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revision 1.1280 by jmc, Tue May 25 22:22:11 2010 UTC revision 1.1408 by dimitri, Wed Apr 20 13:45:13 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 adding allowInteriorFreezing option to check for water below freezing point
8      at depth and bring the negative heat anomaly to the surface level
9    o external_fields_load:
10      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
11       interpolation weights) to use in a periodic time-series ; do not divide by
12       time-step to convert to integer:
13       - this fixes case where externForcingPeriod is not multiple of time-step
14          (Thanks to Christopher L. Wolfe)
15       - this fixes case where externForcingPeriod is an odd multiple of time-step
16         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
17      store index of time-record which is currently loaded:
18       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
19       - needed for the adjoint but not yet used because of extensive recomputations;
20         (to be fixed soon)
21    
22    checkpoint62v (2011/04/02)
23    o verification/1D_ocean_ice_column added to test Ian Fenty's
24      pkg/seaice_growth.F modifications for improving sea ice code differentiability
25    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
26      (new velocity statistics after changing maskInW & maskInS definition)
27    o pkg/generic_advdiff with OBCS:
28      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
29      equivalent to assumption of no tracer gradient outside the OB region.
30      This will affect the results if using obcs+biharmonic diffusion.
31      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
32    o pkg/obcs:
33      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
34      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
35      in Interior region. No impact on solution but affects Velocity monitor stats.
36    o pkg/ptracers (adjoint)
37      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
38      tape file for each tracer
39    o model/inc/src and pkg/autodiff: add parameters that allow to turn
40      of parts of the adjoint code at run time. For now, there are only
41      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
42      parameters are set in data.pkg.
43      This is the lazy coward's version of doing this, but still useful for
44      debugging. In order to do it right, everything needs to be moved to
45      pkg/autodiff.
46    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
47      the end; this fixes the adjoint balancing code for open boundaries.
48    o pkg/ctrl:
49      - change behavior of xx_${varname}period to be analogous to exf-conventions:
50        xx_${varname}period =   0.,  means time-independent control part
51        xx_${varname}period = -12., means one-year-periodic monthly control part
52      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
53        clean up ctrl_init a little, remove unused variables
54      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
55      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
56    
57    checkpoint62u (2011/03/15)
58    o model/src:
59      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
60        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
61      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
62        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
63    o pkg/ctrl/obcs/ecco:
64      - remove obsolete, unused, and partially broken code:
65        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
66        ALLOW_CTRL_OBCS_BALANCE
67      - put a stop statement into ecco/cost_obcsvol.F, but also add
68        cost_obcsvol to ecco_ad_diff.list
69    o pkg/ecco: fix counting cost function contributions for obcs (code
70      by Matt M.) and diffkr for diagnostics
71    o pkg/ecco, pkg/ctrl, pkg/grdchk:
72      add cost penalty terms for initial uvel, vvel, eta controls
73      and I/O for prior error files
74    o pkg/mdsio:
75       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
76       (new argument) to check for tiled file in mdsioLocalDir : this fix the
77       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
78    o pkg/ctrl:
79     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
80       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
81       unused and superfluous variables
82     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
83    o pkg/ecco
84     - enable adjoint of Stevens OB
85    o pkg/ctrl/ecco/grdchk:
86      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
87        Fortunately, we do not have any tests for the numerous cpp-flagged
88        option of "obcs as control parameters" so we will never know
89        if this is an improvement (but at least now things compile).
90      - remove an obsolete initialization from ecco_cost_init_barfiles.F
91      - fix some problems within never used ifdefs to make the code compile
92    o pkg/obcs:
93     - Refine Interior mask definition to work with more complex OB (e.g.
94       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
95       read in Interior mask from file. Check if Interior mask is consistent
96       with OB list of indices.
97    o pkg/seaice
98     - beginning code for a seaice tracer package,
99       but currently only used for seaice age: SEAICE_AGE
100       SEAICE_num = 4
101       iTracer = 1: area-weighted ice age
102               = 2: volume-weighted ice age
103               = 3, 4: template for one-year vs. multi-year ice
104       data.seaice has new namelist SEAICE_PARM03 for arrays related to
105       SEAICE_num
106    
107    checkpoint62t (2011/03/05)
108    o pkg/obcs:
109     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
110       then normal component. This ensures that the normal component is set
111       correctly even when it conficts with tangential setting from an other OB.
