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revision 1.1258 by mlosch, Wed Apr 28 08:37:41 2010 UTC revision 1.1364 by gforget, Fri Jan 14 01:42:22 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/src, pkg/autodiff, pkg/ecco, pkg/seaice:
8      alleviate the need for additional 3D tapes when using
9      the non-inear free surface in the adjoint. This is done
10      by adding an 'update' of hfacc etc. to their current
11      value at the beginning of forward_step.F.
12    o pkg/seaice
13      seaice_lsr: move stress-divergence computations out of outer pseudo-
14      timestepping loop
15    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
16      up, so that the calls of the ctrl_* subroutines are really at the end
17      of the routine.
18    o pkg/gmredi:
19      allow to specify a 2-D horizontal map and a 1-D vertical profil
20      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
21    o pkg/seaice:
22      move lsr iterations from seaice_dynsolver to seaice_lsr.
23    o pkg/seaice:
24      reduce memory footprint of seaice mutldim advection tapes,
25      by using a 2D tape independent of the generic_advdiff ones,
26      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
27    
28    checkpoint62q (2010/12/29)
29    o model/src:
30      - check horizontal grid-spacing for unset or zero/negative values.
31      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
32    o pkg/flt:
33      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
34      - precision of input and output files set according to readBinaryPrec
35        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
36      - initial float position from tiled file was not converted to index space
37        (looks like a bug): fixed to make it similar to initial pos. global file.
38    o global_ocean.cs32x15:
39       change SIZE.h of AD set-up to get same tiling as with MPI.
40       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
41    o model/src:
42       add flag to control printing of domain fields (bathymetry, hFac ...) in
43       ini_mask_etc (call to plot_fieds_xy*).
44    o pkg/thsice:
45       if useEXF, some forcing fields are not valid in overlap: fixed by computing
46       over the interior only + apply EXCH at the end (like with SEAICE advection).
47    o pkg/mdsio:
48      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
49        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
50      - change barrier call for safe multi-threads access to 3-D shared buffer.
51      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
52      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
53        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
54    o pkg/flt:
55      - add fourth-order Runge-Kutta integration
56      - add basic exch2 support (only 1 facet supported so far!)
57    o pkg/mdsio+rw:
58      new S/R to read local (or tile independent) vector (read counterpart of
59       mds_writevec_loc, and front-end write_glvec_rl/rs).
60    o global_ocean.cs32x15: additional input_ad.seaice experiment
61        that uses pkg/seaice rather than pkg/thsice.
62        (using multidim advection for seaice)
63    o towards more F95 syntax for array specification in namelist:
64      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
65        of all verification experiments.
66           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
67          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
68      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
69    o global_ocean.cs32x15: additional input.seaice experiment
70        that uses pkg/seaice rather than pkg/thsice.
71    
72    checkpoint62p (2010/12/17)
73    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
74        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
75    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
76        allow for use of multim. advection in seaice adjoint.
77    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
78      - first attempt to close budgets by taking into account the freshwater
79        flux implied by the sublimation of snow and ice. So far only the
80        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
81        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
82    o eesupp/src:
83      new S/R with new option (NML_EXTENDED_F77) to change array specification
84      from F95 standard to commonly accepted extended F77 form.
85      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
86      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
87      for less tolerant f77 compiler (e.g., pgf77, g77).
88    o globalFiles:
89      commented out in parameter file "data" since it's not safe with MPI
90      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
91      in this case); no longer commented out in restart test (tst_2+2).
92    o add adTapeDir to specify a special directory where adjoint tapes are
93      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
94      and cannot be used together with mdsioLocalDir.
95    o nesting pkgs:
96      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
97      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
98      - add parameter files + utils dir + output from short run on beagle.
99    o pkg/seaice:
100        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
101    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
102      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
103    
104    checkpoint62o (2010/11/25)
105    o pkg/exf:
106      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
107    o pkg/seaice:
108      - seaice_ocean_stress: split a loop for better vectorization of the
109        adjoint code
110      - seaice_growth.F: fix bug in conservation of freshwater connected to
111        capping of heff, put contribution into d_HEFFbyNEG
112      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
113        by something more sensible (parameters that are what their name implies)
114      - change some defaults, so that by default exf-parameters are used for
115        things like rhoAir, cpAir,latent/sensible heat parameters, in order
116        to reproduce the old results, many data.seaice now contain funny values
117        for cpAir and latent heat of sublimation
118    o packages_readparms.F: move exf_readparms up in line so that
119        exf-parameters are visible for other packages (e.g. seaice)
120    o debugMode & debugLevel=2:
121      - differentiate between debugMode & debugLevel=2:
122        debugMode: controls printing of debug messages (sequence of S/R calls).
