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revision 1.1223 by dimitri, Wed Jan 20 23:33:45 2010 UTC revision 1.1370 by jmc, Thu Jan 27 20:52:10 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/icefront: adding the shell of, and the hooks to, a new package that  o pkg/gmredi:
8     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
9       (needed for multi-dim advection).
10    o model/src:
11     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
12    
13    checkpoint62r (2011/01/24)
14    o testreport:
15     - add option -deloutp (-do) to remove output file after successful run
16     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
17       extract exact list of procs from this file ; adjust COMMAND by
18       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
19    o pkg/ecco: replace old ineffective way of penalizing deviations from
20      first guess (of obcs) with code by Matt Mazloff
21    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
22      exf/cal
23      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
24        and handle case of obcs?period == 0
25        Not affected by these changes: There is still an inconsistency in
26        the computation of start/endrec for the obcs variables for ALLOW_CAL
27        defined (see comment by Menemenlis, 7-Mar-2003)
28      - make S/R ctrl_get_gen_rec return something meaningful even if
29        ALLOW_CAL is not defined
30      - ctrl_getobcs?: simplify code so that it does not need to use
31                       S/R exf_swapfields
32    o testreport:
33       allow to test MPI with different number of processors for each experiment:
34       create file "SIZE.h.mpi" in each build dir.
35       Note: update of "-command" argument not yet implemented.
36    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
37      alleviate the need for additional 3D tapes when using
38      the non-inear free surface in the adjoint. This is done
39      by adding an 'update' of hfacc etc. to their current
40      value at the beginning of forward_step.F.
41    o pkg/seaice
42      seaice_lsr: move stress-divergence computations out of outer pseudo-
43      timestepping loop
44    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
45      up, so that the calls of the ctrl_* subroutines are really at the end
46      of the routine.
47    o pkg/gmredi:
48      allow to specify a 2-D horizontal map and a 1-D vertical profil
49      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
50    o pkg/seaice:
51      move lsr iterations from seaice_dynsolver to seaice_lsr.
52    o pkg/seaice:
53      reduce memory footprint of seaice mutldim advection tapes,
54      by using a 2D tape independent of the generic_advdiff ones,
55      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
56    
57    checkpoint62q (2010/12/29)
58    o model/src:
59      - check horizontal grid-spacing for unset or zero/negative values.
60      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
61    o pkg/flt:
62      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
63      - precision of input and output files set according to readBinaryPrec
64        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
65      - initial float position from tiled file was not converted to index space
66        (looks like a bug): fixed to make it similar to initial pos. global file.
67    o global_ocean.cs32x15:
68       change SIZE.h of AD set-up to get same tiling as with MPI.
69       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
70    o model/src:
71       add flag to control printing of domain fields (bathymetry, hFac ...) in
72       ini_mask_etc (call to plot_fieds_xy*).
73    o pkg/thsice:
74       if useEXF, some forcing fields are not valid in overlap: fixed by computing
75       over the interior only + apply EXCH at the end (like with SEAICE advection).
76    o pkg/mdsio:
77      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
78        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
79      - change barrier call for safe multi-threads access to 3-D shared buffer.
80      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
81      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
82        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
83    o pkg/flt:
84      - add fourth-order Runge-Kutta integration
85      - add basic exch2 support (only 1 facet supported so far!)
86    o pkg/mdsio+rw:
87      new S/R to read local (or tile independent) vector (read counterpart of
88       mds_writevec_loc, and front-end write_glvec_rl/rs).
89    o global_ocean.cs32x15: additional input_ad.seaice experiment
90        that uses pkg/seaice rather than pkg/thsice.
91        (using multidim advection for seaice)
92    o towards more F95 syntax for array specification in namelist:
93      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
94        of all verification experiments.
95           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
96          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
97      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
98    o global_ocean.cs32x15: additional input.seaice experiment
99        that uses pkg/seaice rather than pkg/thsice.
100    
101    checkpoint62p (2010/12/17)
102    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
103        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
104    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
105        allow for use of multim. advection in seaice adjoint.
106    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
107      - first attempt to close budgets by taking into account the freshwater
108        flux implied by the sublimation of snow and ice. So far only the
109        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
110        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
111    o eesupp/src:
112      new S/R with new option (NML_EXTENDED_F77) to change array specification
113      from F95 standard to commonly accepted extended F77 form.
114      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
115      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
116      for less tolerant f77 compiler (e.g., pgf77, g77).
