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revision 1.1233 by jmc, Tue Mar 2 19:43:17 2010 UTC revision 1.1380 by jmc, Tue Feb 22 18:44:22 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:
8     - add new param to scale curvilinear grid distance and area when using
9       a different sphere radius from the grid-files.
10     - test/check multi-threads EXCH applied to local variable (cg2d_x)
11    
12    checkpoint62s (2011/02/15)
13    o pkg/seaice:
14     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
15       computing the ice cover tendency from effective thickness tendencies. Include
16       Ian Fenty's formula.
17     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
18       SEAICEareaFormula.
19     - simplify notations for the various d_HEFF/d_AREA terms.
20    o pkg/gmredi:
21     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
22       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
23       add a verification test-run (front_relax.bvp) to test GM_useBVP.
24    o pkg/seaice:
25     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
26     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
27       also melt ice.
28    o pkg/seaice:
29     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
30     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
31    o pkg/cheapaml:
32     - from Nico Wienders: New version of this package.
33    o pkg/flt:
34     - add CPP options to prevent floats to re-enter the opposite side of
35       a periodic domain (default: keep periodicity)
36    o pkg/gmredi:
37     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
38       (needed for multi-dim advection).
39     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
40    o model/src:
41     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
42    o tutorial_tracer_adjsens
43     - extend to NLFS and replace maskC by hFacC
44       (change reference output accordingly)
45    
46    checkpoint62r (2011/01/24)
47    o testreport:
48     - add option -deloutp (-do) to remove output file after successful run
49     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
50       extract exact list of procs from this file ; adjust COMMAND by
51       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
52    o pkg/ecco: replace old ineffective way of penalizing deviations from
53      first guess (of obcs) with code by Matt Mazloff
54    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
55      exf/cal
56      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
57        and handle case of obcs?period == 0
58        Not affected by these changes: There is still an inconsistency in
59        the computation of start/endrec for the obcs variables for ALLOW_CAL
60        defined (see comment by Menemenlis, 7-Mar-2003)
61      - make S/R ctrl_get_gen_rec return something meaningful even if
62        ALLOW_CAL is not defined
63      - ctrl_getobcs?: simplify code so that it does not need to use
64                       S/R exf_swapfields
65    o testreport:
66       allow to test MPI with different number of processors for each experiment:
67       create file "SIZE.h.mpi" in each build dir.
68       Note: update of "-command" argument not yet implemented.
69    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
70      alleviate the need for additional 3D tapes when using
71      the non-inear free surface in the adjoint. This is done
72      by adding an 'update' of hfacc etc. to their current
73      value at the beginning of forward_step.F.
74    o pkg/seaice
75      seaice_lsr: move stress-divergence computations out of outer pseudo-
76      timestepping loop
77    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
78      up, so that the calls of the ctrl_* subroutines are really at the end
79      of the routine.
80    o pkg/gmredi:
81      allow to specify a 2-D horizontal map and a 1-D vertical profil
82      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
83    o pkg/seaice:
84      move lsr iterations from seaice_dynsolver to seaice_lsr.
85    o pkg/seaice:
86      reduce memory footprint of seaice mutldim advection tapes,
87      by using a 2D tape independent of the generic_advdiff ones,
88      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
89    
90    checkpoint62q (2010/12/29)
91    o model/src:
92      - check horizontal grid-spacing for unset or zero/negative values.
93      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
94    o pkg/flt:
95      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
96      - precision of input and output files set according to readBinaryPrec
97        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
98      - initial float position from tiled file was not converted to index space
99        (looks like a bug): fixed to make it similar to initial pos. global file.
100    o global_ocean.cs32x15:
101       change SIZE.h of AD set-up to get same tiling as with MPI.
102       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
103    o model/src:
104       add flag to control printing of domain fields (bathymetry, hFac ...) in
105       ini_mask_etc (call to plot_fieds_xy*).
106    o pkg/thsice:
107       if useEXF, some forcing fields are not valid in overlap: fixed by computing
108       over the interior only + apply EXCH at the end (like with SEAICE advection).
109    o pkg/mdsio:
110      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
111        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
112      - change barrier call for safe multi-threads access to 3-D shared buffer.
113      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
114      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
115        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
116    o pkg/flt:
117      - add fourth-order Runge-Kutta integration
118      - add basic exch2 support (only 1 facet supported so far!)
