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revision 1.1245 by jmc, Thu Apr 1 15:32:08 2010 UTC revision 1.1361 by jmc, Wed Dec 29 16:41:28 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62q (2010/12/29)
8    o model/src:
9      - check horizontal grid-spacing for unset or zero/negative values.
10      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
11    o pkg/flt:
12      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
13      - precision of input and output files set according to readBinaryPrec
14        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
15      - initial float position from tiled file was not converted to index space
16        (looks like a bug): fixed to make it similar to initial pos. global file.
17    o global_ocean.cs32x15:
18       change SIZE.h of AD set-up to get same tiling as with MPI.
19       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
20    o model/src:
21       add flag to control printing of domain fields (bathymetry, hFac ...) in
22       ini_mask_etc (call to plot_fieds_xy*).
23    o pkg/thsice:
24       if useEXF, some forcing fields are not valid in overlap: fixed by computing
25       over the interior only + apply EXCH at the end (like with SEAICE advection).
26    o pkg/mdsio:
27      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
28        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
29      - change barrier call for safe multi-threads access to 3-D shared buffer.
30      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
31      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
32        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
33    o pkg/flt:
34      - add fourth-order Runge-Kutta integration
35      - add basic exch2 support (only 1 facet supported so far!)
36    o pkg/mdsio+rw:
37      new S/R to read local (or tile independent) vector (read counterpart of
38       mds_writevec_loc, and front-end write_glvec_rl/rs).
39    o global_ocean.cs32x15: additional input_ad.seaice experiment
40        that uses pkg/seaice rather than pkg/thsice.
41        (using multidim advection for seaice)
42    o towards more F95 syntax for array specification in namelist:
43      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
44        of all verification experiments.
45           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
46          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
47      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
48    o global_ocean.cs32x15: additional input.seaice experiment
49        that uses pkg/seaice rather than pkg/thsice.
50    
51    checkpoint62p (2010/12/17)
52    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
53        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
54    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
55        allow for use of multim. advection in seaice adjoint.
56    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
57      - first attempt to close budgets by taking into account the freshwater
58        flux implied by the sublimation of snow and ice. So far only the
59        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
60        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
61    o eesupp/src:
62      new S/R with new option (NML_EXTENDED_F77) to change array specification
63      from F95 standard to commonly accepted extended F77 form.
64      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
65      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
66      for less tolerant f77 compiler (e.g., pgf77, g77).
67    o globalFiles:
68      commented out in parameter file "data" since it's not safe with MPI
69      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
70      in this case); no longer commented out in restart test (tst_2+2).
71    o add adTapeDir to specify a special directory where adjoint tapes are
72      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
73      and cannot be used together with mdsioLocalDir.
74    o nesting pkgs:
75      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
76      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
77      - add parameter files + utils dir + output from short run on beagle.
78    o pkg/seaice:
79        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
80    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
81      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
82    
83    checkpoint62o (2010/11/25)
84    o pkg/exf:
85      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
86    o pkg/seaice:
87      - seaice_ocean_stress: split a loop for better vectorization of the
88        adjoint code
89      - seaice_growth.F: fix bug in conservation of freshwater connected to
90        capping of heff, put contribution into d_HEFFbyNEG
91      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
92        by something more sensible (parameters that are what their name implies)
93      - change some defaults, so that by default exf-parameters are used for
94        things like rhoAir, cpAir,latent/sensible heat parameters, in order
95        to reproduce the old results, many data.seaice now contain funny values
96        for cpAir and latent heat of sublimation
97    o packages_readparms.F: move exf_readparms up in line so that
98        exf-parameters are visible for other packages (e.g. seaice)
99    o debugMode & debugLevel=2:
100      - differentiate between debugMode & debugLevel=2:
101        debugMode: controls printing of debug messages (sequence of S/R calls).
102        debugLevel: controls printing of algorithm intermediate results and stats.
103      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
104        => allows to print debug-stats without all sequence of call messages.
105      - switch control of debug print from debugLevel to debugMode in many S/R.
106    o pkg/obcs (obcs-sponge):
107        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
108        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
109    o pkg/generic_advdiff:
110      - record overlap minimum size for each advection scheme;
111      - refine criteria on overlap minimum size;
112      - check and stop (in gad_check) if overlap size is too small.
