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revision 1.1242 by heimbach, Wed Mar 24 21:56:45 2010 UTC revision 1.1336 by jmc, Fri Nov 19 00:29:08 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o debugMode & debugLevel=2:
8      - differentiate between debugMode & debugLevel=2:
9        debugMode: controls printing of debug messages (sequence of S/R calls).
10        debugLevel: controls printing of algorithm intermediate results and stats.
11      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
12        => allows to print debug-stats without all sequence of call messages.
13      - switch control of debug print from debugLevel to debugMode in many S/R.
14    o pkg/obcs (obcs-sponge):
15        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
16        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
17    o pkg/generic_advdiff:
18      - record overlap minimum size for each advection scheme;
19      - refine criteria on overlap minimum size;
20      - check and stop (in gad_check) if overlap size is too small.
21    o pkg/obcs:
22      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
23        once, in ptracers_implicit.F)
24      - with seaice: remove test on empty file name in obcs_apply_seaice (always
25        apply OB values when tile has OB)
26    o model/src, coriolis setting:
27      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
28        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
29        files (selectCoriMap=3) with any grid.
30      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
31    o pkg/seaice/seaice_growth.F:
32        a few cosmetic changes that reduce the number of lines of code
33    o pkg/obcs: add boundary conditions following Stevens (1990)
34      - the code follows old MOM/NAOSIM code
35      - so far it is only implemented for the eastern and western boundaries
36        and NOT for pTracers
37    o pkg/rbcs:
38      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
39        beginning of the first rbcs forcing period.
40      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
41        offline package, i.e., one file per time, labeled by iteration number;
42        deltaTrbcs sets the timestep with which the data was generated;
43        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
44      - rbcsForcingCycle=0 makes forcing non-cyclic.
45      - make arithmetic safe for negative times and odd forcing periods.
46    
47    checkpoint62n (2010/11/09)
48    o pkg/seaice:
49        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
50    o pkg/obcs:
51       New S/R to copy tracer value from the OB location to narrow band region
52        (width = same as overlap) beyond the OB: preserve OB value (needed for
53        high-order scheme) which were overwritten by EXCH call if in overlap
54        region. Applied to theta, salt, ptracer and advected seaice variables.
55       With seaice: use maskInC in similar way as in gad_advection.F,
56        in seaice_advection.F and advect.F.
57       Update output of experiment seaice_obcs and change exp4 to test OBCS with
58        4th order Adv.Scheme. for pasive salt and ptracer.
59    o tools/genmake2:
60      - when looking for an optfile (not specified), only search for Fortran compiler
61        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
62      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
63        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
64      - set default for CPP to "cpp -traditional -P" (was the case without specifying
65        an optfile, but otherwise default was just "cpp".
66      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
67      - when "CC" is not set in the optfile, look for possible C compiler
68        (instead of just setting CC=cc)
69      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
70        => add a ".F" to ".o" rule for source files with no "#include" (such as
71           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
72      - move gfortran before g77 in list of possible Fortran compiler (consistent
73        with reference compiler switch from g77 to gfortran)
74    o pkg/seaice:
75      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
76        seaice_check that stops the model, when the CPP flag is used.
77      o seaice_growth.F: make capping of ice volume conserving by returning the
78        capped ice as freshwater to EmPmR. This does not change the verification
79        experiments but will change runs where the capping is acutally active
80    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
81      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
82         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
83         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
84    o tools/genmake2:
85      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
86      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
87      - clean previous genmake log files before anything else.
88      - change Makefile to remove testreport log files (*.tr_log) and genmake log
89        files only with "CLEAN" target (instead of "Clean");
90    o pkg/generic_advdiff:
91      Change OBCS in multiDim advection (gad_advection.F):
92       Use maskInC to prevent intermediate update of tracer-field in OB regions,
93       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
94       which were applying future time-step OB values.
95      This way, all explicit calculations use current-time-step OB values
96       (simpler and more consistent).
97      Affects results when set-up uses time-varying OBC and multi-dim advection;
98       update output of experiment seaice_obcs.
99    o pkg/seaice:
100      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
101       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
102         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
103      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
104       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
105       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
106    o pkg aim (2010/10/26):
107      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
108        formulation with obliquity, eccentricity, ... as run-time parameters,
109      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
110        upward shortwave radition at the surface (all-sky and clear-sky).
111    o pkg/obcs:
112      - writing sections with globalFiles=T does not work: switch to tiled-files
113        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
114      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
115      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
116    
117    checkpoint62m (2010/10/21)
118    o pkg/seaice: vectorize seaice_solve4temp.F
119      - move iterations loops outside of i/j-loops
120      - requires 2D arrays for TB and effConduct
121      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
122        modified in this routine
123      - a little bit of clean up, adjusting indentation, etc.