119    o pkg/mdsio+rw:
120      new S/R to read local (or tile independent) vector (read counterpart of
121       mds_writevec_loc, and front-end write_glvec_rl/rs).
122    o global_ocean.cs32x15: additional input_ad.seaice experiment
123        that uses pkg/seaice rather than pkg/thsice.
124        (using multidim advection for seaice)
125    o towards more F95 syntax for array specification in namelist:
126      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
127        of all verification experiments.
128           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
129          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
130      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
131    o global_ocean.cs32x15: additional input.seaice experiment
132        that uses pkg/seaice rather than pkg/thsice.
133    
134    checkpoint62p (2010/12/17)
135    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
136        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
137    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
138        allow for use of multim. advection in seaice adjoint.
139    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
140      - first attempt to close budgets by taking into account the freshwater
141        flux implied by the sublimation of snow and ice. So far only the
142        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
143        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
144    o eesupp/src:
145      new S/R with new option (NML_EXTENDED_F77) to change array specification
146      from F95 standard to commonly accepted extended F77 form.
147      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
148      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
149      for less tolerant f77 compiler (e.g., pgf77, g77).
150    o globalFiles:
151      commented out in parameter file "data" since it's not safe with MPI
152      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
153      in this case); no longer commented out in restart test (tst_2+2).
154    o add adTapeDir to specify a special directory where adjoint tapes are
155      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
156      and cannot be used together with mdsioLocalDir.
157    o nesting pkgs:
158      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
159      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
160      - add parameter files + utils dir + output from short run on beagle.
161    o pkg/seaice:
162        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
163    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
164      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
165    
166    checkpoint62o (2010/11/25)
167    o pkg/exf:
168      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
169    o pkg/seaice:
170      - seaice_ocean_stress: split a loop for better vectorization of the
171        adjoint code
172      - seaice_growth.F: fix bug in conservation of freshwater connected to
173        capping of heff, put contribution into d_HEFFbyNEG
174      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
175        by something more sensible (parameters that are what their name implies)
176      - change some defaults, so that by default exf-parameters are used for
177        things like rhoAir, cpAir,latent/sensible heat parameters, in order
178        to reproduce the old results, many data.seaice now contain funny values
179        for cpAir and latent heat of sublimation
180    o packages_readparms.F: move exf_readparms up in line so that
181        exf-parameters are visible for other packages (e.g. seaice)
182    o debugMode & debugLevel=2:
183      - differentiate between debugMode & debugLevel=2:
184        debugMode: controls printing of debug messages (sequence of S/R calls).
185        debugLevel: controls printing of algorithm intermediate results and stats.
186      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
187        => allows to print debug-stats without all sequence of call messages.
188      - switch control of debug print from debugLevel to debugMode in many S/R.
189    o pkg/obcs (obcs-sponge):
190        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
191        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
192    o pkg/generic_advdiff:
193      - record overlap minimum size for each advection scheme;
194      - refine criteria on overlap minimum size;
195      - check and stop (in gad_check) if overlap size is too small.
196    o pkg/obcs:
197      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
198        once, in ptracers_implicit.F)
199      - with seaice: remove test on empty file name in obcs_apply_seaice (always
200        apply OB values when tile has OB)
201    o model/src, coriolis setting:
202      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
203        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
204        files (selectCoriMap=3) with any grid.
205      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
206    o pkg/seaice/seaice_growth.F:
207        a few cosmetic changes that reduce the number of lines of code
208    o pkg/obcs: add boundary conditions following Stevens (1990)
209      - the code follows old MOM/NAOSIM code
210      - so far it is only implemented for the eastern and western boundaries
211        and NOT for pTracers
212    o pkg/rbcs:
213      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
214        beginning of the first rbcs forcing period.
215      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
216        offline package, i.e., one file per time, labeled by iteration number;
217        deltaTrbcs sets the timestep with which the data was generated;
218        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
219      - rbcsForcingCycle=0 makes forcing non-cyclic.
220      - make arithmetic safe for negative times and odd forcing periods.
221    
222    checkpoint62n (2010/11/09)
223    o pkg/seaice:
224        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
225    o pkg/obcs:
226       New S/R to copy tracer value from the OB location to narrow band region
227        (width = same as overlap) beyond the OB: preserve OB value (needed for
228        high-order scheme) which were overwritten by EXCH call if in overlap
229        region. Applied to theta, salt, ptracer and advected seaice variables.
