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revision 1.1258 by mlosch, Wed Apr 28 08:37:41 2010 UTC revision 1.1376 by gforget, Thu Feb 10 12:09:57 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 pkg/seaice:
8     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
9     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to also melt ice.
10    o pkg/seaice:
11     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
12     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
13    o pkg/cheapaml:
14     - from Nico Wienders: New version of this package.
15    o pkg/flt:
16     - add CPP options to prevent floats to re-enter the opposite side of
17       a periodic domain (default: keep periodicity)
18    o pkg/gmredi:
19     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
20       (needed for multi-dim advection).
21     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
22    o model/src:
23     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
24    o tutorial_tracer_adjsens
25     - extend to NLFS and replace maskC by hFacC
26       (change reference output accordingly)
27    
28    checkpoint62r (2011/01/24)
29    o testreport:
30     - add option -deloutp (-do) to remove output file after successful run
31     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
32       extract exact list of procs from this file ; adjust COMMAND by
33       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
34    o pkg/ecco: replace old ineffective way of penalizing deviations from
35      first guess (of obcs) with code by Matt Mazloff
36    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
37      exf/cal
38      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
39        and handle case of obcs?period == 0
40        Not affected by these changes: There is still an inconsistency in
41        the computation of start/endrec for the obcs variables for ALLOW_CAL
42        defined (see comment by Menemenlis, 7-Mar-2003)
43      - make S/R ctrl_get_gen_rec return something meaningful even if
44        ALLOW_CAL is not defined
45      - ctrl_getobcs?: simplify code so that it does not need to use
46                       S/R exf_swapfields
47    o testreport:
48       allow to test MPI with different number of processors for each experiment:
49       create file "SIZE.h.mpi" in each build dir.
50       Note: update of "-command" argument not yet implemented.
51    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
52      alleviate the need for additional 3D tapes when using
53      the non-inear free surface in the adjoint. This is done
54      by adding an 'update' of hfacc etc. to their current
55      value at the beginning of forward_step.F.
56    o pkg/seaice
57      seaice_lsr: move stress-divergence computations out of outer pseudo-
58      timestepping loop
59    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
60      up, so that the calls of the ctrl_* subroutines are really at the end
61      of the routine.
62    o pkg/gmredi:
63      allow to specify a 2-D horizontal map and a 1-D vertical profil
64      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
65    o pkg/seaice:
66      move lsr iterations from seaice_dynsolver to seaice_lsr.
67    o pkg/seaice:
68      reduce memory footprint of seaice mutldim advection tapes,
69      by using a 2D tape independent of the generic_advdiff ones,
70      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
71    
72    checkpoint62q (2010/12/29)
73    o model/src:
74      - check horizontal grid-spacing for unset or zero/negative values.
75      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
76    o pkg/flt:
77      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
78      - precision of input and output files set according to readBinaryPrec
79        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
80      - initial float position from tiled file was not converted to index space
81        (looks like a bug): fixed to make it similar to initial pos. global file.
82    o global_ocean.cs32x15:
83       change SIZE.h of AD set-up to get same tiling as with MPI.
84       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
85    o model/src:
86       add flag to control printing of domain fields (bathymetry, hFac ...) in
87       ini_mask_etc (call to plot_fieds_xy*).
88    o pkg/thsice:
89       if useEXF, some forcing fields are not valid in overlap: fixed by computing
90       over the interior only + apply EXCH at the end (like with SEAICE advection).
91    o pkg/mdsio:
92      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
93        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
94      - change barrier call for safe multi-threads access to 3-D shared buffer.
95      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
96      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
97        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
98    o pkg/flt:
99      - add fourth-order Runge-Kutta integration
100      - add basic exch2 support (only 1 facet supported so far!)
101    o pkg/mdsio+rw:
102      new S/R to read local (or tile independent) vector (read counterpart of
103       mds_writevec_loc, and front-end write_glvec_rl/rs).
104    o global_ocean.cs32x15: additional input_ad.seaice experiment
105        that uses pkg/seaice rather than pkg/thsice.
106        (using multidim advection for seaice)
107    o towards more F95 syntax for array specification in namelist:
108      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
109        of all verification experiments.
110           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
111          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
112      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
113    o global_ocean.cs32x15: additional input.seaice experiment
114        that uses pkg/seaice rather than pkg/thsice.
115    
116    checkpoint62p (2010/12/17)
117    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
118        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
119    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
120        allow for use of multim. advection in seaice adjoint.
