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revision 1.1240 by jmc, Wed Mar 24 02:12:51 2010 UTC revision 1.1401 by mlosch, Fri Mar 18 10:50:53 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 model/inc/scr and pkg/autodiff: add parameters that allow to turn
8      of parts of the adjoint code at run time. For now, there are only
9      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
10      parameters are set in data.pkg.
11      This is the lazy coward's version of doing this, but still useful for
12      debugging. In order to do it right, everything needs to be moved to
13      pkg/autodiff.
14    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
15      the end; this fixes the adjoint balancing code for open boundaries.
16    o pkg/ctrl:
17      - change behavior of xx_${varname}period to be analogous to exf-conventions:
18        xx_${varname}period =   0.,  means time-independent control part
19        xx_${varname}period = -12., means one-year-periodic monthly control part
20      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
21        clean up ctrl_init a little, remove unused variables
22      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
23      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
24    
25    checkpoint62u (2011/03/15)
26    o model/src:
27      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
28        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
29      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
30        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
31    o pkg/ctrl/obcs/ecco:
32      - remove obsolete, unused, and partially broken code:
33        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
34        ALLOW_CTRL_OBCS_BALANCE
35      - put a stop statement into ecco/cost_obcsvol.F, but also add
36        cost_obcsvol to ecco_ad_diff.list
37    o pkg/ecco: fix counting cost function contributions for obcs (code
38      by Matt M.) and diffkr for diagnostics
39    o pkg/ecco, pkg/ctrl, pkg/grdchk:
40      add cost penalty terms for initial uvel, vvel, eta controls
41      and I/O for prior error files
42    o pkg/mdsio:
43       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
44       (new argument) to check for tiled file in mdsioLocalDir : this fix the
45       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
46    o pkg/ctrl:
47     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
48       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
49       unused and superfluous variables
50     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
51    o pkg/ecco
52     - enable adjoint of Stevens OB
53    o pkg/ctrl/ecco/grdchk:
54      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
55        Fortunately, we do not have any tests for the numerous cpp-flagged
56        option of "obcs as control parameters" so we will never know
57        if this is an improvement (but at least now things compile).
58      - remove an obsolete initialization from ecco_cost_init_barfiles.F
59      - fix some problems within never used ifdefs to make the code compile
60    o pkg/obcs:
61     - Refine Interior mask definition to work with more complex OB (e.g.
62       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
63       read in Interior mask from file. Check if Interior mask is consistent
64       with OB list of indices.
65    o pkg/seaice
66     - beginning code for a seaice tracer package,
67       but currently only used for seaice age: SEAICE_AGE
68       SEAICE_num = 4
69       iTracer = 1: area-weighted ice age
70               = 2: volume-weighted ice age
71               = 3, 4: template for one-year vs. multi-year ice
72       data.seaice has new namelist SEAICE_PARM03 for arrays related to
73       SEAICE_num
74    
75    checkpoint62t (2011/03/05)
76    o pkg/obcs:
77     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
78       then normal component. This ensures that the normal component is set
79       correctly even when it conficts with tangential setting from an other OB.
80       Affects results of test-experiment seaice_obcs: update the output.txt
81    o pkg/obcs:
82     - add code to monitor statistics of dynamical fields at OB.
83     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
84       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
85       - change default: balance the Net inflow through all OB (instead of balancing
86         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
87     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
88       to match Nortern OB inflow (OBCS_balanceFacN=0).
89    o pkg/seaice:
90     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
91    o pkg/seaice (seaice_growth v 1.113):
92     - reverting seaice_growth to v 1.111 in order to have code with exact bit
93       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
94       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
95       runtime flag SEAICEareaFormula is kept but is inactive
96    o model/src:
97     - add new param to scale curvilinear grid distance and area when using
98       a different sphere radius from the grid-files.
99     - test/check multi-threads EXCH applied to local variable (cg2d_x)
100    o adjoint:
101     - enable adjoint of Stevens OB
102     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
103       (a bit delicate because of potentially modified adj. common block structure;
104       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
105    
106    checkpoint62s (2011/02/15)
107    o pkg/seaice (seaice_growth v 1.112):
108     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
109       computing the ice cover tendency from effective thickness tendencies. Include
110       Ian Fenty's formula.
111     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
112       SEAICEareaFormula.
113     - simplify notations for the various d_HEFF/d_AREA terms.