113    o pkg/obcs:
114      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
115        once, in ptracers_implicit.F)
116      - with seaice: remove test on empty file name in obcs_apply_seaice (always
117        apply OB values when tile has OB)
118    o model/src, coriolis setting:
119      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
120        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
121        files (selectCoriMap=3) with any grid.
122      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
123    o pkg/seaice/seaice_growth.F:
124        a few cosmetic changes that reduce the number of lines of code
125    o pkg/obcs: add boundary conditions following Stevens (1990)
126      - the code follows old MOM/NAOSIM code
127      - so far it is only implemented for the eastern and western boundaries
128        and NOT for pTracers
129    o pkg/rbcs:
130      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
131        beginning of the first rbcs forcing period.
132      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
133        offline package, i.e., one file per time, labeled by iteration number;
134        deltaTrbcs sets the timestep with which the data was generated;
135        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
136      - rbcsForcingCycle=0 makes forcing non-cyclic.
137      - make arithmetic safe for negative times and odd forcing periods.
138    
139    checkpoint62n (2010/11/09)
140    o pkg/seaice:
141        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
142    o pkg/obcs:
143       New S/R to copy tracer value from the OB location to narrow band region
144        (width = same as overlap) beyond the OB: preserve OB value (needed for
145        high-order scheme) which were overwritten by EXCH call if in overlap
146        region. Applied to theta, salt, ptracer and advected seaice variables.
147       With seaice: use maskInC in similar way as in gad_advection.F,
148        in seaice_advection.F and advect.F.
149       Update output of experiment seaice_obcs and change exp4 to test OBCS with
150        4th order Adv.Scheme. for pasive salt and ptracer.
151    o tools/genmake2:
152      - when looking for an optfile (not specified), only search for Fortran compiler
153        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
154      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
155        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
156      - set default for CPP to "cpp -traditional -P" (was the case without specifying
157        an optfile, but otherwise default was just "cpp".
158      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
159      - when "CC" is not set in the optfile, look for possible C compiler
160        (instead of just setting CC=cc)
161      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
162        => add a ".F" to ".o" rule for source files with no "#include" (such as
163           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
164      - move gfortran before g77 in list of possible Fortran compiler (consistent
165        with reference compiler switch from g77 to gfortran)
166    o pkg/seaice:
167      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
168        seaice_check that stops the model, when the CPP flag is used.
169      o seaice_growth.F: make capping of ice volume conserving by returning the
170        capped ice as freshwater to EmPmR. This does not change the verification
171        experiments but will change runs where the capping is acutally active
172    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
173      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
174         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
175         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
176    o tools/genmake2:
177      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
178      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
179      - clean previous genmake log files before anything else.
180      - change Makefile to remove testreport log files (*.tr_log) and genmake log
181        files only with "CLEAN" target (instead of "Clean");
182    o pkg/generic_advdiff:
183      Change OBCS in multiDim advection (gad_advection.F):
184       Use maskInC to prevent intermediate update of tracer-field in OB regions,
185       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
186       which were applying future time-step OB values.
187      This way, all explicit calculations use current-time-step OB values
188       (simpler and more consistent).
189      Affects results when set-up uses time-varying OBC and multi-dim advection;
190       update output of experiment seaice_obcs.
191    o pkg/seaice:
192      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
193       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
194         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
195      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
196       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
197       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
198    o pkg aim (2010/10/26):
199      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
200        formulation with obliquity, eccentricity, ... as run-time parameters,
201      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
202        upward shortwave radition at the surface (all-sky and clear-sky).
203    o pkg/obcs:
204      - writing sections with globalFiles=T does not work: switch to tiled-files
205        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
206      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
207      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
208    
209    checkpoint62m (2010/10/21)
210    o pkg/seaice: vectorize seaice_solve4temp.F
211      - move iterations loops outside of i/j-loops
212      - requires 2D arrays for TB and effConduct
213      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
214        modified in this routine
215      - a little bit of clean up, adjusting indentation, etc.