123        debugLevel: controls printing of algorithm intermediate results and stats.
124      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
125        => allows to print debug-stats without all sequence of call messages.
126      - switch control of debug print from debugLevel to debugMode in many S/R.
127    o pkg/obcs (obcs-sponge):
128        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
129        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
130    o pkg/generic_advdiff:
131      - record overlap minimum size for each advection scheme;
132      - refine criteria on overlap minimum size;
133      - check and stop (in gad_check) if overlap size is too small.
134    o pkg/obcs:
135      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
136        once, in ptracers_implicit.F)
137      - with seaice: remove test on empty file name in obcs_apply_seaice (always
138        apply OB values when tile has OB)
139    o model/src, coriolis setting:
140      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
141        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
142        files (selectCoriMap=3) with any grid.
143      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
144    o pkg/seaice/seaice_growth.F:
145        a few cosmetic changes that reduce the number of lines of code
146    o pkg/obcs: add boundary conditions following Stevens (1990)
147      - the code follows old MOM/NAOSIM code
148      - so far it is only implemented for the eastern and western boundaries
149        and NOT for pTracers
150    o pkg/rbcs:
151      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
152        beginning of the first rbcs forcing period.
153      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
154        offline package, i.e., one file per time, labeled by iteration number;
155        deltaTrbcs sets the timestep with which the data was generated;
156        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
157      - rbcsForcingCycle=0 makes forcing non-cyclic.
158      - make arithmetic safe for negative times and odd forcing periods.
159    
160    checkpoint62n (2010/11/09)
161    o pkg/seaice:
162        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
163    o pkg/obcs:
164       New S/R to copy tracer value from the OB location to narrow band region
165        (width = same as overlap) beyond the OB: preserve OB value (needed for
166        high-order scheme) which were overwritten by EXCH call if in overlap
167        region. Applied to theta, salt, ptracer and advected seaice variables.
168       With seaice: use maskInC in similar way as in gad_advection.F,
169        in seaice_advection.F and advect.F.
170       Update output of experiment seaice_obcs and change exp4 to test OBCS with
171        4th order Adv.Scheme. for pasive salt and ptracer.
172    o tools/genmake2:
173      - when looking for an optfile (not specified), only search for Fortran compiler
174        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
175      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
176        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
177      - set default for CPP to "cpp -traditional -P" (was the case without specifying
178        an optfile, but otherwise default was just "cpp".
179      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
180      - when "CC" is not set in the optfile, look for possible C compiler
181        (instead of just setting CC=cc)
182      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
183        => add a ".F" to ".o" rule for source files with no "#include" (such as
184           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
185      - move gfortran before g77 in list of possible Fortran compiler (consistent
186        with reference compiler switch from g77 to gfortran)
187    o pkg/seaice:
188      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
189        seaice_check that stops the model, when the CPP flag is used.
190      o seaice_growth.F: make capping of ice volume conserving by returning the
191        capped ice as freshwater to EmPmR. This does not change the verification
192        experiments but will change runs where the capping is acutally active
193    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
194      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
195         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
196         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
197    o tools/genmake2:
198      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
199      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
200      - clean previous genmake log files before anything else.
201      - change Makefile to remove testreport log files (*.tr_log) and genmake log
202        files only with "CLEAN" target (instead of "Clean");
203    o pkg/generic_advdiff:
204      Change OBCS in multiDim advection (gad_advection.F):
205       Use maskInC to prevent intermediate update of tracer-field in OB regions,
206       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
207       which were applying future time-step OB values.
208      This way, all explicit calculations use current-time-step OB values
209       (simpler and more consistent).
210      Affects results when set-up uses time-varying OBC and multi-dim advection;
211       update output of experiment seaice_obcs.
212    o pkg/seaice:
213      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
214       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
215         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
216      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
217       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
218       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
219    o pkg aim (2010/10/26):
220      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
221        formulation with obliquity, eccentricity, ... as run-time parameters,
222      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
223        upward shortwave radition at the surface (all-sky and clear-sky).
