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revision 1.1303 by gforget, Fri Sep 24 23:25:45 2010 UTC revision 1.1412 by jmc, Mon Apr 25 23:03:41 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 pkg/mom_fluxform:
8      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
9      - use parameter "sideDragFactor" in no-slip BC side-drag part.
10      - update output of exp. global_ocean.90x40x15
11    o pkg/mom_vecinv:
12      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
13    o update test-exp global_ocean.90x40x15:
14      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
15      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
16      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
17      o turn on zStar & viscA4 in standard set-up (dir input/)
18        and update output files: output.txt & output.dwnslp.txt
19    o new AD-test experiment: obcs_ctrl
20      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
21    o pkg/dic:
22      fix two bugs in handling water vapour pressure in carbonate chemistry
23      and air-sea fluxes. Found by Val Bennington and Galen McKinley
24      (add DIC Option = WATERVAP_BUG to recover old results)
25      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
26    o adding allowInteriorFreezing option to check for water below freezing point
27      at depth and bring the negative heat anomaly to the surface level
28    o pkgs _fields_load:
29      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
30      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
31        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
32        rbcs to get interpolation weights and time reccord number.
33      - fix multi-threading in aim_fields_load.F
34      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
35    o external_fields_load:
36      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
37       interpolation weights) to use in a periodic time-series ; do not divide by
38       time-step to convert to integer:
39       - this fixes case where externForcingPeriod is not multiple of time-step
40          (Thanks to Christopher L. Wolfe)
41       - this fixes case where externForcingPeriod is an odd multiple of time-step
42         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
43      store index of time-record which is currently loaded:
44       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
45       - needed for the adjoint but not yet used because of extensive recomputations;
46         (to be fixed soon)
47    
48    checkpoint62v (2011/04/02)
49    o verification/1D_ocean_ice_column added to test Ian Fenty's
50      pkg/seaice_growth.F modifications for improving sea ice code differentiability
51    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
52      (new velocity statistics after changing maskInW & maskInS definition)
53    o pkg/generic_advdiff with OBCS:
54      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
55      equivalent to assumption of no tracer gradient outside the OB region.
56      This will affect the results if using obcs+biharmonic diffusion.
57      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
58    o pkg/obcs:
59      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
60      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
61      in Interior region. No impact on solution but affects Velocity monitor stats.
62    o pkg/ptracers (adjoint)
63      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
64      tape file for each tracer
65    o model/inc/src and pkg/autodiff: add parameters that allow to turn
66      of parts of the adjoint code at run time. For now, there are only
67      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
68      parameters are set in data.pkg.
69      This is the lazy coward's version of doing this, but still useful for
70      debugging. In order to do it right, everything needs to be moved to
71      pkg/autodiff.
72    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
73      the end; this fixes the adjoint balancing code for open boundaries.
74    o pkg/ctrl:
75      - change behavior of xx_${varname}period to be analogous to exf-conventions:
76        xx_${varname}period =   0.,  means time-independent control part
77        xx_${varname}period = -12., means one-year-periodic monthly control part
78      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
79        clean up ctrl_init a little, remove unused variables
80      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
81      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
82    
83    checkpoint62u (2011/03/15)
84    o model/src:
85      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
86        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
87      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
88        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
89    o pkg/ctrl/obcs/ecco:
90      - remove obsolete, unused, and partially broken code:
91        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
92        ALLOW_CTRL_OBCS_BALANCE
93      - put a stop statement into ecco/cost_obcsvol.F, but also add
94        cost_obcsvol to ecco_ad_diff.list
95    o pkg/ecco: fix counting cost function contributions for obcs (code
96      by Matt M.) and diffkr for diagnostics
97    o pkg/ecco, pkg/ctrl, pkg/grdchk:
98      add cost penalty terms for initial uvel, vvel, eta controls
99      and I/O for prior error files
100    o pkg/mdsio:
101       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
102       (new argument) to check for tiled file in mdsioLocalDir : this fix the
103       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
104    o pkg/ctrl:
105     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
106       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
107       unused and superfluous variables
108     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
109    o pkg/ecco
110     - enable adjoint of Stevens OB
111    o pkg/ctrl/ecco/grdchk:
112      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
113        Fortunately, we do not have any tests for the numerous cpp-flagged
114        option of "obcs as control parameters" so we will never know
115        if this is an improvement (but at least now things compile).