117    o globalFiles:
118      commented out in parameter file "data" since it's not safe with MPI
119      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
120      in this case); no longer commented out in restart test (tst_2+2).
121    o add adTapeDir to specify a special directory where adjoint tapes are
122      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
123      and cannot be used together with mdsioLocalDir.
124    o nesting pkgs:
125      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
126      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
127      - add parameter files + utils dir + output from short run on beagle.
128    o pkg/seaice:
129        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
130    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
131      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
132    
133    checkpoint62o (2010/11/25)
134    o pkg/exf:
135      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
136    o pkg/seaice:
137      - seaice_ocean_stress: split a loop for better vectorization of the
138        adjoint code
139      - seaice_growth.F: fix bug in conservation of freshwater connected to
140        capping of heff, put contribution into d_HEFFbyNEG
141      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
142        by something more sensible (parameters that are what their name implies)
143      - change some defaults, so that by default exf-parameters are used for
144        things like rhoAir, cpAir,latent/sensible heat parameters, in order
145        to reproduce the old results, many data.seaice now contain funny values
146        for cpAir and latent heat of sublimation
147    o packages_readparms.F: move exf_readparms up in line so that
148        exf-parameters are visible for other packages (e.g. seaice)
149    o debugMode & debugLevel=2:
150      - differentiate between debugMode & debugLevel=2:
151        debugMode: controls printing of debug messages (sequence of S/R calls).
152        debugLevel: controls printing of algorithm intermediate results and stats.
153      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
154        => allows to print debug-stats without all sequence of call messages.
155      - switch control of debug print from debugLevel to debugMode in many S/R.
156    o pkg/obcs (obcs-sponge):
157        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
158        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
159    o pkg/generic_advdiff:
160      - record overlap minimum size for each advection scheme;
161      - refine criteria on overlap minimum size;
162      - check and stop (in gad_check) if overlap size is too small.
163    o pkg/obcs:
164      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
165        once, in ptracers_implicit.F)
166      - with seaice: remove test on empty file name in obcs_apply_seaice (always
167        apply OB values when tile has OB)
168    o model/src, coriolis setting:
169      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
170        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
171        files (selectCoriMap=3) with any grid.
172      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
173    o pkg/seaice/seaice_growth.F:
174        a few cosmetic changes that reduce the number of lines of code
175    o pkg/obcs: add boundary conditions following Stevens (1990)
176      - the code follows old MOM/NAOSIM code
177      - so far it is only implemented for the eastern and western boundaries
178        and NOT for pTracers
179    o pkg/rbcs:
180      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
181        beginning of the first rbcs forcing period.
182      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
183        offline package, i.e., one file per time, labeled by iteration number;
184        deltaTrbcs sets the timestep with which the data was generated;
185        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
186      - rbcsForcingCycle=0 makes forcing non-cyclic.
187      - make arithmetic safe for negative times and odd forcing periods.
188    
189    checkpoint62n (2010/11/09)
190    o pkg/seaice:
191        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
192    o pkg/obcs:
193       New S/R to copy tracer value from the OB location to narrow band region
194        (width = same as overlap) beyond the OB: preserve OB value (needed for
195        high-order scheme) which were overwritten by EXCH call if in overlap
196        region. Applied to theta, salt, ptracer and advected seaice variables.
197       With seaice: use maskInC in similar way as in gad_advection.F,
198        in seaice_advection.F and advect.F.
199       Update output of experiment seaice_obcs and change exp4 to test OBCS with
200        4th order Adv.Scheme. for pasive salt and ptracer.
201    o tools/genmake2:
202      - when looking for an optfile (not specified), only search for Fortran compiler
203        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
204      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
205        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
206      - set default for CPP to "cpp -traditional -P" (was the case without specifying
207        an optfile, but otherwise default was just "cpp".
208      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
209      - when "CC" is not set in the optfile, look for possible C compiler
210        (instead of just setting CC=cc)
211      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
212        => add a ".F" to ".o" rule for source files with no "#include" (such as
213           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
214      - move gfortran before g77 in list of possible Fortran compiler (consistent
215        with reference compiler switch from g77 to gfortran)
216    o pkg/seaice:
217      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
218        seaice_check that stops the model, when the CPP flag is used.
219      o seaice_growth.F: make capping of ice volume conserving by returning the
220        capped ice as freshwater to EmPmR. This does not change the verification
221        experiments but will change runs where the capping is acutally active
222    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
223      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
224         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
225         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
226    o tools/genmake2:
227      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
228      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
229      - clean previous genmake log files before anything else.