124      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
125        performance and '**TWO' by '**2' (because TWO is a float),
126        replaced ONE, ZERO
127    o eesupp/src:
128       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
129    o pkg/seaice/seaice_growth.F
130      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
131      merging process. The merged routine has two branches, and one activates the 'evolution'
132      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
133      In summary, here is what the '10/10 revision' did consist of
134        part 1: seaice_growth.F revisions 1.71 to 1.75
135          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
136            The emphasis here was on improving readability (e.g. by trying to use meaningful
137            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
138        part 1.5:
139          - revising the lab_sea experiment to make it a more useful (i.e. stable
140            and representative of an actual model run). This was done by generating a
141            (winter) pickup to start from, switching back the main experiment dynamic
142            solver from evp to lsr, having one of the experiments use the free drift solution.
143        part 2: seaice_growth.F revisions 1.76 to 1.85
144          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
145          - Sorting out the various fields units and sign (set early on and reset at the end)
146            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
147            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
148          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
149            and simplifying logical expressions to further improve readibility.
150        part 3: seaice_growth.F revisions 1.86 to 1.89
151          - Re-organize the blocks of code more logically.
152          - Merging the '_if.F' pieces that add something new.
153    o pkg/thsice:
154      - vectorize thsice_solve4temp and thsice_get_exf.
155        Problem: thsice_solve4temp has an unvectorizable statement that
156        might also be problematic for TAF
157      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
158        does not change the verifcation experiment, but will change all
159        experiments that have this flag undefined (not tested in verification);
160        a little reorganization to save a few 2D fields and recomputations
161      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
162      - 2nd step:  fix some store dirs
163        o seems to work somewhat, i.e. using ifort but not g77
164        o likely cause are incomplete init. or recomputation
165        o start verification/global_ocean.cs32x15/input_ad.thsice
166    o pkg/obcs: add support for exch2
167      - the position of the boundary and prescribed values are specified using
168        a global domain with exch2 facets stacked
169        - in x for N,S boundaries (like W2_mapIO=-1)
170        - in y for E,W boundaries (so E,W boundaries do not overlap)
171    o pkg/mdsio: add support for writing global sections with exch2
172        file layout is as for obcs described above:
173        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
174        - for y-z sections, facets are stacked in y
175    o pkg/thsice:
176       - change a few routines for better vectorization: thsice_albedo.F,
177         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
178         not affected, but in particular the latter routine has changed
179         dramatically (not necessarily easier to read now).
180       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
181       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
182    o verification/lab_sea:
183      - overhaul of the forward model experiments. The main motivation
184        for this revision is that lab_sea has proven quite fragile (when
185        changing the sea-ice code, and switching platforms) to a point
186        when failures were very hard to attribute to specific code problems.
187      - the suspected reason for this fragility is noise amplification by evp so,
188        to start with, we decided to replace evp with lsr in the main experiment.
189      - the input.lsr experiment thus became obsolete and was removed.
190      - it was replaced with the input.fd experiment that uses an
191        analytical "free drift" solution as the ice velocity field.
192      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
193        will hopefully allow us to discriminate problems due to dynamic solvers
194        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
195        us to test additional options, along with the salt plume package.
196      - Finally a pickup was generated (at the end of a one year run) to
197        make the tests more representative of an actual model run. Previously
198        the tests starting point was a 1m thickness of ice everywhere.
199    o pkg/seaice:
200      - introducing S\R seaice_freedrift.F that compute the
201        analytical solution to an approximate ice momentum
202        equation (i.e. the simple stress/coriolis balance).
203      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
204        of the free drift velocity field, and enable its use.
205        To actually use the free drift solution as the model ice
206        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
207    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
208    
209    checkpoint62l (2010/10/04)
210    o pkg/seaice:
211      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
212      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
213       version (with USE_ORIGINAL_SBI undef);
214    o add hooks for new packages OASIS, the package will follow
215      (hooks exclude the seaice pkg for now)
216    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
217      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
218      rather than mdsio_readvector.F/mdsio_writevector.F, within
219      adread_adwrite.F to read/write adjoint-related tapes to disk.
220    o eesupp and pkg/mdsio: ALLOW_WHIO
221      Option to write/read 2D fields to files including tiles halos.
222      The main purpose is for adjoint related "tape I/O".
223      The secondary purpose is for debugging phases.
224      A word on those rather specifically intended purposes.
225      The code was meant to be stripped down to the bare minimum.
226      Typically, there is a unique and basic mapping to the global
227      buffer (tile by tile, then proc by proc, then level by level), and
228      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
229      meant to generate user friendly outputs of various shapes and forms.