114    o pkg/gmredi:
115     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
116       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
117       add a verification test-run (front_relax.bvp) to test GM_useBVP.
118    o pkg/seaice (seaice_growth v 1.111):
119     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
120     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
121       also melt ice.
122    o pkg/seaice:
123     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
124     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
125    o pkg/cheapaml:
126     - from Nico Wienders: New version of this package.
127    o pkg/flt:
128     - add CPP options to prevent floats to re-enter the opposite side of
129       a periodic domain (default: keep periodicity)
130    o pkg/gmredi:
131     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
132       (needed for multi-dim advection).
133     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
134    o model/src:
135     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
136    o tutorial_tracer_adjsens
137     - extend to NLFS and replace maskC by hFacC
138       (change reference output accordingly)
139    
140    checkpoint62r (2011/01/24)
141    o testreport:
142     - add option -deloutp (-do) to remove output file after successful run
143     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
144       extract exact list of procs from this file ; adjust COMMAND by
145       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
146    o pkg/ecco: replace old ineffective way of penalizing deviations from
147      first guess (of obcs) with code by Matt Mazloff
148    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
149      exf/cal
150      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
151        and handle case of obcs?period == 0
152        Not affected by these changes: There is still an inconsistency in
153        the computation of start/endrec for the obcs variables for ALLOW_CAL
154        defined (see comment by Menemenlis, 7-Mar-2003)
155      - make S/R ctrl_get_gen_rec return something meaningful even if
156        ALLOW_CAL is not defined
157      - ctrl_getobcs?: simplify code so that it does not need to use
158                       S/R exf_swapfields
159    o testreport:
160       allow to test MPI with different number of processors for each experiment:
161       create file "SIZE.h.mpi" in each build dir.
162       Note: update of "-command" argument not yet implemented.
163    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
164      alleviate the need for additional 3D tapes when using
165      the non-inear free surface in the adjoint. This is done
166      by adding an 'update' of hfacc etc. to their current
167      value at the beginning of forward_step.F.
168    o pkg/seaice
169      seaice_lsr: move stress-divergence computations out of outer pseudo-
170      timestepping loop
171    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
172      up, so that the calls of the ctrl_* subroutines are really at the end
173      of the routine.
174    o pkg/gmredi:
175      allow to specify a 2-D horizontal map and a 1-D vertical profil
176      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
177    o pkg/seaice:
178      move lsr iterations from seaice_dynsolver to seaice_lsr.
179    o pkg/seaice:
180      reduce memory footprint of seaice mutldim advection tapes,
181      by using a 2D tape independent of the generic_advdiff ones,
182      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
183    
184    checkpoint62q (2010/12/29)
185    o model/src:
186      - check horizontal grid-spacing for unset or zero/negative values.
187      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
188    o pkg/flt:
189      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
190      - precision of input and output files set according to readBinaryPrec
191        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
192      - initial float position from tiled file was not converted to index space
193        (looks like a bug): fixed to make it similar to initial pos. global file.
194    o global_ocean.cs32x15:
195       change SIZE.h of AD set-up to get same tiling as with MPI.
196       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
197    o model/src:
198       add flag to control printing of domain fields (bathymetry, hFac ...) in
199       ini_mask_etc (call to plot_fieds_xy*).
200    o pkg/thsice:
201       if useEXF, some forcing fields are not valid in overlap: fixed by computing
202       over the interior only + apply EXCH at the end (like with SEAICE advection).
203    o pkg/mdsio:
204      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
205        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
206      - change barrier call for safe multi-threads access to 3-D shared buffer.
207      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
208      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
209        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
210    o pkg/flt:
211      - add fourth-order Runge-Kutta integration
212      - add basic exch2 support (only 1 facet supported so far!)
213    o pkg/mdsio+rw:
214      new S/R to read local (or tile independent) vector (read counterpart of
215       mds_writevec_loc, and front-end write_glvec_rl/rs).