116      - remove an obsolete initialization from ecco_cost_init_barfiles.F
117      - fix some problems within never used ifdefs to make the code compile
118    o pkg/obcs:
119     - Refine Interior mask definition to work with more complex OB (e.g.
120       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
121       read in Interior mask from file. Check if Interior mask is consistent
122       with OB list of indices.
123    o pkg/seaice
124     - beginning code for a seaice tracer package,
125       but currently only used for seaice age: SEAICE_AGE
126       SEAICE_num = 4
127       iTracer = 1: area-weighted ice age
128               = 2: volume-weighted ice age
129               = 3, 4: template for one-year vs. multi-year ice
130       data.seaice has new namelist SEAICE_PARM03 for arrays related to
131       SEAICE_num
132    
133    checkpoint62t (2011/03/05)
134    o pkg/obcs:
135     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
136       then normal component. This ensures that the normal component is set
137       correctly even when it conficts with tangential setting from an other OB.
138       Affects results of test-experiment seaice_obcs: update the output.txt
139    o pkg/obcs:
140     - add code to monitor statistics of dynamical fields at OB.
141     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
142       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
143       - change default: balance the Net inflow through all OB (instead of balancing
144         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
145     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
146       to match Nortern OB inflow (OBCS_balanceFacN=0).
147    o pkg/seaice:
148     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
149    o pkg/seaice (seaice_growth v 1.113):
150     - reverting seaice_growth to v 1.111 in order to have code with exact bit
151       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
152       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
153       runtime flag SEAICEareaFormula is kept but is inactive
154    o model/src:
155     - add new param to scale curvilinear grid distance and area when using
156       a different sphere radius from the grid-files.
157     - test/check multi-threads EXCH applied to local variable (cg2d_x)
158    o adjoint:
159     - enable adjoint of Stevens OB
160     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
161       (a bit delicate because of potentially modified adj. common block structure;
162       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
163    
164    checkpoint62s (2011/02/15)
165    o pkg/seaice (seaice_growth v 1.112):
166     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
167       computing the ice cover tendency from effective thickness tendencies. Include
168       Ian Fenty's formula.
169     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
170       SEAICEareaFormula.
171     - simplify notations for the various d_HEFF/d_AREA terms.
172    o pkg/gmredi:
173     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
174       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
175       add a verification test-run (front_relax.bvp) to test GM_useBVP.
176    o pkg/seaice (seaice_growth v 1.111):
177     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
178     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
179       also melt ice.
180    o pkg/seaice:
181     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
182     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
183    o pkg/cheapaml:
184     - from Nico Wienders: New version of this package.
185    o pkg/flt:
186     - add CPP options to prevent floats to re-enter the opposite side of
187       a periodic domain (default: keep periodicity)
188    o pkg/gmredi:
189     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
190       (needed for multi-dim advection).
191     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
192    o model/src:
193     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
194    o tutorial_tracer_adjsens
195     - extend to NLFS and replace maskC by hFacC
196       (change reference output accordingly)
197    
198    checkpoint62r (2011/01/24)
199    o testreport:
200     - add option -deloutp (-do) to remove output file after successful run
201     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
202       extract exact list of procs from this file ; adjust COMMAND by
203       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
204    o pkg/ecco: replace old ineffective way of penalizing deviations from
205      first guess (of obcs) with code by Matt Mazloff
206    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
207      exf/cal
208      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
209        and handle case of obcs?period == 0
210        Not affected by these changes: There is still an inconsistency in
211        the computation of start/endrec for the obcs variables for ALLOW_CAL
212        defined (see comment by Menemenlis, 7-Mar-2003)
213      - make S/R ctrl_get_gen_rec return something meaningful even if
214        ALLOW_CAL is not defined
215      - ctrl_getobcs?: simplify code so that it does not need to use
216                       S/R exf_swapfields
217    o testreport:
218       allow to test MPI with different number of processors for each experiment:
219       create file "SIZE.h.mpi" in each build dir.
