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1113       => addition to the viscosity field as computed by others schemes
1114    o tools/build_options:
1115      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1116        but keep the former optfile for few weeks for smooth transition
1117    o pkg/ecco
1118      - allow user defined cost function contributions
1119         CPP: ALLOW_USERCOST_CONTRIBUTION
1120         USAGE: compute contributions in cost_usercost_all.F
1121      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1122          the two options are complementary.
1123    o pkg/smooth
1124      - migration from contrib to the main repository
1125    
1126    checkpoint62b (2010/01/26)
1127    o pkg/monitor:
1128      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1129        (in case someone forgot to update customized pieces of code)
1130    o nonHydrostatic:
1131      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1132      - add a simple 2-D experiment (short_surf_wave) to test it.
1133    o pkg/icefront:
1134       adding the shell of, and the hooks to, a new package that
1135       will model melting and freezing of vertical glacier ice fronts
1136    o momentum:
1137      add diagnostics of momentum tendency from Hydrostatic pressure gradient
1138       (without surf.pressure term: would need a 2nd filling since implicit term).
1139    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1140      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1141      cannot deal with the former
1142    o cleaning:
1143      - remove all (except OpenAD) old TLM output from results_ad dirs.
1144      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1145      - comment out maskH definition (replaced by maskInC)
1146    o pkg/monitor:
1147      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1148        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1149    
1150    checkpoint62a (2010/01/15)
1151    o model/src:
1152      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1153  o pkg/diagnostics:  o pkg/diagnostics:
1154    - add optional level number diagnostics (i.e., level number to be define    - add optional level number diagnostics (i.e., level number to be define
1155      explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".      explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
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