230      - change Makefile to remove testreport log files (*.tr_log) and genmake log
231        files only with "CLEAN" target (instead of "Clean");
232    o pkg/generic_advdiff:
233      Change OBCS in multiDim advection (gad_advection.F):
234       Use maskInC to prevent intermediate update of tracer-field in OB regions,
235       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
236       which were applying future time-step OB values.
237      This way, all explicit calculations use current-time-step OB values
238       (simpler and more consistent).
239      Affects results when set-up uses time-varying OBC and multi-dim advection;
240       update output of experiment seaice_obcs.
241    o pkg/seaice:
242      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
243       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
244         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
245      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
246       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
247       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
248    o pkg aim (2010/10/26):
249      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
250        formulation with obliquity, eccentricity, ... as run-time parameters,
251      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
252        upward shortwave radition at the surface (all-sky and clear-sky).
253    o pkg/obcs:
254      - writing sections with globalFiles=T does not work: switch to tiled-files
255        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
256      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
257      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
258    
259    checkpoint62m (2010/10/21)
260    o pkg/seaice: vectorize seaice_solve4temp.F
261      - move iterations loops outside of i/j-loops
262      - requires 2D arrays for TB and effConduct
263      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
264        modified in this routine
265      - a little bit of clean up, adjusting indentation, etc.
266      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
267        performance and '**TWO' by '**2' (because TWO is a float),
268        replaced ONE, ZERO
269    o eesupp/src:
270       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
271    o pkg/seaice/seaice_growth.F
272      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
273      merging process. The merged routine has two branches, and one activates the 'evolution'
274      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
275      In summary, here is what the '10/10 revision' did consist of
276        part 1: seaice_growth.F revisions 1.71 to 1.75
277          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
278            The emphasis here was on improving readability (e.g. by trying to use meaningful
279            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
280        part 1.5:
281          - revising the lab_sea experiment to make it a more useful (i.e. stable
282            and representative of an actual model run). This was done by generating a
283            (winter) pickup to start from, switching back the main experiment dynamic
284            solver from evp to lsr, having one of the experiments use the free drift solution.
285        part 2: seaice_growth.F revisions 1.76 to 1.85
286          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
287          - Sorting out the various fields units and sign (set early on and reset at the end)
288            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
289            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
290          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
291            and simplifying logical expressions to further improve readibility.
292        part 3: seaice_growth.F revisions 1.86 to 1.89
293          - Re-organize the blocks of code more logically.
294          - Merging the '_if.F' pieces that add something new.
295    o pkg/thsice:
296      - vectorize thsice_solve4temp and thsice_get_exf.
297        Problem: thsice_solve4temp has an unvectorizable statement that
298        might also be problematic for TAF
299      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
300        does not change the verifcation experiment, but will change all
301        experiments that have this flag undefined (not tested in verification);
302        a little reorganization to save a few 2D fields and recomputations
303      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
304      - 2nd step:  fix some store dirs
305        o seems to work somewhat, i.e. using ifort but not g77
306        o likely cause are incomplete init. or recomputation
307        o start verification/global_ocean.cs32x15/input_ad.thsice
308    o pkg/obcs: add support for exch2
309      - the position of the boundary and prescribed values are specified using
310        a global domain with exch2 facets stacked
311        - in x for N,S boundaries (like W2_mapIO=-1)
312        - in y for E,W boundaries (so E,W boundaries do not overlap)
313    o pkg/mdsio: add support for writing global sections with exch2
314        file layout is as for obcs described above:
315        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
316        - for y-z sections, facets are stacked in y
317    o pkg/thsice:
318       - change a few routines for better vectorization: thsice_albedo.F,
319         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
320         not affected, but in particular the latter routine has changed
321         dramatically (not necessarily easier to read now).
322       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
323       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
324    o verification/lab_sea:
325      - overhaul of the forward model experiments. The main motivation
326        for this revision is that lab_sea has proven quite fragile (when
327        changing the sea-ice code, and switching platforms) to a point
328        when failures were very hard to attribute to specific code problems.
329      - the suspected reason for this fragility is noise amplification by evp so,
330        to start with, we decided to replace evp with lsr in the main experiment.
331      - the input.lsr experiment thus became obsolete and was removed.
332      - it was replaced with the input.fd experiment that uses an
333        analytical "free drift" solution as the ice velocity field.