216    o global_ocean.cs32x15: additional input_ad.seaice experiment
217        that uses pkg/seaice rather than pkg/thsice.
218        (using multidim advection for seaice)
219    o towards more F95 syntax for array specification in namelist:
220      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
221        of all verification experiments.
222           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
223          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
224      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
225    o global_ocean.cs32x15: additional input.seaice experiment
226        that uses pkg/seaice rather than pkg/thsice.
227    
228    checkpoint62p (2010/12/17)
229    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
230        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
231    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
232        allow for use of multim. advection in seaice adjoint.
233    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
234      - first attempt to close budgets by taking into account the freshwater
235        flux implied by the sublimation of snow and ice. So far only the
236        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
237        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
238    o eesupp/src:
239      new S/R with new option (NML_EXTENDED_F77) to change array specification
240      from F95 standard to commonly accepted extended F77 form.
241      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
242      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
243      for less tolerant f77 compiler (e.g., pgf77, g77).
244    o globalFiles:
245      commented out in parameter file "data" since it's not safe with MPI
246      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
247      in this case); no longer commented out in restart test (tst_2+2).
248    o add adTapeDir to specify a special directory where adjoint tapes are
249      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
250      and cannot be used together with mdsioLocalDir.
251    o nesting pkgs:
252      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
253      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
254      - add parameter files + utils dir + output from short run on beagle.
255    o pkg/seaice:
256        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
257    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
258      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
259    
260    checkpoint62o (2010/11/25)
261    o pkg/exf:
262      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
263    o pkg/seaice:
264      - seaice_ocean_stress: split a loop for better vectorization of the
265        adjoint code
266      - seaice_growth.F: fix bug in conservation of freshwater connected to
267        capping of heff, put contribution into d_HEFFbyNEG
268      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
269        by something more sensible (parameters that are what their name implies)
270      - change some defaults, so that by default exf-parameters are used for
271        things like rhoAir, cpAir,latent/sensible heat parameters, in order
272        to reproduce the old results, many data.seaice now contain funny values
273        for cpAir and latent heat of sublimation
274    o packages_readparms.F: move exf_readparms up in line so that
275        exf-parameters are visible for other packages (e.g. seaice)
276    o debugMode & debugLevel=2:
277      - differentiate between debugMode & debugLevel=2:
278        debugMode: controls printing of debug messages (sequence of S/R calls).
279        debugLevel: controls printing of algorithm intermediate results and stats.
280      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
281        => allows to print debug-stats without all sequence of call messages.
282      - switch control of debug print from debugLevel to debugMode in many S/R.
283    o pkg/obcs (obcs-sponge):
284        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
285        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
286    o pkg/generic_advdiff:
287      - record overlap minimum size for each advection scheme;
288      - refine criteria on overlap minimum size;
289      - check and stop (in gad_check) if overlap size is too small.
290    o pkg/obcs:
291      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
292        once, in ptracers_implicit.F)
293      - with seaice: remove test on empty file name in obcs_apply_seaice (always
294        apply OB values when tile has OB)
295    o model/src, coriolis setting:
296      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
297        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
298        files (selectCoriMap=3) with any grid.
299      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
300    o pkg/seaice/seaice_growth.F:
301        a few cosmetic changes that reduce the number of lines of code
302    o pkg/obcs: add boundary conditions following Stevens (1990)
303      - the code follows old MOM/NAOSIM code
304      - so far it is only implemented for the eastern and western boundaries
305        and NOT for pTracers
306    o pkg/rbcs:
307      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
308        beginning of the first rbcs forcing period.
309      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
310        offline package, i.e., one file per time, labeled by iteration number;
311        deltaTrbcs sets the timestep with which the data was generated;
312        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
313      - rbcsForcingCycle=0 makes forcing non-cyclic.
314      - make arithmetic safe for negative times and odd forcing periods.
315    
316    checkpoint62n (2010/11/09)
317    o pkg/seaice:
318        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
319    o pkg/obcs:
320       New S/R to copy tracer value from the OB location to narrow band region
321        (width = same as overlap) beyond the OB: preserve OB value (needed for
322        high-order scheme) which were overwritten by EXCH call if in overlap
323        region. Applied to theta, salt, ptracer and advected seaice variables.