216      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
217        performance and '**TWO' by '**2' (because TWO is a float),
218        replaced ONE, ZERO
219    o eesupp/src:
220       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
221    o pkg/seaice/seaice_growth.F
222      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
223      merging process. The merged routine has two branches, and one activates the 'evolution'
224      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
225      In summary, here is what the '10/10 revision' did consist of
226        part 1: seaice_growth.F revisions 1.71 to 1.75
227          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
228            The emphasis here was on improving readability (e.g. by trying to use meaningful
229            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
230        part 1.5:
231          - revising the lab_sea experiment to make it a more useful (i.e. stable
232            and representative of an actual model run). This was done by generating a
233            (winter) pickup to start from, switching back the main experiment dynamic
234            solver from evp to lsr, having one of the experiments use the free drift solution.
235        part 2: seaice_growth.F revisions 1.76 to 1.85
236          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
237          - Sorting out the various fields units and sign (set early on and reset at the end)
238            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
239            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
240          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
241            and simplifying logical expressions to further improve readibility.
242        part 3: seaice_growth.F revisions 1.86 to 1.89
243          - Re-organize the blocks of code more logically.
244          - Merging the '_if.F' pieces that add something new.
245    o pkg/thsice:
246      - vectorize thsice_solve4temp and thsice_get_exf.
247        Problem: thsice_solve4temp has an unvectorizable statement that
248        might also be problematic for TAF
249      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
250        does not change the verifcation experiment, but will change all
251        experiments that have this flag undefined (not tested in verification);
252        a little reorganization to save a few 2D fields and recomputations
253      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
254      - 2nd step:  fix some store dirs
255        o seems to work somewhat, i.e. using ifort but not g77
256        o likely cause are incomplete init. or recomputation
257        o start verification/global_ocean.cs32x15/input_ad.thsice
258    o pkg/obcs: add support for exch2
259      - the position of the boundary and prescribed values are specified using
260        a global domain with exch2 facets stacked
261        - in x for N,S boundaries (like W2_mapIO=-1)
262        - in y for E,W boundaries (so E,W boundaries do not overlap)
263    o pkg/mdsio: add support for writing global sections with exch2
264        file layout is as for obcs described above:
265        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
266        - for y-z sections, facets are stacked in y
267    o pkg/thsice:
268       - change a few routines for better vectorization: thsice_albedo.F,
269         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
270         not affected, but in particular the latter routine has changed
271         dramatically (not necessarily easier to read now).
272       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
273       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
274    o verification/lab_sea:
275      - overhaul of the forward model experiments. The main motivation
276        for this revision is that lab_sea has proven quite fragile (when
277        changing the sea-ice code, and switching platforms) to a point
278        when failures were very hard to attribute to specific code problems.
279      - the suspected reason for this fragility is noise amplification by evp so,
280        to start with, we decided to replace evp with lsr in the main experiment.
281      - the input.lsr experiment thus became obsolete and was removed.
282      - it was replaced with the input.fd experiment that uses an
283        analytical "free drift" solution as the ice velocity field.
284      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
285        will hopefully allow us to discriminate problems due to dynamic solvers
286        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
287        us to test additional options, along with the salt plume package.
288      - Finally a pickup was generated (at the end of a one year run) to
289        make the tests more representative of an actual model run. Previously
290        the tests starting point was a 1m thickness of ice everywhere.
291    o pkg/seaice:
292      - introducing S\R seaice_freedrift.F that compute the
293        analytical solution to an approximate ice momentum
294        equation (i.e. the simple stress/coriolis balance).
295      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
296        of the free drift velocity field, and enable its use.
297        To actually use the free drift solution as the model ice
298        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
299    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
300    
301    checkpoint62l (2010/10/04)
302    o pkg/seaice:
303      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
304      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
305       version (with USE_ORIGINAL_SBI undef);
306    o add hooks for new packages OASIS, the package will follow
307      (hooks exclude the seaice pkg for now)
308    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
309      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
310      rather than mdsio_readvector.F/mdsio_writevector.F, within
311      adread_adwrite.F to read/write adjoint-related tapes to disk.
312    o eesupp and pkg/mdsio: ALLOW_WHIO
313      Option to write/read 2D fields to files including tiles halos.
314      The main purpose is for adjoint related "tape I/O".
315      The secondary purpose is for debugging phases.
316      A word on those rather specifically intended purposes.
317      The code was meant to be stripped down to the bare minimum.
318      Typically, there is a unique and basic mapping to the global
319      buffer (tile by tile, then proc by proc, then level by level), and
320      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
321      meant to generate user friendly outputs of various shapes and forms.