334      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
335        will hopefully allow us to discriminate problems due to dynamic solvers
336        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
337        us to test additional options, along with the salt plume package.
338      - Finally a pickup was generated (at the end of a one year run) to
339        make the tests more representative of an actual model run. Previously
340        the tests starting point was a 1m thickness of ice everywhere.
341    o pkg/seaice:
342      - introducing S\R seaice_freedrift.F that compute the
343        analytical solution to an approximate ice momentum
344        equation (i.e. the simple stress/coriolis balance).
345      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
346        of the free drift velocity field, and enable its use.
347        To actually use the free drift solution as the model ice
348        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
349    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
350    
351    checkpoint62l (2010/10/04)
352    o pkg/seaice:
353      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
354      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
355       version (with USE_ORIGINAL_SBI undef);
356    o add hooks for new packages OASIS, the package will follow
357      (hooks exclude the seaice pkg for now)
358    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
359      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
360      rather than mdsio_readvector.F/mdsio_writevector.F, within
361      adread_adwrite.F to read/write adjoint-related tapes to disk.
362    o eesupp and pkg/mdsio: ALLOW_WHIO
363      Option to write/read 2D fields to files including tiles halos.
364      The main purpose is for adjoint related "tape I/O".
365      The secondary purpose is for debugging phases.
366      A word on those rather specifically intended purposes.
367      The code was meant to be stripped down to the bare minimum.
368      Typically, there is a unique and basic mapping to the global
369      buffer (tile by tile, then proc by proc, then level by level), and
370      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
371      meant to generate user friendly outputs of various shapes and forms.
372      Rather it is intended, for the knowledgeabale developers,
373      to be largely independent of the many mdsio options, to allow
374      outputs of tiles+halos in debugging phases and in adjoint runs,
375      and to allow some flexibility in tuning (adoint) I/O depending on each
376      file system behavior. With regard to tuning, most of the potential knobs
377      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
378      to specify directories, to specify the typical size of I/O calls, etc.)
379      are not yet included, and will be added if they prove useful.
380    o pkg/seaice:
381       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
382    o pkg/seaice:
383       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
384       code (seaice_budget_ice_if.F) which enable to recover old standard
385       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
386       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
387    o model/src (rStar):
388       use simple average (not area weighted) of rStarFac at U,V point when using
389       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
390       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
391    
392    checkpoint62k (2010/09/17)
393    o adjoint
394       * changed verification/global_ocean.cs32x15 ; adjoint now tests
395         Adams-Bashforth 3 + NLFS + RSTAR
396       * some more modifs required for ECCO-GODAE v4
397    o pkg/seaice
398       add SEAICE_AGE_VOL option to use volume instead of area for
399       integrating SEAICE_AGE
400    o model/src:
401       first check-in of sigma & hybrid-sigma coordinate code ; also includes
402       non-linear free-surface parts ; but pressure-gradient not yet coded.
403    o pkg/ptracers:
404       option for ptracer to convert Salt Relax into additional EmP.
405        tested in exp. global_ocean.90x40x15.dwnslp (update output)
406    
407    checkpoint62j (2010/08/25)
408    o pkg/ggl90:
409       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
410    o pkg/dic: car_flux.F, phos_flux.F
411      - reduce number of exp-calls in order to improve performance
412      - clean up a little (replace fields by their macros, etc., fix
413        typo in CPP-flag)
414    o pkg/ggl90: minor changes
415      - GGL90diffKrS was removed --> always use GGL90diffKr
416      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
417      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
418        (commented out for now)
419      - change in max/min operations to ensure that smoothing is ok
420      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
421      - always use diffKrNrT as background profile (i.e. never use diffKr field)
422    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
423    o pkg/dic:
424      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
425        vectorization
426      - small bug fix in insol for the unlikely case of a cartesian grid
427      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
428        + now vectorize, which also removes adjoint recomputations;
429        + replace integer maksp1 by _RL maskp1
430        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
431    
432    checkpoint62i (2010/07/21)
433    o pkg/flt:
434      - with OBCS: stop floats which enter the OB region
435    o model/src:
436      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
437        for implicit vertical advection.
438    o pkg/seaice:
439     - account for melting in seaice age evolution.
440     - remove double counting of seaice ridging effect on seaice age.
441    
442    checkpoint62h (2010/06/18)
443    o pkg/exch2:
444     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
445    o tools/genmake2
446      - remove "-pdefault" option: redundant with the use of "packages.conf";
447      - remove file pkg/pkg_default : set the default as a pkg group
448        ("default_pkg_list") defined in pkg/pkg_groups;
449      - fix for case pkg/pkg_depend is missing (was hanging before);
450      - add option "-pgroups" to specify a different pkg_groups than the default.