121    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
122      - first attempt to close budgets by taking into account the freshwater
123        flux implied by the sublimation of snow and ice. So far only the
124        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
125        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
126    o eesupp/src:
127      new S/R with new option (NML_EXTENDED_F77) to change array specification
128      from F95 standard to commonly accepted extended F77 form.
129      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
130      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
131      for less tolerant f77 compiler (e.g., pgf77, g77).
132    o globalFiles:
133      commented out in parameter file "data" since it's not safe with MPI
134      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
135      in this case); no longer commented out in restart test (tst_2+2).
136    o add adTapeDir to specify a special directory where adjoint tapes are
137      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
138      and cannot be used together with mdsioLocalDir.
139    o nesting pkgs:
140      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
141      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
142      - add parameter files + utils dir + output from short run on beagle.
143    o pkg/seaice:
144        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
145    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
146      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
147    
148    checkpoint62o (2010/11/25)
149    o pkg/exf:
150      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
151    o pkg/seaice:
152      - seaice_ocean_stress: split a loop for better vectorization of the
153        adjoint code
154      - seaice_growth.F: fix bug in conservation of freshwater connected to
155        capping of heff, put contribution into d_HEFFbyNEG
156      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
157        by something more sensible (parameters that are what their name implies)
158      - change some defaults, so that by default exf-parameters are used for
159        things like rhoAir, cpAir,latent/sensible heat parameters, in order
160        to reproduce the old results, many data.seaice now contain funny values
161        for cpAir and latent heat of sublimation
162    o packages_readparms.F: move exf_readparms up in line so that
163        exf-parameters are visible for other packages (e.g. seaice)
164    o debugMode & debugLevel=2:
165      - differentiate between debugMode & debugLevel=2:
166        debugMode: controls printing of debug messages (sequence of S/R calls).
167        debugLevel: controls printing of algorithm intermediate results and stats.
168      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
169        => allows to print debug-stats without all sequence of call messages.
170      - switch control of debug print from debugLevel to debugMode in many S/R.
171    o pkg/obcs (obcs-sponge):
172        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
173        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
174    o pkg/generic_advdiff:
175      - record overlap minimum size for each advection scheme;
176      - refine criteria on overlap minimum size;
177      - check and stop (in gad_check) if overlap size is too small.
178    o pkg/obcs:
179      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
180        once, in ptracers_implicit.F)
181      - with seaice: remove test on empty file name in obcs_apply_seaice (always
182        apply OB values when tile has OB)
183    o model/src, coriolis setting:
184      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
185        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
186        files (selectCoriMap=3) with any grid.
187      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
188    o pkg/seaice/seaice_growth.F:
189        a few cosmetic changes that reduce the number of lines of code
190    o pkg/obcs: add boundary conditions following Stevens (1990)
191      - the code follows old MOM/NAOSIM code
192      - so far it is only implemented for the eastern and western boundaries
193        and NOT for pTracers
194    o pkg/rbcs:
195      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
196        beginning of the first rbcs forcing period.
197      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
198        offline package, i.e., one file per time, labeled by iteration number;
199        deltaTrbcs sets the timestep with which the data was generated;
200        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
201      - rbcsForcingCycle=0 makes forcing non-cyclic.
202      - make arithmetic safe for negative times and odd forcing periods.
203    
204    checkpoint62n (2010/11/09)
205    o pkg/seaice:
206        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
207    o pkg/obcs:
208       New S/R to copy tracer value from the OB location to narrow band region
209        (width = same as overlap) beyond the OB: preserve OB value (needed for
210        high-order scheme) which were overwritten by EXCH call if in overlap
211        region. Applied to theta, salt, ptracer and advected seaice variables.
212       With seaice: use maskInC in similar way as in gad_advection.F,
213        in seaice_advection.F and advect.F.
214       Update output of experiment seaice_obcs and change exp4 to test OBCS with
215        4th order Adv.Scheme. for pasive salt and ptracer.
216    o tools/genmake2:
217      - when looking for an optfile (not specified), only search for Fortran compiler
218        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
219      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
220        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
221      - set default for CPP to "cpp -traditional -P" (was the case without specifying
222        an optfile, but otherwise default was just "cpp".
223      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
224      - when "CC" is not set in the optfile, look for possible C compiler
225        (instead of just setting CC=cc)
226      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
227        => add a ".F" to ".o" rule for source files with no "#include" (such as
228           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
229      - move gfortran before g77 in list of possible Fortran compiler (consistent
230        with reference compiler switch from g77 to gfortran)
231    o pkg/seaice:
232      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
233        seaice_check that stops the model, when the CPP flag is used.