112       Affects results of test-experiment seaice_obcs: update the output.txt
113    o pkg/obcs:
114     - add code to monitor statistics of dynamical fields at OB.
115     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
116       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
117       - change default: balance the Net inflow through all OB (instead of balancing
118         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
119     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
120       to match Nortern OB inflow (OBCS_balanceFacN=0).
121    o pkg/seaice:
122     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
123    o pkg/seaice (seaice_growth v 1.113):
124     - reverting seaice_growth to v 1.111 in order to have code with exact bit
125       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
126       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
127       runtime flag SEAICEareaFormula is kept but is inactive
128    o model/src:
129     - add new param to scale curvilinear grid distance and area when using
130       a different sphere radius from the grid-files.
131     - test/check multi-threads EXCH applied to local variable (cg2d_x)
132    o adjoint:
133     - enable adjoint of Stevens OB
134     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
135       (a bit delicate because of potentially modified adj. common block structure;
136       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
137    
138    checkpoint62s (2011/02/15)
139    o pkg/seaice (seaice_growth v 1.112):
140     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
141       computing the ice cover tendency from effective thickness tendencies. Include
142       Ian Fenty's formula.
143     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
144       SEAICEareaFormula.
145     - simplify notations for the various d_HEFF/d_AREA terms.
146    o pkg/gmredi:
147     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
148       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
149       add a verification test-run (front_relax.bvp) to test GM_useBVP.
150    o pkg/seaice (seaice_growth v 1.111):
151     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
152     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
153       also melt ice.
154    o pkg/seaice:
155     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
156     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
157    o pkg/cheapaml:
158     - from Nico Wienders: New version of this package.
159    o pkg/flt:
160     - add CPP options to prevent floats to re-enter the opposite side of
161       a periodic domain (default: keep periodicity)
162    o pkg/gmredi:
163     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
164       (needed for multi-dim advection).
165     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
166    o model/src:
167     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
168    o tutorial_tracer_adjsens
169     - extend to NLFS and replace maskC by hFacC
170       (change reference output accordingly)
171    
172    checkpoint62r (2011/01/24)
173    o testreport:
174     - add option -deloutp (-do) to remove output file after successful run
175     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
176       extract exact list of procs from this file ; adjust COMMAND by
177       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
178    o pkg/ecco: replace old ineffective way of penalizing deviations from
179      first guess (of obcs) with code by Matt Mazloff
180    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
181      exf/cal
182      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
183        and handle case of obcs?period == 0
184        Not affected by these changes: There is still an inconsistency in
185        the computation of start/endrec for the obcs variables for ALLOW_CAL
186        defined (see comment by Menemenlis, 7-Mar-2003)
187      - make S/R ctrl_get_gen_rec return something meaningful even if
188        ALLOW_CAL is not defined
189      - ctrl_getobcs?: simplify code so that it does not need to use
190                       S/R exf_swapfields
191    o testreport:
192       allow to test MPI with different number of processors for each experiment:
193       create file "SIZE.h.mpi" in each build dir.
194       Note: update of "-command" argument not yet implemented.
195    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
196      alleviate the need for additional 3D tapes when using
197      the non-inear free surface in the adjoint. This is done
198      by adding an 'update' of hfacc etc. to their current
199      value at the beginning of forward_step.F.
200    o pkg/seaice
201      seaice_lsr: move stress-divergence computations out of outer pseudo-
202      timestepping loop
203    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
204      up, so that the calls of the ctrl_* subroutines are really at the end
205      of the routine.
206    o pkg/gmredi:
207      allow to specify a 2-D horizontal map and a 1-D vertical profil
208      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
209    o pkg/seaice:
210      move lsr iterations from seaice_dynsolver to seaice_lsr.
211    o pkg/seaice:
212      reduce memory footprint of seaice mutldim advection tapes,
213      by using a 2D tape independent of the generic_advdiff ones,
214      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
215    
216    checkpoint62q (2010/12/29)
217    o model/src:
218      - check horizontal grid-spacing for unset or zero/negative values.