220       Note: update of "-command" argument not yet implemented.
221    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
222      alleviate the need for additional 3D tapes when using
223      the non-inear free surface in the adjoint. This is done
224      by adding an 'update' of hfacc etc. to their current
225      value at the beginning of forward_step.F.
226    o pkg/seaice
227      seaice_lsr: move stress-divergence computations out of outer pseudo-
228      timestepping loop
229    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
230      up, so that the calls of the ctrl_* subroutines are really at the end
231      of the routine.
232    o pkg/gmredi:
233      allow to specify a 2-D horizontal map and a 1-D vertical profil
234      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
235    o pkg/seaice:
236      move lsr iterations from seaice_dynsolver to seaice_lsr.
237    o pkg/seaice:
238      reduce memory footprint of seaice mutldim advection tapes,
239      by using a 2D tape independent of the generic_advdiff ones,
240      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
241    
242    checkpoint62q (2010/12/29)
243    o model/src:
244      - check horizontal grid-spacing for unset or zero/negative values.
245      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
246    o pkg/flt:
247      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
248      - precision of input and output files set according to readBinaryPrec
249        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
250      - initial float position from tiled file was not converted to index space
251        (looks like a bug): fixed to make it similar to initial pos. global file.
252    o global_ocean.cs32x15:
253       change SIZE.h of AD set-up to get same tiling as with MPI.
254       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
255    o model/src:
256       add flag to control printing of domain fields (bathymetry, hFac ...) in
257       ini_mask_etc (call to plot_fieds_xy*).
258    o pkg/thsice:
259       if useEXF, some forcing fields are not valid in overlap: fixed by computing
260       over the interior only + apply EXCH at the end (like with SEAICE advection).
261    o pkg/mdsio:
262      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
263        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
264      - change barrier call for safe multi-threads access to 3-D shared buffer.
265      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
266      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
267        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
268    o pkg/flt:
269      - add fourth-order Runge-Kutta integration
270      - add basic exch2 support (only 1 facet supported so far!)
271    o pkg/mdsio+rw:
272      new S/R to read local (or tile independent) vector (read counterpart of
273       mds_writevec_loc, and front-end write_glvec_rl/rs).
274    o global_ocean.cs32x15: additional input_ad.seaice experiment
275        that uses pkg/seaice rather than pkg/thsice.
276        (using multidim advection for seaice)
277    o towards more F95 syntax for array specification in namelist:
278      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
279        of all verification experiments.
280           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
281          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
282      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
283    o global_ocean.cs32x15: additional input.seaice experiment
284        that uses pkg/seaice rather than pkg/thsice.
285    
286    checkpoint62p (2010/12/17)
287    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
288        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
289    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
290        allow for use of multim. advection in seaice adjoint.
291    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
292      - first attempt to close budgets by taking into account the freshwater
293        flux implied by the sublimation of snow and ice. So far only the
294        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
295        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
296    o eesupp/src:
297      new S/R with new option (NML_EXTENDED_F77) to change array specification
298      from F95 standard to commonly accepted extended F77 form.
299      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
300      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
301      for less tolerant f77 compiler (e.g., pgf77, g77).
302    o globalFiles:
303      commented out in parameter file "data" since it's not safe with MPI
304      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
305      in this case); no longer commented out in restart test (tst_2+2).
306    o add adTapeDir to specify a special directory where adjoint tapes are
307      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
308      and cannot be used together with mdsioLocalDir.
309    o nesting pkgs:
310      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
311      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
312      - add parameter files + utils dir + output from short run on beagle.