230       With seaice: use maskInC in similar way as in gad_advection.F,
231        in seaice_advection.F and advect.F.
232       Update output of experiment seaice_obcs and change exp4 to test OBCS with
233        4th order Adv.Scheme. for pasive salt and ptracer.
234    o tools/genmake2:
235      - when looking for an optfile (not specified), only search for Fortran compiler
236        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
237      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
238        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
239      - set default for CPP to "cpp -traditional -P" (was the case without specifying
240        an optfile, but otherwise default was just "cpp".
241      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
242      - when "CC" is not set in the optfile, look for possible C compiler
243        (instead of just setting CC=cc)
244      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
245        => add a ".F" to ".o" rule for source files with no "#include" (such as
246           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
247      - move gfortran before g77 in list of possible Fortran compiler (consistent
248        with reference compiler switch from g77 to gfortran)
249    o pkg/seaice:
250      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
251        seaice_check that stops the model, when the CPP flag is used.
252      o seaice_growth.F: make capping of ice volume conserving by returning the
253        capped ice as freshwater to EmPmR. This does not change the verification
254        experiments but will change runs where the capping is acutally active
255    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
256      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
257         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
258         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
259    o tools/genmake2:
260      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
261      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
262      - clean previous genmake log files before anything else.
263      - change Makefile to remove testreport log files (*.tr_log) and genmake log
264        files only with "CLEAN" target (instead of "Clean");
265    o pkg/generic_advdiff:
266      Change OBCS in multiDim advection (gad_advection.F):
267       Use maskInC to prevent intermediate update of tracer-field in OB regions,
268       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
269       which were applying future time-step OB values.
270      This way, all explicit calculations use current-time-step OB values
271       (simpler and more consistent).
272      Affects results when set-up uses time-varying OBC and multi-dim advection;
273       update output of experiment seaice_obcs.
274    o pkg/seaice:
275      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
276       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
277         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
278      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
279       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
280       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
281    o pkg aim (2010/10/26):
282      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
283        formulation with obliquity, eccentricity, ... as run-time parameters,
284      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
285        upward shortwave radition at the surface (all-sky and clear-sky).
286    o pkg/obcs:
287      - writing sections with globalFiles=T does not work: switch to tiled-files
288        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
289      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
290      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
291    
292    checkpoint62m (2010/10/21)
293    o pkg/seaice: vectorize seaice_solve4temp.F
294      - move iterations loops outside of i/j-loops
295      - requires 2D arrays for TB and effConduct
296      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
297        modified in this routine
298      - a little bit of clean up, adjusting indentation, etc.
299      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
300        performance and '**TWO' by '**2' (because TWO is a float),
301        replaced ONE, ZERO
302    o eesupp/src:
303       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
304    o pkg/seaice/seaice_growth.F
305      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
306      merging process. The merged routine has two branches, and one activates the 'evolution'
307      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
308      In summary, here is what the '10/10 revision' did consist of
309        part 1: seaice_growth.F revisions 1.71 to 1.75
310          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
311            The emphasis here was on improving readability (e.g. by trying to use meaningful
312            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
313        part 1.5:
314          - revising the lab_sea experiment to make it a more useful (i.e. stable
315            and representative of an actual model run). This was done by generating a
316            (winter) pickup to start from, switching back the main experiment dynamic
317            solver from evp to lsr, having one of the experiments use the free drift solution.
318        part 2: seaice_growth.F revisions 1.76 to 1.85
319          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
320          - Sorting out the various fields units and sign (set early on and reset at the end)
321            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
322            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
323          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
324            and simplifying logical expressions to further improve readibility.
325        part 3: seaice_growth.F revisions 1.86 to 1.89
326          - Re-organize the blocks of code more logically.
327          - Merging the '_if.F' pieces that add something new.
328    o pkg/thsice:
329      - vectorize thsice_solve4temp and thsice_get_exf.