451    o verification/adjustment.cs-32x32x1:
452       add a "minimal" set-up test (code_min & input_min) which only compiles
453       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
454    o tools/genmake2
455      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
456      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
457    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
458      files are nearly the same anyway.
459      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
460       - redefinition of tau(i,i) (by a factor of ustar)
461       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
462       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
463       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
464       - replace
465         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
466         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
467         by
468         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
469         (changes results)
470       -> exf_bulkformulae v1.22,
471          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
472          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
473                    output.txt 1.63
474           offline_exf_seaice: output.seaicetd.txt 1.7
475           seaice_obcs: output.txt 1.10)
476      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
477       -> exf_bulkformulae v1.23,
478          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
479          and global_ocean.cs32x15.icedyn (only 11 matching digits)
480      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
481    o adjoint of exch-1:
482     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
483       (note: was already like this when using EXCH-2) and remove flow dir
484       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
485     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
486     - update pkg/exch2 diff list.
487    
488    checkpoint62g (2010/05/19)
489    o eesupp/src (exch-1):
490     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
491       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
492       (renamed to exch1_*rx_cube.F).
493     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
494       to call new exch1 S/R ; update Makefile and .cvsignore.
495     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
496       exch2_xy_rx later)
497      Note: after updating your code, need to run "make clean" in eesupp/src
498    o test experiment bottom_ctrl_5x5:
499       new output_adm.txt with fewer grdchk & less monitor output.
500    o model/src:
501      remove the call to ini_cori in initialise_varia.F (just keep the usual one
502       in initialise_fixed.F). More consistent with coriolis & horizontal grid
503       beeing treated in the same way (ini_grid is not called a 2nd time).
504    o pkg/exf:
505      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
506      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
507      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
508      - cosmetic changes to exf_bulkformulae.F to make it look more like
509        exf_bulk_largeyeager04.F
510    o eesupp/src (exch-1):
511      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
512      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
513        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
514        (even without using MPI).
515      - Message mode: move RecvAck setting (indicator of buffer being ready)
516        from send_put to recv_get S/R (was useless before, but not sure if
517        it's much more useful now);
518      - Switch the order of sync: MPI-proc 1rst and then threads;
519      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
520      - fix AD code for communication mode ='get' (but not used).
521    o model/src:
522      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
523      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
524    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
525    o pkg/ctrl: require a specific set of control variables and exf-flags for
526      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
527    o model/src:
528     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
529       1rst forward sweep, to avoid over-writing output files during recomputations
530       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
531     b) 2nd version:
532      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
533      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
534         writePickupAtEnd) + seaice & ptracers output;
535      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
536    o model/src:
537      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
538    o pkg/exch2:
539      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
540      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
541    o pkg/autodiff & exch2:
542      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
543      (for now, only if ALLOW_EXCH2 is defined).
544    o pkg/autodiff:
545      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
546        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
547       + clean-up comments (_RS is not always real*4)
548      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
549      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
550        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
551    o testreport (AD-tests):
552      no longer link files from dir "../input" (1rst link files from
553      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
554    
555    checkpoint62f (2010/04/29)
556    o model/src/the_main_loop.F:
557      adjust store directives for seaice evp and multicategory according to
558      pkg/ecco/the_main_loop.F
559    o adjoint:
560      global_sum_ad was incomplete (noted many times by many people ;)
561      nice description by Jean U. as follows:
562      * allreduce(var) in global_sum.F can be interpreted as
563        reduce(sum) followed by broadcast of sum.
564      * The adjoint of that is
565        sum(adjoint) followed by broadcast(summed adjoint value)
566        or in other words, allreduce(sum, adjoint vars)
567      We were missing the sum(adjoint)!
568      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
569      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
570      The fix should produce 16-digit accuracy between
571      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
572      multi-CPU single-tile (e.g. nSx=1, nPx-2)
573      We'll probably change this yet again shortly
574    o eesupp/src:
575      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
576    o pkg/icefront
577      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
578        specification of addmass array based on a 2D field, which is added
579        at bottommost wet level at each horizontal location.
580    o model/src:
581     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
582     layout; (not always compatible with delX,delY setting; commented out for now).