324       With seaice: use maskInC in similar way as in gad_advection.F,
325        in seaice_advection.F and advect.F.
326       Update output of experiment seaice_obcs and change exp4 to test OBCS with
327        4th order Adv.Scheme. for pasive salt and ptracer.
328    o tools/genmake2:
329      - when looking for an optfile (not specified), only search for Fortran compiler
330        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
331      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
332        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
333      - set default for CPP to "cpp -traditional -P" (was the case without specifying
334        an optfile, but otherwise default was just "cpp".
335      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
336      - when "CC" is not set in the optfile, look for possible C compiler
337        (instead of just setting CC=cc)
338      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
339        => add a ".F" to ".o" rule for source files with no "#include" (such as
340           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
341      - move gfortran before g77 in list of possible Fortran compiler (consistent
342        with reference compiler switch from g77 to gfortran)
343    o pkg/seaice:
344      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
345        seaice_check that stops the model, when the CPP flag is used.
346      o seaice_growth.F: make capping of ice volume conserving by returning the
347        capped ice as freshwater to EmPmR. This does not change the verification
348        experiments but will change runs where the capping is acutally active
349    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
350      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
351         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
352         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
353    o tools/genmake2:
354      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
355      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
356      - clean previous genmake log files before anything else.
357      - change Makefile to remove testreport log files (*.tr_log) and genmake log
358        files only with "CLEAN" target (instead of "Clean");
359    o pkg/generic_advdiff:
360      Change OBCS in multiDim advection (gad_advection.F):
361       Use maskInC to prevent intermediate update of tracer-field in OB regions,
362       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
363       which were applying future time-step OB values.
364      This way, all explicit calculations use current-time-step OB values
365       (simpler and more consistent).
366      Affects results when set-up uses time-varying OBC and multi-dim advection;
367       update output of experiment seaice_obcs.
368    o pkg/seaice:
369      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
370       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
371         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
372      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
373       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
374       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
375    o pkg aim (2010/10/26):
376      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
377        formulation with obliquity, eccentricity, ... as run-time parameters,
378      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
379        upward shortwave radition at the surface (all-sky and clear-sky).
380    o pkg/obcs:
381      - writing sections with globalFiles=T does not work: switch to tiled-files
382        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
383      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
384      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
385    
386    checkpoint62m (2010/10/21)
387    o pkg/seaice: vectorize seaice_solve4temp.F
388      - move iterations loops outside of i/j-loops
389      - requires 2D arrays for TB and effConduct
390      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
391        modified in this routine
392      - a little bit of clean up, adjusting indentation, etc.
393      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
394        performance and '**TWO' by '**2' (because TWO is a float),
395        replaced ONE, ZERO
396    o eesupp/src:
397       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
398    o pkg/seaice/seaice_growth.F
399      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
400      merging process. The merged routine has two branches, and one activates the 'evolution'
401      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
402      In summary, here is what the '10/10 revision' did consist of
403        part 1: seaice_growth.F revisions 1.71 to 1.75
404          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
405            The emphasis here was on improving readability (e.g. by trying to use meaningful
406            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
407        part 1.5:
408          - revising the lab_sea experiment to make it a more useful (i.e. stable
409            and representative of an actual model run). This was done by generating a
410            (winter) pickup to start from, switching back the main experiment dynamic
411            solver from evp to lsr, having one of the experiments use the free drift solution.
412        part 2: seaice_growth.F revisions 1.76 to 1.85
413          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
414          - Sorting out the various fields units and sign (set early on and reset at the end)
415            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
416            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
417          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
418            and simplifying logical expressions to further improve readibility.
419        part 3: seaice_growth.F revisions 1.86 to 1.89
420          - Re-organize the blocks of code more logically.
421          - Merging the '_if.F' pieces that add something new.
422    o pkg/thsice:
423      - vectorize thsice_solve4temp and thsice_get_exf.