330        Problem: thsice_solve4temp has an unvectorizable statement that
331        might also be problematic for TAF
332      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
333        does not change the verifcation experiment, but will change all
334        experiments that have this flag undefined (not tested in verification);
335        a little reorganization to save a few 2D fields and recomputations
336      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
337      - 2nd step:  fix some store dirs
338        o seems to work somewhat, i.e. using ifort but not g77
339        o likely cause are incomplete init. or recomputation
340        o start verification/global_ocean.cs32x15/input_ad.thsice
341    o pkg/obcs: add support for exch2
342      - the position of the boundary and prescribed values are specified using
343        a global domain with exch2 facets stacked
344        - in x for N,S boundaries (like W2_mapIO=-1)
345        - in y for E,W boundaries (so E,W boundaries do not overlap)
346    o pkg/mdsio: add support for writing global sections with exch2
347        file layout is as for obcs described above:
348        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
349        - for y-z sections, facets are stacked in y
350    o pkg/thsice:
351       - change a few routines for better vectorization: thsice_albedo.F,
352         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
353         not affected, but in particular the latter routine has changed
354         dramatically (not necessarily easier to read now).
355       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
356       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
357    o verification/lab_sea:
358      - overhaul of the forward model experiments. The main motivation
359        for this revision is that lab_sea has proven quite fragile (when
360        changing the sea-ice code, and switching platforms) to a point
361        when failures were very hard to attribute to specific code problems.
362      - the suspected reason for this fragility is noise amplification by evp so,
363        to start with, we decided to replace evp with lsr in the main experiment.
364      - the input.lsr experiment thus became obsolete and was removed.
365      - it was replaced with the input.fd experiment that uses an
366        analytical "free drift" solution as the ice velocity field.
367      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
368        will hopefully allow us to discriminate problems due to dynamic solvers
369        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
370        us to test additional options, along with the salt plume package.
371      - Finally a pickup was generated (at the end of a one year run) to
372        make the tests more representative of an actual model run. Previously
373        the tests starting point was a 1m thickness of ice everywhere.
374    o pkg/seaice:
375      - introducing S\R seaice_freedrift.F that compute the
376        analytical solution to an approximate ice momentum
377        equation (i.e. the simple stress/coriolis balance).
378      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
379        of the free drift velocity field, and enable its use.
380        To actually use the free drift solution as the model ice
381        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
382    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
383    
384    checkpoint62l (2010/10/04)
385    o pkg/seaice:
386      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
387      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
388       version (with USE_ORIGINAL_SBI undef);
389    o add hooks for new packages OASIS, the package will follow
390      (hooks exclude the seaice pkg for now)
391    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
392      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
393      rather than mdsio_readvector.F/mdsio_writevector.F, within
394      adread_adwrite.F to read/write adjoint-related tapes to disk.
395    o eesupp and pkg/mdsio: ALLOW_WHIO
396      Option to write/read 2D fields to files including tiles halos.
397      The main purpose is for adjoint related "tape I/O".
398      The secondary purpose is for debugging phases.
399      A word on those rather specifically intended purposes.
400      The code was meant to be stripped down to the bare minimum.
401      Typically, there is a unique and basic mapping to the global
402      buffer (tile by tile, then proc by proc, then level by level), and
403      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
404      meant to generate user friendly outputs of various shapes and forms.
405      Rather it is intended, for the knowledgeabale developers,
406      to be largely independent of the many mdsio options, to allow
407      outputs of tiles+halos in debugging phases and in adjoint runs,
408      and to allow some flexibility in tuning (adoint) I/O depending on each
409      file system behavior. With regard to tuning, most of the potential knobs
410      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
411      to specify directories, to specify the typical size of I/O calls, etc.)
412      are not yet included, and will be added if they prove useful.
413    o pkg/seaice:
414       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
415    o pkg/seaice:
416       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
417       code (seaice_budget_ice_if.F) which enable to recover old standard
418       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
419       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
420    o model/src (rStar):
421       use simple average (not area weighted) of rStarFac at U,V point when using
422       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
423       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
424    
425    checkpoint62k (2010/09/17)
426    o adjoint
427       * changed verification/global_ocean.cs32x15 ; adjoint now tests
428         Adams-Bashforth 3 + NLFS + RSTAR
429       * some more modifs required for ECCO-GODAE v4
430    o pkg/seaice
431       add SEAICE_AGE_VOL option to use volume instead of area for
432       integrating SEAICE_AGE
433    o model/src:
434       first check-in of sigma & hybrid-sigma coordinate code ; also includes
435       non-linear free-surface parts ; but pressure-gradient not yet coded.
436    o pkg/ptracers:
437       option for ptracer to convert Salt Relax into additional EmP.