219      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
220    o pkg/flt:
221      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
222      - precision of input and output files set according to readBinaryPrec
223        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
224      - initial float position from tiled file was not converted to index space
225        (looks like a bug): fixed to make it similar to initial pos. global file.
226    o global_ocean.cs32x15:
227       change SIZE.h of AD set-up to get same tiling as with MPI.
228       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
229    o model/src:
230       add flag to control printing of domain fields (bathymetry, hFac ...) in
231       ini_mask_etc (call to plot_fieds_xy*).
232    o pkg/thsice:
233       if useEXF, some forcing fields are not valid in overlap: fixed by computing
234       over the interior only + apply EXCH at the end (like with SEAICE advection).
235    o pkg/mdsio:
236      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
237        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
238      - change barrier call for safe multi-threads access to 3-D shared buffer.
239      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
240      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
241        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
242    o pkg/flt:
243      - add fourth-order Runge-Kutta integration
244      - add basic exch2 support (only 1 facet supported so far!)
245    o pkg/mdsio+rw:
246      new S/R to read local (or tile independent) vector (read counterpart of
247       mds_writevec_loc, and front-end write_glvec_rl/rs).
248    o global_ocean.cs32x15: additional input_ad.seaice experiment
249        that uses pkg/seaice rather than pkg/thsice.
250        (using multidim advection for seaice)
251    o towards more F95 syntax for array specification in namelist:
252      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
253        of all verification experiments.
254           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
255          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
256      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
257    o global_ocean.cs32x15: additional input.seaice experiment
258        that uses pkg/seaice rather than pkg/thsice.
259    
260    checkpoint62p (2010/12/17)
261    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
262        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
263    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
264        allow for use of multim. advection in seaice adjoint.
265    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
266      - first attempt to close budgets by taking into account the freshwater
267        flux implied by the sublimation of snow and ice. So far only the
268        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
269        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
270    o eesupp/src:
271      new S/R with new option (NML_EXTENDED_F77) to change array specification
272      from F95 standard to commonly accepted extended F77 form.
273      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
274      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
275      for less tolerant f77 compiler (e.g., pgf77, g77).
276    o globalFiles:
277      commented out in parameter file "data" since it's not safe with MPI
278      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
279      in this case); no longer commented out in restart test (tst_2+2).
280    o add adTapeDir to specify a special directory where adjoint tapes are
281      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
282      and cannot be used together with mdsioLocalDir.
283    o nesting pkgs:
284      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
285      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
286      - add parameter files + utils dir + output from short run on beagle.
287    o pkg/seaice:
288        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
289    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
290      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
291    
292    checkpoint62o (2010/11/25)
293    o pkg/exf:
294      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
295    o pkg/seaice:
296      - seaice_ocean_stress: split a loop for better vectorization of the
297        adjoint code
298      - seaice_growth.F: fix bug in conservation of freshwater connected to
299        capping of heff, put contribution into d_HEFFbyNEG
300      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
301        by something more sensible (parameters that are what their name implies)
302      - change some defaults, so that by default exf-parameters are used for
303        things like rhoAir, cpAir,latent/sensible heat parameters, in order
304        to reproduce the old results, many data.seaice now contain funny values
305        for cpAir and latent heat of sublimation
306    o packages_readparms.F: move exf_readparms up in line so that
307        exf-parameters are visible for other packages (e.g. seaice)
308    o debugMode & debugLevel=2:
309      - differentiate between debugMode & debugLevel=2:
310        debugMode: controls printing of debug messages (sequence of S/R calls).
311        debugLevel: controls printing of algorithm intermediate results and stats.
312      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
313        => allows to print debug-stats without all sequence of call messages.
314      - switch control of debug print from debugLevel to debugMode in many S/R.
315    o pkg/obcs (obcs-sponge):
316        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
317        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
318    o pkg/generic_advdiff:
319      - record overlap minimum size for each advection scheme;
320      - refine criteria on overlap minimum size;
321      - check and stop (in gad_check) if overlap size is too small.