234      o seaice_growth.F: make capping of ice volume conserving by returning the
235        capped ice as freshwater to EmPmR. This does not change the verification
236        experiments but will change runs where the capping is acutally active
237    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
238      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
239         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
240         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
241    o tools/genmake2:
242      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
243      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
244      - clean previous genmake log files before anything else.
245      - change Makefile to remove testreport log files (*.tr_log) and genmake log
246        files only with "CLEAN" target (instead of "Clean");
247    o pkg/generic_advdiff:
248      Change OBCS in multiDim advection (gad_advection.F):
249       Use maskInC to prevent intermediate update of tracer-field in OB regions,
250       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
251       which were applying future time-step OB values.
252      This way, all explicit calculations use current-time-step OB values
253       (simpler and more consistent).
254      Affects results when set-up uses time-varying OBC and multi-dim advection;
255       update output of experiment seaice_obcs.
256    o pkg/seaice:
257      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
258       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
259         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
260      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
261       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
262       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
263    o pkg aim (2010/10/26):
264      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
265        formulation with obliquity, eccentricity, ... as run-time parameters,
266      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
267        upward shortwave radition at the surface (all-sky and clear-sky).
268    o pkg/obcs:
269      - writing sections with globalFiles=T does not work: switch to tiled-files
270        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
271      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
272      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
273    
274    checkpoint62m (2010/10/21)
275    o pkg/seaice: vectorize seaice_solve4temp.F
276      - move iterations loops outside of i/j-loops
277      - requires 2D arrays for TB and effConduct
278      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
279        modified in this routine
280      - a little bit of clean up, adjusting indentation, etc.
281      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
282        performance and '**TWO' by '**2' (because TWO is a float),
283        replaced ONE, ZERO
284    o eesupp/src:
285       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
286    o pkg/seaice/seaice_growth.F
287      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
288      merging process. The merged routine has two branches, and one activates the 'evolution'
289      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
290      In summary, here is what the '10/10 revision' did consist of
291        part 1: seaice_growth.F revisions 1.71 to 1.75
292          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
293            The emphasis here was on improving readability (e.g. by trying to use meaningful
294            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
295        part 1.5:
296          - revising the lab_sea experiment to make it a more useful (i.e. stable
297            and representative of an actual model run). This was done by generating a
298            (winter) pickup to start from, switching back the main experiment dynamic
299            solver from evp to lsr, having one of the experiments use the free drift solution.
300        part 2: seaice_growth.F revisions 1.76 to 1.85
301          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
302          - Sorting out the various fields units and sign (set early on and reset at the end)
303            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
304            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
305          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
306            and simplifying logical expressions to further improve readibility.
307        part 3: seaice_growth.F revisions 1.86 to 1.89
308          - Re-organize the blocks of code more logically.
309          - Merging the '_if.F' pieces that add something new.
310    o pkg/thsice:
311      - vectorize thsice_solve4temp and thsice_get_exf.
312        Problem: thsice_solve4temp has an unvectorizable statement that
313        might also be problematic for TAF
314      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
315        does not change the verifcation experiment, but will change all
316        experiments that have this flag undefined (not tested in verification);
317        a little reorganization to save a few 2D fields and recomputations
318      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
319      - 2nd step:  fix some store dirs
320        o seems to work somewhat, i.e. using ifort but not g77
321        o likely cause are incomplete init. or recomputation
322        o start verification/global_ocean.cs32x15/input_ad.thsice
323    o pkg/obcs: add support for exch2
324      - the position of the boundary and prescribed values are specified using
325        a global domain with exch2 facets stacked
326        - in x for N,S boundaries (like W2_mapIO=-1)
327        - in y for E,W boundaries (so E,W boundaries do not overlap)
328    o pkg/mdsio: add support for writing global sections with exch2
329        file layout is as for obcs described above:
330        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
331        - for y-z sections, facets are stacked in y
332    o pkg/thsice:
333       - change a few routines for better vectorization: thsice_albedo.F,
334         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
335         not affected, but in particular the latter routine has changed
336         dramatically (not necessarily easier to read now).
337       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
338       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
339    o verification/lab_sea:
340      - overhaul of the forward model experiments. The main motivation
341        for this revision is that lab_sea has proven quite fragile (when
342        changing the sea-ice code, and switching platforms) to a point
343        when failures were very hard to attribute to specific code problems.
344      - the suspected reason for this fragility is noise amplification by evp so,
345        to start with, we decided to replace evp with lsr in the main experiment.
346      - the input.lsr experiment thus became obsolete and was removed.
347      - it was replaced with the input.fd experiment that uses an
348        analytical "free drift" solution as the ice velocity field.