224    o pkg/obcs:
225      - writing sections with globalFiles=T does not work: switch to tiled-files
226        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
227      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
228      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
229    
230    checkpoint62m (2010/10/21)
231    o pkg/seaice: vectorize seaice_solve4temp.F
232      - move iterations loops outside of i/j-loops
233      - requires 2D arrays for TB and effConduct
234      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
235        modified in this routine
236      - a little bit of clean up, adjusting indentation, etc.
237      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
238        performance and '**TWO' by '**2' (because TWO is a float),
239        replaced ONE, ZERO
240    o eesupp/src:
241       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
242    o pkg/seaice/seaice_growth.F
243      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
244      merging process. The merged routine has two branches, and one activates the 'evolution'
245      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
246      In summary, here is what the '10/10 revision' did consist of
247        part 1: seaice_growth.F revisions 1.71 to 1.75
248          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
249            The emphasis here was on improving readability (e.g. by trying to use meaningful
250            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
251        part 1.5:
252          - revising the lab_sea experiment to make it a more useful (i.e. stable
253            and representative of an actual model run). This was done by generating a
254            (winter) pickup to start from, switching back the main experiment dynamic
255            solver from evp to lsr, having one of the experiments use the free drift solution.
256        part 2: seaice_growth.F revisions 1.76 to 1.85
257          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
258          - Sorting out the various fields units and sign (set early on and reset at the end)
259            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
260            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
261          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
262            and simplifying logical expressions to further improve readibility.
263        part 3: seaice_growth.F revisions 1.86 to 1.89
264          - Re-organize the blocks of code more logically.
265          - Merging the '_if.F' pieces that add something new.
266    o pkg/thsice:
267      - vectorize thsice_solve4temp and thsice_get_exf.
268        Problem: thsice_solve4temp has an unvectorizable statement that
269        might also be problematic for TAF
270      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
271        does not change the verifcation experiment, but will change all
272        experiments that have this flag undefined (not tested in verification);
273        a little reorganization to save a few 2D fields and recomputations
274      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
275      - 2nd step:  fix some store dirs
276        o seems to work somewhat, i.e. using ifort but not g77
277        o likely cause are incomplete init. or recomputation
278        o start verification/global_ocean.cs32x15/input_ad.thsice
279    o pkg/obcs: add support for exch2
280      - the position of the boundary and prescribed values are specified using
281        a global domain with exch2 facets stacked
282        - in x for N,S boundaries (like W2_mapIO=-1)
283        - in y for E,W boundaries (so E,W boundaries do not overlap)
284    o pkg/mdsio: add support for writing global sections with exch2
285        file layout is as for obcs described above:
286        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
287        - for y-z sections, facets are stacked in y
288    o pkg/thsice:
289       - change a few routines for better vectorization: thsice_albedo.F,
290         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
291         not affected, but in particular the latter routine has changed
292         dramatically (not necessarily easier to read now).
293       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
294       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
295    o verification/lab_sea:
296      - overhaul of the forward model experiments. The main motivation
297        for this revision is that lab_sea has proven quite fragile (when
298        changing the sea-ice code, and switching platforms) to a point
299        when failures were very hard to attribute to specific code problems.
300      - the suspected reason for this fragility is noise amplification by evp so,
301        to start with, we decided to replace evp with lsr in the main experiment.
302      - the input.lsr experiment thus became obsolete and was removed.
303      - it was replaced with the input.fd experiment that uses an
304        analytical "free drift" solution as the ice velocity field.
305      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
306        will hopefully allow us to discriminate problems due to dynamic solvers
307        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
308        us to test additional options, along with the salt plume package.
309      - Finally a pickup was generated (at the end of a one year run) to
310        make the tests more representative of an actual model run. Previously
311        the tests starting point was a 1m thickness of ice everywhere.
312    o pkg/seaice:
313      - introducing S\R seaice_freedrift.F that compute the
314        analytical solution to an approximate ice momentum
315        equation (i.e. the simple stress/coriolis balance).
316      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
317        of the free drift velocity field, and enable its use.