322    o pkg/obcs:
323      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
324        once, in ptracers_implicit.F)
325      - with seaice: remove test on empty file name in obcs_apply_seaice (always
326        apply OB values when tile has OB)
327    o model/src, coriolis setting:
328      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
329        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
330        files (selectCoriMap=3) with any grid.
331      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
332    o pkg/seaice/seaice_growth.F:
333        a few cosmetic changes that reduce the number of lines of code
334    o pkg/obcs: add boundary conditions following Stevens (1990)
335      - the code follows old MOM/NAOSIM code
336      - so far it is only implemented for the eastern and western boundaries
337        and NOT for pTracers
338    o pkg/rbcs:
339      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
340        beginning of the first rbcs forcing period.
341      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
342        offline package, i.e., one file per time, labeled by iteration number;
343        deltaTrbcs sets the timestep with which the data was generated;
344        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
345      - rbcsForcingCycle=0 makes forcing non-cyclic.
346      - make arithmetic safe for negative times and odd forcing periods.
347    
348    checkpoint62n (2010/11/09)
349    o pkg/seaice:
350        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
351    o pkg/obcs:
352       New S/R to copy tracer value from the OB location to narrow band region
353        (width = same as overlap) beyond the OB: preserve OB value (needed for
354        high-order scheme) which were overwritten by EXCH call if in overlap
355        region. Applied to theta, salt, ptracer and advected seaice variables.
356       With seaice: use maskInC in similar way as in gad_advection.F,
357        in seaice_advection.F and advect.F.
358       Update output of experiment seaice_obcs and change exp4 to test OBCS with
359        4th order Adv.Scheme. for pasive salt and ptracer.
360    o tools/genmake2:
361      - when looking for an optfile (not specified), only search for Fortran compiler
362        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
363      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
364        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
365      - set default for CPP to "cpp -traditional -P" (was the case without specifying
366        an optfile, but otherwise default was just "cpp".
367      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
368      - when "CC" is not set in the optfile, look for possible C compiler
369        (instead of just setting CC=cc)
370      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
371        => add a ".F" to ".o" rule for source files with no "#include" (such as
372           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
373      - move gfortran before g77 in list of possible Fortran compiler (consistent
374        with reference compiler switch from g77 to gfortran)
375    o pkg/seaice:
376      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
377        seaice_check that stops the model, when the CPP flag is used.
378      o seaice_growth.F: make capping of ice volume conserving by returning the
379        capped ice as freshwater to EmPmR. This does not change the verification
380        experiments but will change runs where the capping is acutally active
381    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
382      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
383         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
384         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
385    o tools/genmake2:
386      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
387      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
388      - clean previous genmake log files before anything else.
389      - change Makefile to remove testreport log files (*.tr_log) and genmake log
390        files only with "CLEAN" target (instead of "Clean");
391    o pkg/generic_advdiff:
392      Change OBCS in multiDim advection (gad_advection.F):
393       Use maskInC to prevent intermediate update of tracer-field in OB regions,
394       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
395       which were applying future time-step OB values.
396      This way, all explicit calculations use current-time-step OB values
397       (simpler and more consistent).
398      Affects results when set-up uses time-varying OBC and multi-dim advection;
399       update output of experiment seaice_obcs.
400    o pkg/seaice:
401      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
402       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
403         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
404      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
405       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
406       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
407    o pkg aim (2010/10/26):
408      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
409        formulation with obliquity, eccentricity, ... as run-time parameters,
410      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
411        upward shortwave radition at the surface (all-sky and clear-sky).
412    o pkg/obcs:
413      - writing sections with globalFiles=T does not work: switch to tiled-files
414        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
415      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
416      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
417    
418    checkpoint62m (2010/10/21)
419    o pkg/seaice: vectorize seaice_solve4temp.F
420      - move iterations loops outside of i/j-loops
421      - requires 2D arrays for TB and effConduct
422      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
423        modified in this routine
424      - a little bit of clean up, adjusting indentation, etc.