424        Problem: thsice_solve4temp has an unvectorizable statement that
425        might also be problematic for TAF
426      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
427        does not change the verifcation experiment, but will change all
428        experiments that have this flag undefined (not tested in verification);
429        a little reorganization to save a few 2D fields and recomputations
430      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
431      - 2nd step:  fix some store dirs
432        o seems to work somewhat, i.e. using ifort but not g77
433        o likely cause are incomplete init. or recomputation
434        o start verification/global_ocean.cs32x15/input_ad.thsice
435    o pkg/obcs: add support for exch2
436      - the position of the boundary and prescribed values are specified using
437        a global domain with exch2 facets stacked
438        - in x for N,S boundaries (like W2_mapIO=-1)
439        - in y for E,W boundaries (so E,W boundaries do not overlap)
440    o pkg/mdsio: add support for writing global sections with exch2
441        file layout is as for obcs described above:
442        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
443        - for y-z sections, facets are stacked in y
444    o pkg/thsice:
445       - change a few routines for better vectorization: thsice_albedo.F,
446         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
447         not affected, but in particular the latter routine has changed
448         dramatically (not necessarily easier to read now).
449       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
450       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
451    o verification/lab_sea:
452      - overhaul of the forward model experiments. The main motivation
453        for this revision is that lab_sea has proven quite fragile (when
454        changing the sea-ice code, and switching platforms) to a point
455        when failures were very hard to attribute to specific code problems.
456      - the suspected reason for this fragility is noise amplification by evp so,
457        to start with, we decided to replace evp with lsr in the main experiment.
458      - the input.lsr experiment thus became obsolete and was removed.
459      - it was replaced with the input.fd experiment that uses an
460        analytical "free drift" solution as the ice velocity field.
461      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
462        will hopefully allow us to discriminate problems due to dynamic solvers
463        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
464        us to test additional options, along with the salt plume package.
465      - Finally a pickup was generated (at the end of a one year run) to
466        make the tests more representative of an actual model run. Previously
467        the tests starting point was a 1m thickness of ice everywhere.
468    o pkg/seaice:
469      - introducing S\R seaice_freedrift.F that compute the
470        analytical solution to an approximate ice momentum
471        equation (i.e. the simple stress/coriolis balance).
472      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
473        of the free drift velocity field, and enable its use.
474        To actually use the free drift solution as the model ice
475        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
476    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
477    
478    checkpoint62l (2010/10/04)
479    o pkg/seaice:
480      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
481      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
482       version (with USE_ORIGINAL_SBI undef);
483    o add hooks for new packages OASIS, the package will follow
484      (hooks exclude the seaice pkg for now)
485    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
486      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
487      rather than mdsio_readvector.F/mdsio_writevector.F, within
488      adread_adwrite.F to read/write adjoint-related tapes to disk.
489    o eesupp and pkg/mdsio: ALLOW_WHIO
490      Option to write/read 2D fields to files including tiles halos.
491      The main purpose is for adjoint related "tape I/O".
492      The secondary purpose is for debugging phases.
493      A word on those rather specifically intended purposes.
494      The code was meant to be stripped down to the bare minimum.
495      Typically, there is a unique and basic mapping to the global
496      buffer (tile by tile, then proc by proc, then level by level), and
497      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
498      meant to generate user friendly outputs of various shapes and forms.
499      Rather it is intended, for the knowledgeabale developers,
500      to be largely independent of the many mdsio options, to allow
501      outputs of tiles+halos in debugging phases and in adjoint runs,
502      and to allow some flexibility in tuning (adoint) I/O depending on each
503      file system behavior. With regard to tuning, most of the potential knobs
504      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
505      to specify directories, to specify the typical size of I/O calls, etc.)
506      are not yet included, and will be added if they prove useful.
507    o pkg/seaice:
508       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
509    o pkg/seaice:
510       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
511       code (seaice_budget_ice_if.F) which enable to recover old standard
512       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
513       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
514    o model/src (rStar):
515       use simple average (not area weighted) of rStarFac at U,V point when using
516       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
517       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
518    
519    checkpoint62k (2010/09/17)
520    o adjoint
521       * changed verification/global_ocean.cs32x15 ; adjoint now tests
522         Adams-Bashforth 3 + NLFS + RSTAR
523       * some more modifs required for ECCO-GODAE v4
524    o pkg/seaice
525       add SEAICE_AGE_VOL option to use volume instead of area for
526       integrating SEAICE_AGE
527    o model/src:
528       first check-in of sigma & hybrid-sigma coordinate code ; also includes
529       non-linear free-surface parts ; but pressure-gradient not yet coded.