318        To actually use the free drift solution as the model ice
319        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
320    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
321    
322    checkpoint62l (2010/10/04)
323    o pkg/seaice:
324      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
325      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
326       version (with USE_ORIGINAL_SBI undef);
327    o add hooks for new packages OASIS, the package will follow
328      (hooks exclude the seaice pkg for now)
329    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
330      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
331      rather than mdsio_readvector.F/mdsio_writevector.F, within
332      adread_adwrite.F to read/write adjoint-related tapes to disk.
333    o eesupp and pkg/mdsio: ALLOW_WHIO
334      Option to write/read 2D fields to files including tiles halos.
335      The main purpose is for adjoint related "tape I/O".
336      The secondary purpose is for debugging phases.
337      A word on those rather specifically intended purposes.
338      The code was meant to be stripped down to the bare minimum.
339      Typically, there is a unique and basic mapping to the global
340      buffer (tile by tile, then proc by proc, then level by level), and
341      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
342      meant to generate user friendly outputs of various shapes and forms.
343      Rather it is intended, for the knowledgeabale developers,
344      to be largely independent of the many mdsio options, to allow
345      outputs of tiles+halos in debugging phases and in adjoint runs,
346      and to allow some flexibility in tuning (adoint) I/O depending on each
347      file system behavior. With regard to tuning, most of the potential knobs
348      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
349      to specify directories, to specify the typical size of I/O calls, etc.)
350      are not yet included, and will be added if they prove useful.
351    o pkg/seaice:
352       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
353    o pkg/seaice:
354       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
355       code (seaice_budget_ice_if.F) which enable to recover old standard
356       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
357       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
358    o model/src (rStar):
359       use simple average (not area weighted) of rStarFac at U,V point when using
360       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
361       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
362    
363    checkpoint62k (2010/09/17)
364    o adjoint
365       * changed verification/global_ocean.cs32x15 ; adjoint now tests
366         Adams-Bashforth 3 + NLFS + RSTAR
367       * some more modifs required for ECCO-GODAE v4
368    o pkg/seaice
369       add SEAICE_AGE_VOL option to use volume instead of area for
370       integrating SEAICE_AGE
371    o model/src:
372       first check-in of sigma & hybrid-sigma coordinate code ; also includes
373       non-linear free-surface parts ; but pressure-gradient not yet coded.
374    o pkg/ptracers:
375       option for ptracer to convert Salt Relax into additional EmP.
376        tested in exp. global_ocean.90x40x15.dwnslp (update output)
377    
378    checkpoint62j (2010/08/25)
379    o pkg/ggl90:
380       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
381    o pkg/dic: car_flux.F, phos_flux.F
382      - reduce number of exp-calls in order to improve performance
383      - clean up a little (replace fields by their macros, etc., fix
384        typo in CPP-flag)
385    o pkg/ggl90: minor changes
386      - GGL90diffKrS was removed --> always use GGL90diffKr
387      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
388      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
389        (commented out for now)
390      - change in max/min operations to ensure that smoothing is ok
391      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
392      - always use diffKrNrT as background profile (i.e. never use diffKr field)
393    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
394    o pkg/dic:
395      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
396        vectorization
397      - small bug fix in insol for the unlikely case of a cartesian grid
398      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
399        + now vectorize, which also removes adjoint recomputations;
400        + replace integer maksp1 by _RL maskp1
401        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
402    
403    checkpoint62i (2010/07/21)
404    o pkg/flt:
405      - with OBCS: stop floats which enter the OB region
406    o model/src:
407      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
408        for implicit vertical advection.
409    o pkg/seaice:
410     - account for melting in seaice age evolution.
411     - remove double counting of seaice ridging effect on seaice age.
412    
413    checkpoint62h (2010/06/18)
414    o pkg/exch2:
415     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
416    o tools/genmake2
417      - remove "-pdefault" option: redundant with the use of "packages.conf";
418      - remove file pkg/pkg_default : set the default as a pkg group
419        ("default_pkg_list") defined in pkg/pkg_groups;
420      - fix for case pkg/pkg_depend is missing (was hanging before);
421      - add option "-pgroups" to specify a different pkg_groups than the default.
422    o verification/adjustment.cs-32x32x1:
423       add a "minimal" set-up test (code_min & input_min) which only compiles
424       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
425    o tools/genmake2
426      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
427      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
428    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
429      files are nearly the same anyway.