438        tested in exp. global_ocean.90x40x15.dwnslp (update output)
439    
440    checkpoint62j (2010/08/25)
441    o pkg/ggl90:
442       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
443    o pkg/dic: car_flux.F, phos_flux.F
444      - reduce number of exp-calls in order to improve performance
445      - clean up a little (replace fields by their macros, etc., fix
446        typo in CPP-flag)
447    o pkg/ggl90: minor changes
448      - GGL90diffKrS was removed --> always use GGL90diffKr
449      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
450      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
451        (commented out for now)
452      - change in max/min operations to ensure that smoothing is ok
453      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
454      - always use diffKrNrT as background profile (i.e. never use diffKr field)
455    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
456    o pkg/dic:
457      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
458        vectorization
459      - small bug fix in insol for the unlikely case of a cartesian grid
460      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
461        + now vectorize, which also removes adjoint recomputations;
462        + replace integer maksp1 by _RL maskp1
463        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
464    
465    checkpoint62i (2010/07/21)
466    o pkg/flt:
467      - with OBCS: stop floats which enter the OB region
468    o model/src:
469      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
470        for implicit vertical advection.
471    o pkg/seaice:
472     - account for melting in seaice age evolution.
473     - remove double counting of seaice ridging effect on seaice age.
474    
475    checkpoint62h (2010/06/18)
476    o pkg/exch2:
477     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
478    o tools/genmake2
479      - remove "-pdefault" option: redundant with the use of "packages.conf";
480      - remove file pkg/pkg_default : set the default as a pkg group
481        ("default_pkg_list") defined in pkg/pkg_groups;
482      - fix for case pkg/pkg_depend is missing (was hanging before);
483      - add option "-pgroups" to specify a different pkg_groups than the default.
484    o verification/adjustment.cs-32x32x1:
485       add a "minimal" set-up test (code_min & input_min) which only compiles
486       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
487    o tools/genmake2
488      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
489      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
490    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
491      files are nearly the same anyway.
492      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
493       - redefinition of tau(i,i) (by a factor of ustar)
494       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
495       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
496       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
497       - replace
498         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
499         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
500         by
501         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
502         (changes results)
503       -> exf_bulkformulae v1.22,
504          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
505          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
506                    output.txt 1.63
507           offline_exf_seaice: output.seaicetd.txt 1.7
508           seaice_obcs: output.txt 1.10)
509      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
510       -> exf_bulkformulae v1.23,
511          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
512          and global_ocean.cs32x15.icedyn (only 11 matching digits)
513      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
514    o adjoint of exch-1:
515     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
516       (note: was already like this when using EXCH-2) and remove flow dir
517       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
518     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
519     - update pkg/exch2 diff list.
520    
521    checkpoint62g (2010/05/19)
522    o eesupp/src (exch-1):
523     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
524       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
525       (renamed to exch1_*rx_cube.F).
526     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
527       to call new exch1 S/R ; update Makefile and .cvsignore.
528     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
529       exch2_xy_rx later)
530      Note: after updating your code, need to run "make clean" in eesupp/src
531    o test experiment bottom_ctrl_5x5:
532       new output_adm.txt with fewer grdchk & less monitor output.
533    o model/src:
534      remove the call to ini_cori in initialise_varia.F (just keep the usual one
535       in initialise_fixed.F). More consistent with coriolis & horizontal grid
536       beeing treated in the same way (ini_grid is not called a 2nd time).
537    o pkg/exf:
538      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
539      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
540      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
541      - cosmetic changes to exf_bulkformulae.F to make it look more like
542        exf_bulk_largeyeager04.F
543    o eesupp/src (exch-1):
544      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
545      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
546        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
547        (even without using MPI).
548      - Message mode: move RecvAck setting (indicator of buffer being ready)
549        from send_put to recv_get S/R (was useless before, but not sure if
550        it's much more useful now);
551      - Switch the order of sync: MPI-proc 1rst and then threads;
552      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
553      - fix AD code for communication mode ='get' (but not used).
554    o model/src:
555      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
556      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
557    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
558    o pkg/ctrl: require a specific set of control variables and exf-flags for
559      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
560    o model/src:
561     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
562       1rst forward sweep, to avoid over-writing output files during recomputations
563       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
564     b) 2nd version:
565      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
566      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
567         writePickupAtEnd) + seaice & ptracers output;
568      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
569    o model/src:
570      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
571    o pkg/exch2:
572      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
573      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
574    o pkg/autodiff & exch2:
575      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
576      (for now, only if ALLOW_EXCH2 is defined).