230      Rather it is intended, for the knowledgeabale developers,
231      to be largely independent of the many mdsio options, to allow
232      outputs of tiles+halos in debugging phases and in adjoint runs,
233      and to allow some flexibility in tuning (adoint) I/O depending on each
234      file system behavior. With regard to tuning, most of the potential knobs
235      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
236      to specify directories, to specify the typical size of I/O calls, etc.)
237      are not yet included, and will be added if they prove useful.
238    o pkg/seaice:
239       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
240    o pkg/seaice:
241       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
242       code (seaice_budget_ice_if.F) which enable to recover old standard
243       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
244       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
245    o model/src (rStar):
246       use simple average (not area weighted) of rStarFac at U,V point when using
247       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
248       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
249    
250    checkpoint62k (2010/09/17)
251    o adjoint
252       * changed verification/global_ocean.cs32x15 ; adjoint now tests
253         Adams-Bashforth 3 + NLFS + RSTAR
254       * some more modifs required for ECCO-GODAE v4
255    o pkg/seaice
256       add SEAICE_AGE_VOL option to use volume instead of area for
257       integrating SEAICE_AGE
258    o model/src:
259       first check-in of sigma & hybrid-sigma coordinate code ; also includes
260       non-linear free-surface parts ; but pressure-gradient not yet coded.
261    o pkg/ptracers:
262       option for ptracer to convert Salt Relax into additional EmP.
263        tested in exp. global_ocean.90x40x15.dwnslp (update output)
264    
265    checkpoint62j (2010/08/25)
266    o pkg/ggl90:
267       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
268    o pkg/dic: car_flux.F, phos_flux.F
269      - reduce number of exp-calls in order to improve performance
270      - clean up a little (replace fields by their macros, etc., fix
271        typo in CPP-flag)
272    o pkg/ggl90: minor changes
273      - GGL90diffKrS was removed --> always use GGL90diffKr
274      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
275      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
276        (commented out for now)
277      - change in max/min operations to ensure that smoothing is ok
278      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
279      - always use diffKrNrT as background profile (i.e. never use diffKr field)
280    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
281    o pkg/dic:
282      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
283        vectorization
284      - small bug fix in insol for the unlikely case of a cartesian grid
285      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
286        + now vectorize, which also removes adjoint recomputations;
287        + replace integer maksp1 by _RL maskp1
288        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
289    
290    checkpoint62i (2010/07/21)
291    o pkg/flt:
292      - with OBCS: stop floats which enter the OB region
293    o model/src:
294      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
295        for implicit vertical advection.
296    o pkg/seaice:
297     - account for melting in seaice age evolution.
298     - remove double counting of seaice ridging effect on seaice age.
299    
300    checkpoint62h (2010/06/18)
301    o pkg/exch2:
302     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
303    o tools/genmake2
304      - remove "-pdefault" option: redundant with the use of "packages.conf";
305      - remove file pkg/pkg_default : set the default as a pkg group
306        ("default_pkg_list") defined in pkg/pkg_groups;
307      - fix for case pkg/pkg_depend is missing (was hanging before);
308      - add option "-pgroups" to specify a different pkg_groups than the default.
309    o verification/adjustment.cs-32x32x1:
310       add a "minimal" set-up test (code_min & input_min) which only compiles
311       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
312    o tools/genmake2
313      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
314      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
315    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
316      files are nearly the same anyway.
317      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
318       - redefinition of tau(i,i) (by a factor of ustar)
319       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
320       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
321       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
322       - replace
323         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
324         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
325         by
326         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
327         (changes results)
328       -> exf_bulkformulae v1.22,
329          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
330          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
331                    output.txt 1.63
332           offline_exf_seaice: output.seaicetd.txt 1.7
333           seaice_obcs: output.txt 1.10)
334      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
335       -> exf_bulkformulae v1.23,
336          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
337          and global_ocean.cs32x15.icedyn (only 11 matching digits)
338      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
339    o adjoint of exch-1:
340     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
341       (note: was already like this when using EXCH-2) and remove flow dir
342       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
343     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
344     - update pkg/exch2 diff list.
345    
346    checkpoint62g (2010/05/19)
347    o eesupp/src (exch-1):
348     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
349       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
350       (renamed to exch1_*rx_cube.F).
351     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
352       to call new exch1 S/R ; update Makefile and .cvsignore.
353     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
354       exch2_xy_rx later)
355      Note: after updating your code, need to run "make clean" in eesupp/src
356    o test experiment bottom_ctrl_5x5:
357       new output_adm.txt with fewer grdchk & less monitor output.
358    o model/src:
359      remove the call to ini_cori in initialise_varia.F (just keep the usual one
360       in initialise_fixed.F). More consistent with coriolis & horizontal grid
361       beeing treated in the same way (ini_grid is not called a 2nd time).