530    o pkg/ptracers:
531       option for ptracer to convert Salt Relax into additional EmP.
532        tested in exp. global_ocean.90x40x15.dwnslp (update output)
533    
534    checkpoint62j (2010/08/25)
535    o pkg/ggl90:
536       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
537    o pkg/dic: car_flux.F, phos_flux.F
538      - reduce number of exp-calls in order to improve performance
539      - clean up a little (replace fields by their macros, etc., fix
540        typo in CPP-flag)
541    o pkg/ggl90: minor changes
542      - GGL90diffKrS was removed --> always use GGL90diffKr
543      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
544      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
545        (commented out for now)
546      - change in max/min operations to ensure that smoothing is ok
547      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
548      - always use diffKrNrT as background profile (i.e. never use diffKr field)
549    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
550    o pkg/dic:
551      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
552        vectorization
553      - small bug fix in insol for the unlikely case of a cartesian grid
554      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
555        + now vectorize, which also removes adjoint recomputations;
556        + replace integer maksp1 by _RL maskp1
557        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
558    
559    checkpoint62i (2010/07/21)
560    o pkg/flt:
561      - with OBCS: stop floats which enter the OB region
562    o model/src:
563      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
564        for implicit vertical advection.
565    o pkg/seaice:
566     - account for melting in seaice age evolution.
567     - remove double counting of seaice ridging effect on seaice age.
568    
569    checkpoint62h (2010/06/18)
570    o pkg/exch2:
571     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
572    o tools/genmake2
573      - remove "-pdefault" option: redundant with the use of "packages.conf";
574      - remove file pkg/pkg_default : set the default as a pkg group
575        ("default_pkg_list") defined in pkg/pkg_groups;
576      - fix for case pkg/pkg_depend is missing (was hanging before);
577      - add option "-pgroups" to specify a different pkg_groups than the default.
578    o verification/adjustment.cs-32x32x1:
579       add a "minimal" set-up test (code_min & input_min) which only compiles
580       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
581    o tools/genmake2
582      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
583      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
584    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
585      files are nearly the same anyway.
586      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
587       - redefinition of tau(i,i) (by a factor of ustar)
588       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
589       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
590       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
591       - replace
592         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
593         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
594         by
595         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
596         (changes results)
597       -> exf_bulkformulae v1.22,
598          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
599          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
600                    output.txt 1.63
601           offline_exf_seaice: output.seaicetd.txt 1.7
602           seaice_obcs: output.txt 1.10)
603      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
604       -> exf_bulkformulae v1.23,
605          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
606          and global_ocean.cs32x15.icedyn (only 11 matching digits)
607      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
608    o adjoint of exch-1:
609     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
610       (note: was already like this when using EXCH-2) and remove flow dir
611       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
612     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
613     - update pkg/exch2 diff list.
614    
615    checkpoint62g (2010/05/19)
616    o eesupp/src (exch-1):
617     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
618       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
619       (renamed to exch1_*rx_cube.F).
620     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
621       to call new exch1 S/R ; update Makefile and .cvsignore.
622     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
623       exch2_xy_rx later)
624      Note: after updating your code, need to run "make clean" in eesupp/src
625    o test experiment bottom_ctrl_5x5:
626       new output_adm.txt with fewer grdchk & less monitor output.
627    o model/src:
628      remove the call to ini_cori in initialise_varia.F (just keep the usual one
629       in initialise_fixed.F). More consistent with coriolis & horizontal grid
630       beeing treated in the same way (ini_grid is not called a 2nd time).
631    o pkg/exf:
632      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
633      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
634      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
635      - cosmetic changes to exf_bulkformulae.F to make it look more like
636        exf_bulk_largeyeager04.F
637    o eesupp/src (exch-1):
638      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
639      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
640        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
641        (even without using MPI).