425      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
426        performance and '**TWO' by '**2' (because TWO is a float),
427        replaced ONE, ZERO
428    o eesupp/src:
429       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
430    o pkg/seaice/seaice_growth.F
431      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
432      merging process. The merged routine has two branches, and one activates the 'evolution'
433      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
434      In summary, here is what the '10/10 revision' did consist of
435        part 1: seaice_growth.F revisions 1.71 to 1.75
436          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
437            The emphasis here was on improving readability (e.g. by trying to use meaningful
438            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
439        part 1.5:
440          - revising the lab_sea experiment to make it a more useful (i.e. stable
441            and representative of an actual model run). This was done by generating a
442            (winter) pickup to start from, switching back the main experiment dynamic
443            solver from evp to lsr, having one of the experiments use the free drift solution.
444        part 2: seaice_growth.F revisions 1.76 to 1.85
445          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
446          - Sorting out the various fields units and sign (set early on and reset at the end)
447            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
448            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
449          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
450            and simplifying logical expressions to further improve readibility.
451        part 3: seaice_growth.F revisions 1.86 to 1.89
452          - Re-organize the blocks of code more logically.
453          - Merging the '_if.F' pieces that add something new.
454    o pkg/thsice:
455      - vectorize thsice_solve4temp and thsice_get_exf.
456        Problem: thsice_solve4temp has an unvectorizable statement that
457        might also be problematic for TAF
458      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
459        does not change the verifcation experiment, but will change all
460        experiments that have this flag undefined (not tested in verification);
461        a little reorganization to save a few 2D fields and recomputations
462      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
463      - 2nd step:  fix some store dirs
464        o seems to work somewhat, i.e. using ifort but not g77
465        o likely cause are incomplete init. or recomputation
466        o start verification/global_ocean.cs32x15/input_ad.thsice
467    o pkg/obcs: add support for exch2
468      - the position of the boundary and prescribed values are specified using
469        a global domain with exch2 facets stacked
470        - in x for N,S boundaries (like W2_mapIO=-1)
471        - in y for E,W boundaries (so E,W boundaries do not overlap)
472    o pkg/mdsio: add support for writing global sections with exch2
473        file layout is as for obcs described above:
474        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
475        - for y-z sections, facets are stacked in y
476    o pkg/thsice:
477       - change a few routines for better vectorization: thsice_albedo.F,
478         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
479         not affected, but in particular the latter routine has changed
480         dramatically (not necessarily easier to read now).
481       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
482       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
483    o verification/lab_sea:
484      - overhaul of the forward model experiments. The main motivation
485        for this revision is that lab_sea has proven quite fragile (when
486        changing the sea-ice code, and switching platforms) to a point
487        when failures were very hard to attribute to specific code problems.
488      - the suspected reason for this fragility is noise amplification by evp so,
489        to start with, we decided to replace evp with lsr in the main experiment.
490      - the input.lsr experiment thus became obsolete and was removed.
491      - it was replaced with the input.fd experiment that uses an
492        analytical "free drift" solution as the ice velocity field.
493      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
494        will hopefully allow us to discriminate problems due to dynamic solvers
495        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
496        us to test additional options, along with the salt plume package.
497      - Finally a pickup was generated (at the end of a one year run) to
498        make the tests more representative of an actual model run. Previously
499        the tests starting point was a 1m thickness of ice everywhere.
500    o pkg/seaice:
501      - introducing S\R seaice_freedrift.F that compute the
502        analytical solution to an approximate ice momentum
503        equation (i.e. the simple stress/coriolis balance).
504      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
505        of the free drift velocity field, and enable its use.
506        To actually use the free drift solution as the model ice
507        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
508    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
509    
510    checkpoint62l (2010/10/04)
511    o pkg/seaice:
512      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
513      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
514       version (with USE_ORIGINAL_SBI undef);
515    o add hooks for new packages OASIS, the package will follow
516      (hooks exclude the seaice pkg for now)
517    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
518      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
519      rather than mdsio_readvector.F/mdsio_writevector.F, within
520      adread_adwrite.F to read/write adjoint-related tapes to disk.