313    o pkg/seaice:
314        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
315    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
316      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
317    
318    checkpoint62o (2010/11/25)
319    o pkg/exf:
320      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
321    o pkg/seaice:
322      - seaice_ocean_stress: split a loop for better vectorization of the
323        adjoint code
324      - seaice_growth.F: fix bug in conservation of freshwater connected to
325        capping of heff, put contribution into d_HEFFbyNEG
326      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
327        by something more sensible (parameters that are what their name implies)
328      - change some defaults, so that by default exf-parameters are used for
329        things like rhoAir, cpAir,latent/sensible heat parameters, in order
330        to reproduce the old results, many data.seaice now contain funny values
331        for cpAir and latent heat of sublimation
332    o packages_readparms.F: move exf_readparms up in line so that
333        exf-parameters are visible for other packages (e.g. seaice)
334    o debugMode & debugLevel=2:
335      - differentiate between debugMode & debugLevel=2:
336        debugMode: controls printing of debug messages (sequence of S/R calls).
337        debugLevel: controls printing of algorithm intermediate results and stats.
338      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
339        => allows to print debug-stats without all sequence of call messages.
340      - switch control of debug print from debugLevel to debugMode in many S/R.
341    o pkg/obcs (obcs-sponge):
342        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
343        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
344    o pkg/generic_advdiff:
345      - record overlap minimum size for each advection scheme;
346      - refine criteria on overlap minimum size;
347      - check and stop (in gad_check) if overlap size is too small.
348    o pkg/obcs:
349      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
350        once, in ptracers_implicit.F)
351      - with seaice: remove test on empty file name in obcs_apply_seaice (always
352        apply OB values when tile has OB)
353    o model/src, coriolis setting:
354      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
355        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
356        files (selectCoriMap=3) with any grid.
357      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
358    o pkg/seaice/seaice_growth.F:
359        a few cosmetic changes that reduce the number of lines of code
360    o pkg/obcs: add boundary conditions following Stevens (1990)
361      - the code follows old MOM/NAOSIM code
362      - so far it is only implemented for the eastern and western boundaries
363        and NOT for pTracers
364    o pkg/rbcs:
365      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
366        beginning of the first rbcs forcing period.
367      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
368        offline package, i.e., one file per time, labeled by iteration number;
369        deltaTrbcs sets the timestep with which the data was generated;
370        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
371      - rbcsForcingCycle=0 makes forcing non-cyclic.
372      - make arithmetic safe for negative times and odd forcing periods.
373    
374    checkpoint62n (2010/11/09)
375    o pkg/seaice:
376        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
377    o pkg/obcs:
378       New S/R to copy tracer value from the OB location to narrow band region
379        (width = same as overlap) beyond the OB: preserve OB value (needed for
380        high-order scheme) which were overwritten by EXCH call if in overlap
381        region. Applied to theta, salt, ptracer and advected seaice variables.
382       With seaice: use maskInC in similar way as in gad_advection.F,
383        in seaice_advection.F and advect.F.
384       Update output of experiment seaice_obcs and change exp4 to test OBCS with
385        4th order Adv.Scheme. for pasive salt and ptracer.
386    o tools/genmake2:
387      - when looking for an optfile (not specified), only search for Fortran compiler
388        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
389      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
390        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
391      - set default for CPP to "cpp -traditional -P" (was the case without specifying
392        an optfile, but otherwise default was just "cpp".
393      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
394      - when "CC" is not set in the optfile, look for possible C compiler
395        (instead of just setting CC=cc)
396      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
397        => add a ".F" to ".o" rule for source files with no "#include" (such as
398           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
399      - move gfortran before g77 in list of possible Fortran compiler (consistent
400        with reference compiler switch from g77 to gfortran)
401    o pkg/seaice:
402      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
403        seaice_check that stops the model, when the CPP flag is used.
404      o seaice_growth.F: make capping of ice volume conserving by returning the
405        capped ice as freshwater to EmPmR. This does not change the verification
406        experiments but will change runs where the capping is acutally active
407    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
408      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
409         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
410         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
411    o tools/genmake2:
412      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
413      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
414      - clean previous genmake log files before anything else.