322      Rather it is intended, for the knowledgeabale developers,
323      to be largely independent of the many mdsio options, to allow
324      outputs of tiles+halos in debugging phases and in adjoint runs,
325      and to allow some flexibility in tuning (adoint) I/O depending on each
326      file system behavior. With regard to tuning, most of the potential knobs
327      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
328      to specify directories, to specify the typical size of I/O calls, etc.)
329      are not yet included, and will be added if they prove useful.
330    o pkg/seaice:
331       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
332    o pkg/seaice:
333       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
334       code (seaice_budget_ice_if.F) which enable to recover old standard
335       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
336       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
337    o model/src (rStar):
338       use simple average (not area weighted) of rStarFac at U,V point when using
339       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
340       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
341    
342    checkpoint62k (2010/09/17)
343    o adjoint
344       * changed verification/global_ocean.cs32x15 ; adjoint now tests
345         Adams-Bashforth 3 + NLFS + RSTAR
346       * some more modifs required for ECCO-GODAE v4
347    o pkg/seaice
348       add SEAICE_AGE_VOL option to use volume instead of area for
349       integrating SEAICE_AGE
350    o model/src:
351       first check-in of sigma & hybrid-sigma coordinate code ; also includes
352       non-linear free-surface parts ; but pressure-gradient not yet coded.
353    o pkg/ptracers:
354       option for ptracer to convert Salt Relax into additional EmP.
355        tested in exp. global_ocean.90x40x15.dwnslp (update output)
356    
357    checkpoint62j (2010/08/25)
358    o pkg/ggl90:
359       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
360    o pkg/dic: car_flux.F, phos_flux.F
361      - reduce number of exp-calls in order to improve performance
362      - clean up a little (replace fields by their macros, etc., fix
363        typo in CPP-flag)
364    o pkg/ggl90: minor changes
365      - GGL90diffKrS was removed --> always use GGL90diffKr
366      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
367      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
368        (commented out for now)
369      - change in max/min operations to ensure that smoothing is ok
370      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
371      - always use diffKrNrT as background profile (i.e. never use diffKr field)
372    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
373    o pkg/dic:
374      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
375        vectorization
376      - small bug fix in insol for the unlikely case of a cartesian grid
377      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
378        + now vectorize, which also removes adjoint recomputations;
379        + replace integer maksp1 by _RL maskp1
380        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
381    
382    checkpoint62i (2010/07/21)
383    o pkg/flt:
384      - with OBCS: stop floats which enter the OB region
385    o model/src:
386      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
387        for implicit vertical advection.
388    o pkg/seaice:
389     - account for melting in seaice age evolution.
390     - remove double counting of seaice ridging effect on seaice age.
391    
392    checkpoint62h (2010/06/18)
393    o pkg/exch2:
394     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
395    o tools/genmake2
396      - remove "-pdefault" option: redundant with the use of "packages.conf";
397      - remove file pkg/pkg_default : set the default as a pkg group
398        ("default_pkg_list") defined in pkg/pkg_groups;
399      - fix for case pkg/pkg_depend is missing (was hanging before);
400      - add option "-pgroups" to specify a different pkg_groups than the default.
401    o verification/adjustment.cs-32x32x1:
402       add a "minimal" set-up test (code_min & input_min) which only compiles
403       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
404    o tools/genmake2
405      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
406      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
407    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
408      files are nearly the same anyway.
409      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
410       - redefinition of tau(i,i) (by a factor of ustar)
411       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
412       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
413       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
414       - replace
415         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
416         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
417         by
418         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
419         (changes results)
420       -> exf_bulkformulae v1.22,
421          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
422          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
423                    output.txt 1.63
424           offline_exf_seaice: output.seaicetd.txt 1.7
425           seaice_obcs: output.txt 1.10)
426      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
427       -> exf_bulkformulae v1.23,
428          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
429          and global_ocean.cs32x15.icedyn (only 11 matching digits)
430      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
431    o adjoint of exch-1:
432     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
433       (note: was already like this when using EXCH-2) and remove flow dir
434       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
435     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
436     - update pkg/exch2 diff list.
437    
438    checkpoint62g (2010/05/19)
439    o eesupp/src (exch-1):
440     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
441       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
442       (renamed to exch1_*rx_cube.F).