577    o pkg/autodiff:
578      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
579        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
580       + clean-up comments (_RS is not always real*4)
581      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
582      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
583        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
584    o testreport (AD-tests):
585      no longer link files from dir "../input" (1rst link files from
586      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
587    
588    checkpoint62f (2010/04/29)
589    o model/src/the_main_loop.F:
590      adjust store directives for seaice evp and multicategory according to
591      pkg/ecco/the_main_loop.F
592    o adjoint:
593      global_sum_ad was incomplete (noted many times by many people ;)
594      nice description by Jean U. as follows:
595      * allreduce(var) in global_sum.F can be interpreted as
596        reduce(sum) followed by broadcast of sum.
597      * The adjoint of that is
598        sum(adjoint) followed by broadcast(summed adjoint value)
599        or in other words, allreduce(sum, adjoint vars)
600      We were missing the sum(adjoint)!
601      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
602      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
603      The fix should produce 16-digit accuracy between
604      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
605      multi-CPU single-tile (e.g. nSx=1, nPx-2)
606      We'll probably change this yet again shortly
607    o eesupp/src:
608      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
609    o pkg/icefront
610      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
611        specification of addmass array based on a 2D field, which is added
612        at bottommost wet level at each horizontal location.
613    o model/src:
614     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
615     layout; (not always compatible with delX,delY setting; commented out for now).
616    o pkg/exch2:
617     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
618     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
619    
620    checkpoint62e (2010/04/15)
621    o pkg/obcs:
622      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
623    o pkg/dic:
624      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
625        (note: not presently tested in any forward verification exp.)
626       update tutorial_global_oce_biogeo AD output file.
627    o pkg/exf:
628      - account for the variation of albedo as a function of zenith angle
629        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
630    o build_options:
631     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
632    o pkg/dic:
633      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
634      - use binary pickup file for restart;
635      - initialise atmos-CO2 box from dic_pCO2 parameter;
636      - fix multi-threaded.
637    o pkg/rbcs:
638     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
639       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
640     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
641       and update output.txt
642    o pkg/kpp:
643     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
644     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
645       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
646       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
647     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
648       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
649    o pkg/offline:
650      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
651      (bug was added in version 1.10 on 2007-08-23).
652    o pkg/offline:
653      - no need to specify periodicExternalForcing, etc ... to use offline pack
654      - offline input files no longer just single prec --> parameter offlineLoadPrec
655    o verification/lab_sea:
656      change AD test to multi-tile setup and update all 4 AD output.
657      NOTE: while cost function values remain very similar,
658      gradients are very different, although gradient checks are self-consistent
659      Should try to get to the bottom of this (cost function summation order?)
660    o pkg/dic:
661      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
662      a weakness of TAF that drops part of double precision in log10 derivative.
663      <= changes removed since problem has been fixed in current TAF version 1.9.71
664      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
665    o pkg/ecco:
666      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
667      update all 4 lab_sea AD output.
668    
669    checkpoint62d (2010/03/22)
670    o build_options:
671      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
672    o remove unbalanced quote (single or double) in commented line of source code
673      (may cause some warning with some preprocessor/makedepend versions).
674    o pkg/seaice:
675      fix seaice_model.F for adjoint (gael) and update AD results of experiments
676       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
677    o testreport:
678      add option '-runonly' (short: '-ro') to just do the run part (without make).
679    o eesupp: remove JAM communication code (obsolete).
680    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
681      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
682      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
683      (update also the output).
684    
685  checkpoint62c (2010/03/02)  checkpoint62c (2010/03/02)
686  o tools/build_options :  o tools/build_options :
687     move (some) old optfiles from build_options/ to build_options/unsupported/     move (some) old optfiles from build_options/ to build_options/unsupported/
# Line 21  o tools/build_options: Line 699  o tools/build_options:
699      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
700  o pkg/ecco  o pkg/ecco
701    - allow user defined cost function contributions    - allow user defined cost function contributions
702          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
703          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
704    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
705        the two options are complementary.        the two options are complementary.
706  o pkg/smooth  o pkg/smooth
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