430      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
431       - redefinition of tau(i,i) (by a factor of ustar)
432       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
433       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
434       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
435       - replace
436         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
437         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
438         by
439         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
440         (changes results)
441       -> exf_bulkformulae v1.22,
442          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
443          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
444                    output.txt 1.63
445           offline_exf_seaice: output.seaicetd.txt 1.7
446           seaice_obcs: output.txt 1.10)
447      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
448       -> exf_bulkformulae v1.23,
449          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
450          and global_ocean.cs32x15.icedyn (only 11 matching digits)
451      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
452    o adjoint of exch-1:
453     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
454       (note: was already like this when using EXCH-2) and remove flow dir
455       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
456     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
457     - update pkg/exch2 diff list.
458    
459    checkpoint62g (2010/05/19)
460    o eesupp/src (exch-1):
461     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
462       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
463       (renamed to exch1_*rx_cube.F).
464     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
465       to call new exch1 S/R ; update Makefile and .cvsignore.
466     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
467       exch2_xy_rx later)
468      Note: after updating your code, need to run "make clean" in eesupp/src
469    o test experiment bottom_ctrl_5x5:
470       new output_adm.txt with fewer grdchk & less monitor output.
471    o model/src:
472      remove the call to ini_cori in initialise_varia.F (just keep the usual one
473       in initialise_fixed.F). More consistent with coriolis & horizontal grid
474       beeing treated in the same way (ini_grid is not called a 2nd time).
475    o pkg/exf:
476      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
477      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
478      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
479      - cosmetic changes to exf_bulkformulae.F to make it look more like
480        exf_bulk_largeyeager04.F
481    o eesupp/src (exch-1):
482      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
483      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
484        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
485        (even without using MPI).
486      - Message mode: move RecvAck setting (indicator of buffer being ready)
487        from send_put to recv_get S/R (was useless before, but not sure if
488        it's much more useful now);
489      - Switch the order of sync: MPI-proc 1rst and then threads;
490      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
491      - fix AD code for communication mode ='get' (but not used).
492    o model/src:
493      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
494      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
495    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
496    o pkg/ctrl: require a specific set of control variables and exf-flags for
497      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
498    o model/src:
499     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
500       1rst forward sweep, to avoid over-writing output files during recomputations
501       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
502     b) 2nd version:
503      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
504      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
505         writePickupAtEnd) + seaice & ptracers output;
506      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
507    o model/src:
508      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
509    o pkg/exch2:
510      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
511      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
512    o pkg/autodiff & exch2:
513      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
514      (for now, only if ALLOW_EXCH2 is defined).
515    o pkg/autodiff:
516      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
517        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
518       + clean-up comments (_RS is not always real*4)
519      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
520      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
521        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
522    o testreport (AD-tests):
523      no longer link files from dir "../input" (1rst link files from
524      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
525    
526    checkpoint62f (2010/04/29)
527  o model/src/the_main_loop.F:  o model/src/the_main_loop.F:
528    adjust store directives for seaice evp and multicategory according to    adjust store directives for seaice evp and multicategory according to
529    pkg/ecco/the_main_loop.F    pkg/ecco/the_main_loop.F
530  o adjoint:  o adjoint:
531    global_sum_ad was incomplete (noted many times by many people ;)    global_sum_ad was incomplete (noted many times by many people ;)
532    nice description by Jean U. as follows:    nice description by Jean U. as follows:
533    * allreduce(var) in global_sum.F can be interpreted as    * allreduce(var) in global_sum.F can be interpreted as
534      reduce(sum) followed by broadcast of sum.        reduce(sum) followed by broadcast of sum.
535    * The adjoint of that is    * The adjoint of that is
536      sum(adjoint) followed by broadcast(summed adjoint value)      sum(adjoint) followed by broadcast(summed adjoint value)
537      or in other words, allreduce(sum, adjoint vars)      or in other words, allreduce(sum, adjoint vars)
538    We were missing the sum(adjoint)!    We were missing the sum(adjoint)!
539    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
# Line 117  o tools/build_options: Line 637  o tools/build_options:
637      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
638  o pkg/ecco  o pkg/ecco
639    - allow user defined cost function contributions    - allow user defined cost function contributions
640          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
641          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
642    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
643        the two options are complementary.        the two options are complementary.
644  o pkg/smooth  o pkg/smooth
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