415      - change Makefile to remove testreport log files (*.tr_log) and genmake log
416        files only with "CLEAN" target (instead of "Clean");
417    o pkg/generic_advdiff:
418      Change OBCS in multiDim advection (gad_advection.F):
419       Use maskInC to prevent intermediate update of tracer-field in OB regions,
420       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
421       which were applying future time-step OB values.
422      This way, all explicit calculations use current-time-step OB values
423       (simpler and more consistent).
424      Affects results when set-up uses time-varying OBC and multi-dim advection;
425       update output of experiment seaice_obcs.
426    o pkg/seaice:
427      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
428       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
429         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
430      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
431       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
432       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
433    o pkg aim (2010/10/26):
434      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
435        formulation with obliquity, eccentricity, ... as run-time parameters,
436      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
437        upward shortwave radition at the surface (all-sky and clear-sky).
438    o pkg/obcs:
439      - writing sections with globalFiles=T does not work: switch to tiled-files
440        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
441      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
442      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
443    
444    checkpoint62m (2010/10/21)
445    o pkg/seaice: vectorize seaice_solve4temp.F
446      - move iterations loops outside of i/j-loops
447      - requires 2D arrays for TB and effConduct
448      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
449        modified in this routine
450      - a little bit of clean up, adjusting indentation, etc.
451      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
452        performance and '**TWO' by '**2' (because TWO is a float),
453        replaced ONE, ZERO
454    o eesupp/src:
455       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
456    o pkg/seaice/seaice_growth.F
457      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
458      merging process. The merged routine has two branches, and one activates the 'evolution'
459      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
460      In summary, here is what the '10/10 revision' did consist of
461        part 1: seaice_growth.F revisions 1.71 to 1.75
462          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
463            The emphasis here was on improving readability (e.g. by trying to use meaningful
464            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
465        part 1.5:
466          - revising the lab_sea experiment to make it a more useful (i.e. stable
467            and representative of an actual model run). This was done by generating a
468            (winter) pickup to start from, switching back the main experiment dynamic
469            solver from evp to lsr, having one of the experiments use the free drift solution.
470        part 2: seaice_growth.F revisions 1.76 to 1.85
471          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
472          - Sorting out the various fields units and sign (set early on and reset at the end)
473            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
474            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
475          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
476            and simplifying logical expressions to further improve readibility.
477        part 3: seaice_growth.F revisions 1.86 to 1.89
478          - Re-organize the blocks of code more logically.
479          - Merging the '_if.F' pieces that add something new.
480    o pkg/thsice:
481      - vectorize thsice_solve4temp and thsice_get_exf.
482        Problem: thsice_solve4temp has an unvectorizable statement that
483        might also be problematic for TAF
484      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
485        does not change the verifcation experiment, but will change all
486        experiments that have this flag undefined (not tested in verification);
487        a little reorganization to save a few 2D fields and recomputations
488      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
489      - 2nd step:  fix some store dirs
490        o seems to work somewhat, i.e. using ifort but not g77
491        o likely cause are incomplete init. or recomputation
492        o start verification/global_ocean.cs32x15/input_ad.thsice
493    o pkg/obcs: add support for exch2
494      - the position of the boundary and prescribed values are specified using
495        a global domain with exch2 facets stacked
496        - in x for N,S boundaries (like W2_mapIO=-1)
497        - in y for E,W boundaries (so E,W boundaries do not overlap)
498    o pkg/mdsio: add support for writing global sections with exch2
499        file layout is as for obcs described above:
500        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
501        - for y-z sections, facets are stacked in y
502    o pkg/thsice:
503       - change a few routines for better vectorization: thsice_albedo.F,
504         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
505         not affected, but in particular the latter routine has changed
506         dramatically (not necessarily easier to read now).