349      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
350        will hopefully allow us to discriminate problems due to dynamic solvers
351        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
352        us to test additional options, along with the salt plume package.
353      - Finally a pickup was generated (at the end of a one year run) to
354        make the tests more representative of an actual model run. Previously
355        the tests starting point was a 1m thickness of ice everywhere.
356    o pkg/seaice:
357      - introducing S\R seaice_freedrift.F that compute the
358        analytical solution to an approximate ice momentum
359        equation (i.e. the simple stress/coriolis balance).
360      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
361        of the free drift velocity field, and enable its use.
362        To actually use the free drift solution as the model ice
363        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
364    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
365    
366    checkpoint62l (2010/10/04)
367    o pkg/seaice:
368      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
369      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
370       version (with USE_ORIGINAL_SBI undef);
371    o add hooks for new packages OASIS, the package will follow
372      (hooks exclude the seaice pkg for now)
373    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
374      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
375      rather than mdsio_readvector.F/mdsio_writevector.F, within
376      adread_adwrite.F to read/write adjoint-related tapes to disk.
377    o eesupp and pkg/mdsio: ALLOW_WHIO
378      Option to write/read 2D fields to files including tiles halos.
379      The main purpose is for adjoint related "tape I/O".
380      The secondary purpose is for debugging phases.
381      A word on those rather specifically intended purposes.
382      The code was meant to be stripped down to the bare minimum.
383      Typically, there is a unique and basic mapping to the global
384      buffer (tile by tile, then proc by proc, then level by level), and
385      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
386      meant to generate user friendly outputs of various shapes and forms.
387      Rather it is intended, for the knowledgeabale developers,
388      to be largely independent of the many mdsio options, to allow
389      outputs of tiles+halos in debugging phases and in adjoint runs,
390      and to allow some flexibility in tuning (adoint) I/O depending on each
391      file system behavior. With regard to tuning, most of the potential knobs
392      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
393      to specify directories, to specify the typical size of I/O calls, etc.)
394      are not yet included, and will be added if they prove useful.
395    o pkg/seaice:
396       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
397    o pkg/seaice:
398       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
399       code (seaice_budget_ice_if.F) which enable to recover old standard
400       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
401       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
402    o model/src (rStar):
403       use simple average (not area weighted) of rStarFac at U,V point when using
404       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
405       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
406    
407    checkpoint62k (2010/09/17)
408    o adjoint
409       * changed verification/global_ocean.cs32x15 ; adjoint now tests
410         Adams-Bashforth 3 + NLFS + RSTAR
411       * some more modifs required for ECCO-GODAE v4
412    o pkg/seaice
413       add SEAICE_AGE_VOL option to use volume instead of area for
414       integrating SEAICE_AGE
415    o model/src:
416       first check-in of sigma & hybrid-sigma coordinate code ; also includes
417       non-linear free-surface parts ; but pressure-gradient not yet coded.
418    o pkg/ptracers:
419       option for ptracer to convert Salt Relax into additional EmP.
420        tested in exp. global_ocean.90x40x15.dwnslp (update output)
421    
422    checkpoint62j (2010/08/25)
423    o pkg/ggl90:
424       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
425    o pkg/dic: car_flux.F, phos_flux.F
426      - reduce number of exp-calls in order to improve performance
427      - clean up a little (replace fields by their macros, etc., fix
428        typo in CPP-flag)
429    o pkg/ggl90: minor changes
430      - GGL90diffKrS was removed --> always use GGL90diffKr
431      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
432      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
433        (commented out for now)
434      - change in max/min operations to ensure that smoothing is ok
435      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
436      - always use diffKrNrT as background profile (i.e. never use diffKr field)
437    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
438    o pkg/dic:
439      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
440        vectorization
441      - small bug fix in insol for the unlikely case of a cartesian grid
442      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
443        + now vectorize, which also removes adjoint recomputations;
444        + replace integer maksp1 by _RL maskp1
445        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
446    
447    checkpoint62i (2010/07/21)
448    o pkg/flt:
449      - with OBCS: stop floats which enter the OB region
450    o model/src:
451      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
452        for implicit vertical advection.
453    o pkg/seaice:
454     - account for melting in seaice age evolution.
455     - remove double counting of seaice ridging effect on seaice age.
456    
457    checkpoint62h (2010/06/18)
458    o pkg/exch2:
459     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
460    o tools/genmake2
461      - remove "-pdefault" option: redundant with the use of "packages.conf";
462      - remove file pkg/pkg_default : set the default as a pkg group
463        ("default_pkg_list") defined in pkg/pkg_groups;
464      - fix for case pkg/pkg_depend is missing (was hanging before);
465      - add option "-pgroups" to specify a different pkg_groups than the default.