642      - Message mode: move RecvAck setting (indicator of buffer being ready)
643        from send_put to recv_get S/R (was useless before, but not sure if
644        it's much more useful now);
645      - Switch the order of sync: MPI-proc 1rst and then threads;
646      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
647      - fix AD code for communication mode ='get' (but not used).
648    o model/src:
649      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
650      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
651    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
652    o pkg/ctrl: require a specific set of control variables and exf-flags for
653      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
654    o model/src:
655     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
656       1rst forward sweep, to avoid over-writing output files during recomputations
657       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
658     b) 2nd version:
659      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
660      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
661         writePickupAtEnd) + seaice & ptracers output;
662      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
663    o model/src:
664      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
665    o pkg/exch2:
666      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
667      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
668    o pkg/autodiff & exch2:
669      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
670      (for now, only if ALLOW_EXCH2 is defined).
671    o pkg/autodiff:
672      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
673        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
674       + clean-up comments (_RS is not always real*4)
675      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
676      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
677        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
678    o testreport (AD-tests):
679      no longer link files from dir "../input" (1rst link files from
680      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
681    
682    checkpoint62f (2010/04/29)
683    o model/src/the_main_loop.F:
684      adjust store directives for seaice evp and multicategory according to
685      pkg/ecco/the_main_loop.F
686    o adjoint:
687      global_sum_ad was incomplete (noted many times by many people ;)
688      nice description by Jean U. as follows:
689      * allreduce(var) in global_sum.F can be interpreted as
690        reduce(sum) followed by broadcast of sum.
691      * The adjoint of that is
692        sum(adjoint) followed by broadcast(summed adjoint value)
693        or in other words, allreduce(sum, adjoint vars)
694      We were missing the sum(adjoint)!
695      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
696      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
697      The fix should produce 16-digit accuracy between
698      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
699      multi-CPU single-tile (e.g. nSx=1, nPx-2)
700      We'll probably change this yet again shortly
701    o eesupp/src:
702      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
703    o pkg/icefront
704      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
705        specification of addmass array based on a 2D field, which is added
706        at bottommost wet level at each horizontal location.
707    o model/src:
708     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
709     layout; (not always compatible with delX,delY setting; commented out for now).
710    o pkg/exch2:
711     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
712     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
713    
714    checkpoint62e (2010/04/15)
715    o pkg/obcs:
716      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
717    o pkg/dic:
718      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
719        (note: not presently tested in any forward verification exp.)
720       update tutorial_global_oce_biogeo AD output file.
721    o pkg/exf:
722      - account for the variation of albedo as a function of zenith angle
723        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
724    o build_options:
725     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
726    o pkg/dic:
727      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
728      - use binary pickup file for restart;
729      - initialise atmos-CO2 box from dic_pCO2 parameter;
730      - fix multi-threaded.
731    o pkg/rbcs:
732     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
733       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
734     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
735       and update output.txt
736    o pkg/kpp:
737     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
738     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
739       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
740       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
741     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
742       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
743    o pkg/offline:
744      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
745      (bug was added in version 1.10 on 2007-08-23).
746    o pkg/offline:
747      - no need to specify periodicExternalForcing, etc ... to use offline pack
748      - offline input files no longer just single prec --> parameter offlineLoadPrec
749    o verification/lab_sea:
750      change AD test to multi-tile setup and update all 4 AD output.
751      NOTE: while cost function values remain very similar,
752      gradients are very different, although gradient checks are self-consistent
753      Should try to get to the bottom of this (cost function summation order?)
754    o pkg/dic:
755      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
756      a weakness of TAF that drops part of double precision in log10 derivative.
757      <= changes removed since problem has been fixed in current TAF version 1.9.71
758      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
759  o pkg/ecco:  o pkg/ecco:
760    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
761    update all 4 lab_sea AD output.    update all 4 lab_sea AD output.
# Line 41  o tools/build_options: Line 793  o tools/build_options:
793      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
794  o pkg/ecco  o pkg/ecco
795    - allow user defined cost function contributions    - allow user defined cost function contributions
796          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
797          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
798    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
799        the two options are complementary.        the two options are complementary.
800  o pkg/smooth  o pkg/smooth
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