507       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
508       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
509    o verification/lab_sea:
510      - overhaul of the forward model experiments. The main motivation
511        for this revision is that lab_sea has proven quite fragile (when
512        changing the sea-ice code, and switching platforms) to a point
513        when failures were very hard to attribute to specific code problems.
514      - the suspected reason for this fragility is noise amplification by evp so,
515        to start with, we decided to replace evp with lsr in the main experiment.
516      - the input.lsr experiment thus became obsolete and was removed.
517      - it was replaced with the input.fd experiment that uses an
518        analytical "free drift" solution as the ice velocity field.
519      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
520        will hopefully allow us to discriminate problems due to dynamic solvers
521        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
522        us to test additional options, along with the salt plume package.
523      - Finally a pickup was generated (at the end of a one year run) to
524        make the tests more representative of an actual model run. Previously
525        the tests starting point was a 1m thickness of ice everywhere.
526    o pkg/seaice:
527      - introducing S\R seaice_freedrift.F that compute the
528        analytical solution to an approximate ice momentum
529        equation (i.e. the simple stress/coriolis balance).
530      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
531        of the free drift velocity field, and enable its use.
532        To actually use the free drift solution as the model ice
533        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
534    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
535    
536    checkpoint62l (2010/10/04)
537    o pkg/seaice:
538      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
539      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
540       version (with USE_ORIGINAL_SBI undef);
541    o add hooks for new packages OASIS, the package will follow
542      (hooks exclude the seaice pkg for now)
543  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
544    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
545    rather than mdsio_readvector.F/mdsio_writevector.F, within    rather than mdsio_readvector.F/mdsio_writevector.F, within
546    adread_adwrite.F to read/write adjoint-related tapes to disk.    adread_adwrite.F to read/write adjoint-related tapes to disk.
547  o eesup and pkg/mdsio: ALLOW_WHIO  o eesupp and pkg/mdsio: ALLOW_WHIO
548      Option to write/read 2D fields to files including tiles halos.
549    Option to write/read 2D fields to files including tiles halos.    The main purpose is for adjoint related "tape I/O".
   The main purpose is for adjoint related "tape I/O".  
550    The secondary purpose is for debugging phases.    The secondary purpose is for debugging phases.
   
551    A word on those rather specifically intended purposes.    A word on those rather specifically intended purposes.
552    The code was meant to be stripped down to the bare minimum.    The code was meant to be stripped down to the bare minimum.
553    Typically, there is a unique and basic mapping to the global    Typically, there is a unique and basic mapping to the global
554    buffer (tile by tile, then proc by proc, then level by level), and    buffer (tile by tile, then proc by proc, then level by level), and
555    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
556    meant to generate user friendly outputs of various shapes and forms.    meant to generate user friendly outputs of various shapes and forms.
557    Rather it is intended, for the knowledgeabale developers,    Rather it is intended, for the knowledgeabale developers,
558    to be largely independent of the many mdsio options, to allow    to be largely independent of the many mdsio options, to allow
559    outputs of tiles+halos in debugging phases and in adjoint runs,    outputs of tiles+halos in debugging phases and in adjoint runs,
560    and to allow some flexibility in tuning (adoint) I/O depending on each    and to allow some flexibility in tuning (adoint) I/O depending on each
561    file system behavior. With regard to tuning, most of the potential knobs    file system behavior. With regard to tuning, most of the potential knobs
562    (to leave files open, to allocate the I/O indep. of usesinglecpuio,    (to leave files open, to allocate the I/O indep. of usesinglecpuio,
563    to specify directories, to specify the typical size of I/O calls, etc.)    to specify directories, to specify the typical size of I/O calls, etc.)
564    are not yet included, and will be added if they prove useful.    are not yet included, and will be added if they prove useful.
# Line 317  o tools/build_options: Line 851  o tools/build_options:
851      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
852  o pkg/ecco  o pkg/ecco
853    - allow user defined cost function contributions    - allow user defined cost function contributions
854          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
855          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
856    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
857        the two options are complementary.        the two options are complementary.
858  o pkg/smooth  o pkg/smooth
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