443     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
444       to call new exch1 S/R ; update Makefile and .cvsignore.
445     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
446       exch2_xy_rx later)
447      Note: after updating your code, need to run "make clean" in eesupp/src
448    o test experiment bottom_ctrl_5x5:
449       new output_adm.txt with fewer grdchk & less monitor output.
450    o model/src:
451      remove the call to ini_cori in initialise_varia.F (just keep the usual one
452       in initialise_fixed.F). More consistent with coriolis & horizontal grid
453       beeing treated in the same way (ini_grid is not called a 2nd time).
454    o pkg/exf:
455      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
456      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
457      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
458      - cosmetic changes to exf_bulkformulae.F to make it look more like
459        exf_bulk_largeyeager04.F
460    o eesupp/src (exch-1):
461      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
462      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
463        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
464        (even without using MPI).
465      - Message mode: move RecvAck setting (indicator of buffer being ready)
466        from send_put to recv_get S/R (was useless before, but not sure if
467        it's much more useful now);
468      - Switch the order of sync: MPI-proc 1rst and then threads;
469      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
470      - fix AD code for communication mode ='get' (but not used).
471    o model/src:
472      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
473      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
474    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
475    o pkg/ctrl: require a specific set of control variables and exf-flags for
476      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
477    o model/src:
478     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
479       1rst forward sweep, to avoid over-writing output files during recomputations
480       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
481     b) 2nd version:
482      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
483      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
484         writePickupAtEnd) + seaice & ptracers output;
485      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
486    o model/src:
487      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
488    o pkg/exch2:
489      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
490      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
491    o pkg/autodiff & exch2:
492      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
493      (for now, only if ALLOW_EXCH2 is defined).
494    o pkg/autodiff:
495      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
496        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
497       + clean-up comments (_RS is not always real*4)
498      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
499      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
500        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
501    o testreport (AD-tests):
502      no longer link files from dir "../input" (1rst link files from
503      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
504    
505    checkpoint62f (2010/04/29)
506    o model/src/the_main_loop.F:
507      adjust store directives for seaice evp and multicategory according to
508      pkg/ecco/the_main_loop.F
509    o adjoint:
510      global_sum_ad was incomplete (noted many times by many people ;)
511      nice description by Jean U. as follows:
512      * allreduce(var) in global_sum.F can be interpreted as
513        reduce(sum) followed by broadcast of sum.
514      * The adjoint of that is
515        sum(adjoint) followed by broadcast(summed adjoint value)
516        or in other words, allreduce(sum, adjoint vars)
517      We were missing the sum(adjoint)!
518      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
519      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
520      The fix should produce 16-digit accuracy between
521      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
522      multi-CPU single-tile (e.g. nSx=1, nPx-2)
523      We'll probably change this yet again shortly
524    o eesupp/src:
525      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
526    o pkg/icefront
527      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
528        specification of addmass array based on a 2D field, which is added
529        at bottommost wet level at each horizontal location.
530    o model/src:
531     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
532     layout; (not always compatible with delX,delY setting; commented out for now).
533    o pkg/exch2:
534     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
535     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
536    
537    checkpoint62e (2010/04/15)
538    o pkg/obcs:
539      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
540    o pkg/dic:
541      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
542        (note: not presently tested in any forward verification exp.)
543       update tutorial_global_oce_biogeo AD output file.
544    o pkg/exf:
545      - account for the variation of albedo as a function of zenith angle
546        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
547    o build_options:
548     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
549    o pkg/dic:
550      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
551      - use binary pickup file for restart;
552      - initialise atmos-CO2 box from dic_pCO2 parameter;
553      - fix multi-threaded.
554    o pkg/rbcs:
555     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
556       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
557     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
558       and update output.txt
559    o pkg/kpp:
560     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
561     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
562       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
563       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
564     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
565       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
566  o pkg/offline:  o pkg/offline:
567    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
568    (bug was added in version 1.10 on 2007-08-23).    (bug was added in version 1.10 on 2007-08-23).
# Line 57  o tools/build_options: Line 616  o tools/build_options:
616      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
617  o pkg/ecco  o pkg/ecco
618    - allow user defined cost function contributions    - allow user defined cost function contributions
619          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
620          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
621    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
622        the two options are complementary.        the two options are complementary.
623  o pkg/smooth  o pkg/smooth
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