521    o eesupp and pkg/mdsio: ALLOW_WHIO
522      Option to write/read 2D fields to files including tiles halos.
523      The main purpose is for adjoint related "tape I/O".
524      The secondary purpose is for debugging phases.
525      A word on those rather specifically intended purposes.
526      The code was meant to be stripped down to the bare minimum.
527      Typically, there is a unique and basic mapping to the global
528      buffer (tile by tile, then proc by proc, then level by level), and
529      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
530      meant to generate user friendly outputs of various shapes and forms.
531      Rather it is intended, for the knowledgeabale developers,
532      to be largely independent of the many mdsio options, to allow
533      outputs of tiles+halos in debugging phases and in adjoint runs,
534      and to allow some flexibility in tuning (adoint) I/O depending on each
535      file system behavior. With regard to tuning, most of the potential knobs
536      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
537      to specify directories, to specify the typical size of I/O calls, etc.)
538      are not yet included, and will be added if they prove useful.
539    o pkg/seaice:
540       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
541    o pkg/seaice:
542       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
543       code (seaice_budget_ice_if.F) which enable to recover old standard
544       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
545       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
546    o model/src (rStar):
547       use simple average (not area weighted) of rStarFac at U,V point when using
548       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
549       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
550    
551    checkpoint62k (2010/09/17)
552    o adjoint
553       * changed verification/global_ocean.cs32x15 ; adjoint now tests
554         Adams-Bashforth 3 + NLFS + RSTAR
555       * some more modifs required for ECCO-GODAE v4
556    o pkg/seaice
557       add SEAICE_AGE_VOL option to use volume instead of area for
558       integrating SEAICE_AGE
559    o model/src:
560       first check-in of sigma & hybrid-sigma coordinate code ; also includes
561       non-linear free-surface parts ; but pressure-gradient not yet coded.
562    o pkg/ptracers:
563       option for ptracer to convert Salt Relax into additional EmP.
564        tested in exp. global_ocean.90x40x15.dwnslp (update output)
565    
566    checkpoint62j (2010/08/25)
567    o pkg/ggl90:
568       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
569    o pkg/dic: car_flux.F, phos_flux.F
570      - reduce number of exp-calls in order to improve performance
571      - clean up a little (replace fields by their macros, etc., fix
572        typo in CPP-flag)
573    o pkg/ggl90: minor changes
574      - GGL90diffKrS was removed --> always use GGL90diffKr
575      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
576      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
577        (commented out for now)
578      - change in max/min operations to ensure that smoothing is ok
579      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
580      - always use diffKrNrT as background profile (i.e. never use diffKr field)
581    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
582    o pkg/dic:
583      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
584        vectorization
585      - small bug fix in insol for the unlikely case of a cartesian grid
586      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
587        + now vectorize, which also removes adjoint recomputations;
588        + replace integer maksp1 by _RL maskp1
589        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
590    
591    checkpoint62i (2010/07/21)
592    o pkg/flt:
593      - with OBCS: stop floats which enter the OB region
594    o model/src:
595      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
596        for implicit vertical advection.
597    o pkg/seaice:
598     - account for melting in seaice age evolution.
599     - remove double counting of seaice ridging effect on seaice age.
600    
601    checkpoint62h (2010/06/18)
602    o pkg/exch2:
603     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
604    o tools/genmake2
605      - remove "-pdefault" option: redundant with the use of "packages.conf";
606      - remove file pkg/pkg_default : set the default as a pkg group
607        ("default_pkg_list") defined in pkg/pkg_groups;
608      - fix for case pkg/pkg_depend is missing (was hanging before);
609      - add option "-pgroups" to specify a different pkg_groups than the default.
610  o verification/adjustment.cs-32x32x1:  o verification/adjustment.cs-32x32x1:
611     add a "minimal" set-up test (code_min & input_min) which only compiles     add a "minimal" set-up test (code_min & input_min) which only compiles
612     eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.     eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
# Line 222  o tools/build_options: Line 825  o tools/build_options:
825      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
826  o pkg/ecco  o pkg/ecco
827    - allow user defined cost function contributions    - allow user defined cost function contributions
828          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
829          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
830    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
831        the two options are complementary.        the two options are complementary.
832  o pkg/smooth  o pkg/smooth
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