466    o verification/adjustment.cs-32x32x1:
467       add a "minimal" set-up test (code_min & input_min) which only compiles
468       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
469    o tools/genmake2
470      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
471      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
472    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
473      files are nearly the same anyway.
474      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
475       - redefinition of tau(i,i) (by a factor of ustar)
476       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
477       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
478       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
479       - replace
480         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
481         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
482         by
483         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
484         (changes results)
485       -> exf_bulkformulae v1.22,
486          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
487          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
488                    output.txt 1.63
489           offline_exf_seaice: output.seaicetd.txt 1.7
490           seaice_obcs: output.txt 1.10)
491      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
492       -> exf_bulkformulae v1.23,
493          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
494          and global_ocean.cs32x15.icedyn (only 11 matching digits)
495      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
496    o adjoint of exch-1:
497     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
498       (note: was already like this when using EXCH-2) and remove flow dir
499       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
500     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
501     - update pkg/exch2 diff list.
502    
503    checkpoint62g (2010/05/19)
504    o eesupp/src (exch-1):
505     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
506       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
507       (renamed to exch1_*rx_cube.F).
508     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
509       to call new exch1 S/R ; update Makefile and .cvsignore.
510     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
511       exch2_xy_rx later)
512      Note: after updating your code, need to run "make clean" in eesupp/src
513    o test experiment bottom_ctrl_5x5:
514       new output_adm.txt with fewer grdchk & less monitor output.
515    o model/src:
516      remove the call to ini_cori in initialise_varia.F (just keep the usual one
517       in initialise_fixed.F). More consistent with coriolis & horizontal grid
518       beeing treated in the same way (ini_grid is not called a 2nd time).
519    o pkg/exf:
520      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
521      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
522      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
523      - cosmetic changes to exf_bulkformulae.F to make it look more like
524        exf_bulk_largeyeager04.F
525    o eesupp/src (exch-1):
526      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
527      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
528        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
529        (even without using MPI).
530      - Message mode: move RecvAck setting (indicator of buffer being ready)
531        from send_put to recv_get S/R (was useless before, but not sure if
532        it's much more useful now);
533      - Switch the order of sync: MPI-proc 1rst and then threads;
534      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
535      - fix AD code for communication mode ='get' (but not used).
536    o model/src:
537      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
538      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
539    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
540    o pkg/ctrl: require a specific set of control variables and exf-flags for
541      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
542    o model/src:
543     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
544       1rst forward sweep, to avoid over-writing output files during recomputations
545       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
546     b) 2nd version:
547      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
548      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
549         writePickupAtEnd) + seaice & ptracers output;
550      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
551    o model/src:
552      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
553    o pkg/exch2:
554      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
555      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
556    o pkg/autodiff & exch2:
557      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
558      (for now, only if ALLOW_EXCH2 is defined).
559    o pkg/autodiff:
560      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
561        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
562       + clean-up comments (_RS is not always real*4)
563      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
564      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
565        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
566    o testreport (AD-tests):
567      no longer link files from dir "../input" (1rst link files from
568      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
569    
570    checkpoint62f (2010/04/29)
571  o model/src/the_main_loop.F:  o model/src/the_main_loop.F:
572    adjust store directives for seaice evp and multicategory according to    adjust store directives for seaice evp and multicategory according to
573    pkg/ecco/the_main_loop.F    pkg/ecco/the_main_loop.F
574  o adjoint:  o adjoint:
575    global_sum_ad was incomplete (noted many times by many people ;)    global_sum_ad was incomplete (noted many times by many people ;)
576    nice description by Jean U. as follows:    nice description by Jean U. as follows:
577    * allreduce(var) in global_sum.F can be interpreted as    * allreduce(var) in global_sum.F can be interpreted as
578      reduce(sum) followed by broadcast of sum.        reduce(sum) followed by broadcast of sum.
579    * The adjoint of that is    * The adjoint of that is
580      sum(adjoint) followed by broadcast(summed adjoint value)      sum(adjoint) followed by broadcast(summed adjoint value)
581      or in other words, allreduce(sum, adjoint vars)      or in other words, allreduce(sum, adjoint vars)
582    We were missing the sum(adjoint)!    We were missing the sum(adjoint)!
583    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 681  o tools/build_options:
681      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
682  o pkg/ecco  o pkg/ecco
683    - allow user defined cost function contributions    - allow user defined cost function contributions
684          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
685          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
686    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
687        the two options are complementary.        the two options are complementary.
688  o pkg/smooth  o pkg/smooth
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