362    o pkg/exf:
363      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
364      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
365      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
366      - cosmetic changes to exf_bulkformulae.F to make it look more like
367        exf_bulk_largeyeager04.F
368    o eesupp/src (exch-1):
369      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
370      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
371        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
372        (even without using MPI).
373      - Message mode: move RecvAck setting (indicator of buffer being ready)
374        from send_put to recv_get S/R (was useless before, but not sure if
375        it's much more useful now);
376      - Switch the order of sync: MPI-proc 1rst and then threads;
377      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
378      - fix AD code for communication mode ='get' (but not used).
379    o model/src:
380      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
381      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
382    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
383    o pkg/ctrl: require a specific set of control variables and exf-flags for
384      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
385    o model/src:
386     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
387       1rst forward sweep, to avoid over-writing output files during recomputations
388       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
389     b) 2nd version:
390      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
391      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
392         writePickupAtEnd) + seaice & ptracers output;
393      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
394    o model/src:
395      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
396    o pkg/exch2:
397      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
398      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
399    o pkg/autodiff & exch2:
400      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
401      (for now, only if ALLOW_EXCH2 is defined).
402    o pkg/autodiff:
403      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
404        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
405       + clean-up comments (_RS is not always real*4)
406      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
407      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
408        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
409    o testreport (AD-tests):
410      no longer link files from dir "../input" (1rst link files from
411      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
412    
413    checkpoint62f (2010/04/29)
414    o model/src/the_main_loop.F:
415      adjust store directives for seaice evp and multicategory according to
416      pkg/ecco/the_main_loop.F
417    o adjoint:
418      global_sum_ad was incomplete (noted many times by many people ;)
419      nice description by Jean U. as follows:
420      * allreduce(var) in global_sum.F can be interpreted as
421        reduce(sum) followed by broadcast of sum.
422      * The adjoint of that is
423        sum(adjoint) followed by broadcast(summed adjoint value)
424        or in other words, allreduce(sum, adjoint vars)
425      We were missing the sum(adjoint)!
426      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
427      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
428      The fix should produce 16-digit accuracy between
429      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
430      multi-CPU single-tile (e.g. nSx=1, nPx-2)
431      We'll probably change this yet again shortly
432    o eesupp/src:
433      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
434    o pkg/icefront
435      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
436        specification of addmass array based on a 2D field, which is added
437        at bottommost wet level at each horizontal location.
438    o model/src:
439     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
440     layout; (not always compatible with delX,delY setting; commented out for now).
441    o pkg/exch2:
442     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
443     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
444    
445    checkpoint62e (2010/04/15)
446    o pkg/obcs:
447      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
448    o pkg/dic:
449      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
450        (note: not presently tested in any forward verification exp.)
451       update tutorial_global_oce_biogeo AD output file.
452    o pkg/exf:
453      - account for the variation of albedo as a function of zenith angle
454        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
455    o build_options:
456     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
457    o pkg/dic:
458      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
459      - use binary pickup file for restart;
460      - initialise atmos-CO2 box from dic_pCO2 parameter;
461      - fix multi-threaded.
462    o pkg/rbcs:
463     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
464       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
465     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
466       and update output.txt
467    o pkg/kpp:
468     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
469     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
470       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
471       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
472     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
473       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
474    o pkg/offline:
475      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
476      (bug was added in version 1.10 on 2007-08-23).
477    o pkg/offline:
478      - no need to specify periodicExternalForcing, etc ... to use offline pack
479      - offline input files no longer just single prec --> parameter offlineLoadPrec
480  o verification/lab_sea:  o verification/lab_sea:
481    change to multi-tile setup.    change AD test to multi-tile setup and update all 4 AD output.
482    NOTE: while cost function values remain very similar,    NOTE: while cost function values remain very similar,
483    gradients are very different, although gradient checks are self-consistent    gradients are very different, although gradient checks are self-consistent
484    Should try to get to the bottom of this (cost function summation order?)    Should try to get to the bottom of this (cost function summation order?)
485  o pkg/dic:  o pkg/dic:
486    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
487    a weakness of TAF that drops part of double precision in log10 derivative.    a weakness of TAF that drops part of double precision in log10 derivative.
488      <= changes removed since problem has been fixed in current TAF version 1.9.71
489    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
490  o pkg/ecco:  o pkg/ecco:
491    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
# Line 50  o tools/build_options: Line 524  o tools/build_options:
524      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
525  o pkg/ecco  o pkg/ecco
526    - allow user defined cost function contributions    - allow user defined cost function contributions
527          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
528          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
529    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
530        the two options are complementary.        the two options are complementary.
531  o pkg/smooth  o pkg/smooth
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