583    o pkg/exch2:
584     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
585     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
586    
587    checkpoint62e (2010/04/15)
588    o pkg/obcs:
589      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
590    o pkg/dic:
591      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
592        (note: not presently tested in any forward verification exp.)
593       update tutorial_global_oce_biogeo AD output file.
594    o pkg/exf:
595      - account for the variation of albedo as a function of zenith angle
596        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
597    o build_options:
598     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
599    o pkg/dic:
600      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
601      - use binary pickup file for restart;
602      - initialise atmos-CO2 box from dic_pCO2 parameter;
603      - fix multi-threaded.
604    o pkg/rbcs:
605     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
606       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
607     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
608       and update output.txt
609    o pkg/kpp:
610     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
611     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
612       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
613       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
614     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
615       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
616    o pkg/offline:
617      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
618      (bug was added in version 1.10 on 2007-08-23).
619    o pkg/offline:
620      - no need to specify periodicExternalForcing, etc ... to use offline pack
621      - offline input files no longer just single prec --> parameter offlineLoadPrec
622    o verification/lab_sea:
623      change AD test to multi-tile setup and update all 4 AD output.
624      NOTE: while cost function values remain very similar,
625      gradients are very different, although gradient checks are self-consistent
626      Should try to get to the bottom of this (cost function summation order?)
627    o pkg/dic:
628      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
629      a weakness of TAF that drops part of double precision in log10 derivative.
630      <= changes removed since problem has been fixed in current TAF version 1.9.71
631      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
632    o pkg/ecco:
633      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
634      update all 4 lab_sea AD output.
635    
636    checkpoint62d (2010/03/22)
637    o build_options:
638      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
639    o remove unbalanced quote (single or double) in commented line of source code
640      (may cause some warning with some preprocessor/makedepend versions).
641    o pkg/seaice:
642      fix seaice_model.F for adjoint (gael) and update AD results of experiments
643       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
644    o testreport:
645      add option '-runonly' (short: '-ro') to just do the run part (without make).
646    o eesupp: remove JAM communication code (obsolete).
647    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
648      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
649      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
650      (update also the output).
651    
652    checkpoint62c (2010/03/02)
653    o tools/build_options :
654       move (some) old optfiles from build_options/ to build_options/unsupported/
655    o model/src and pkg/exf
656       surface relaxation -- separating data and data.exf options
657       The point is to ensure that we specify the surface relaxation
658       either in data or in data.exf (but not half and half) and to
659       avoid an accidental relaxation to 0 (which happened if a time
660       scale was specified but the file name was left empty)
661    o model/src model/inc and pkg/mom_common
662       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
663       => addition to the viscosity field as computed by others schemes
664    o tools/build_options:
665      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
666        but keep the former optfile for few weeks for smooth transition
667    o pkg/ecco
668      - allow user defined cost function contributions
669         CPP: ALLOW_USERCOST_CONTRIBUTION
670         USAGE: compute contributions in cost_usercost_all.F
671      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
672          the two options are complementary.
673    o pkg/smooth
674      - migration from contrib to the main repository
675    
676    checkpoint62b (2010/01/26)
677    o pkg/monitor:
678      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
679        (in case someone forgot to update customized pieces of code)
680    o nonHydrostatic:
681      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
682      - add a simple 2-D experiment (short_surf_wave) to test it.
683    o pkg/icefront:
684       adding the shell of, and the hooks to, a new package that
685     will model melting and freezing of vertical glacier ice fronts     will model melting and freezing of vertical glacier ice fronts
686  o momentum:  o momentum:
687    add diagnostics of momentum tendency from Hydrostatic pressure gradient    add diagnostics of momentum tendency from Hydrostatic pressure gradient
688     (without surf.pressure term: would need a 2nd filling since implicit term).     (without surf.pressure term: would need a 2nd filling since implicit term).
689  o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace  o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
690    two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR    two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
691    cannot deal with the former    cannot deal with the former
692  o cleaning:  o cleaning:
693    - remove all (except OpenAD) old TLM output from results_ad dirs.    - remove all (except OpenAD) old TLM output from results_ad dirs.
694    - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)    - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
695    - comment out maskH definition (replaced by maskInC)    - comment out maskH definition (replaced by maskInC)
696  o pkg/monitor:  o pkg/monitor:
697    - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl    - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
698      & mon_calc_stats_rl) to be the RL pendant to mon_printstats_rs & mon_stats_rs.      & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
699    
700  checkpoint62a (2010/01/15)  checkpoint62a (2010/01/15)
701  o model/src:  o model/src:
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