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revision 1.1240 by jmc, Wed Mar 24 02:12:51 2010 UTC revision 1.1378 by gforget, Mon Feb 14 23:59:10 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/seaice:
8     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
9     computing the ice cover tendency from effective thickness tendencies. Include Ian Fenty's formula.
10     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using SEAICEareaFormula.
11     - simplify notations for the various d_HEFF/d_AREA terms.
12    o pkg/gmredi:
13     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
14       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
15       add a verification test-run (front_relax.bvp) to test GM_useBVP.
16    o pkg/seaice:
17     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
18     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to also melt ice.
19    o pkg/seaice:
20     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
21     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
22    o pkg/cheapaml:
23     - from Nico Wienders: New version of this package.
24    o pkg/flt:
25     - add CPP options to prevent floats to re-enter the opposite side of
26       a periodic domain (default: keep periodicity)
27    o pkg/gmredi:
28     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
29       (needed for multi-dim advection).
30     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
31    o model/src:
32     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
33    o tutorial_tracer_adjsens
34     - extend to NLFS and replace maskC by hFacC
35       (change reference output accordingly)
36    
37    checkpoint62r (2011/01/24)
38    o testreport:
39     - add option -deloutp (-do) to remove output file after successful run
40     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
41       extract exact list of procs from this file ; adjust COMMAND by
42       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
43    o pkg/ecco: replace old ineffective way of penalizing deviations from
44      first guess (of obcs) with code by Matt Mazloff
45    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
46      exf/cal
47      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
48        and handle case of obcs?period == 0
49        Not affected by these changes: There is still an inconsistency in
50        the computation of start/endrec for the obcs variables for ALLOW_CAL
51        defined (see comment by Menemenlis, 7-Mar-2003)
52      - make S/R ctrl_get_gen_rec return something meaningful even if
53        ALLOW_CAL is not defined
54      - ctrl_getobcs?: simplify code so that it does not need to use
55                       S/R exf_swapfields
56    o testreport:
57       allow to test MPI with different number of processors for each experiment:
58       create file "SIZE.h.mpi" in each build dir.
59       Note: update of "-command" argument not yet implemented.
60    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
61      alleviate the need for additional 3D tapes when using
62      the non-inear free surface in the adjoint. This is done
63      by adding an 'update' of hfacc etc. to their current
64      value at the beginning of forward_step.F.
65    o pkg/seaice
66      seaice_lsr: move stress-divergence computations out of outer pseudo-
67      timestepping loop
68    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
69      up, so that the calls of the ctrl_* subroutines are really at the end
70      of the routine.
71    o pkg/gmredi:
72      allow to specify a 2-D horizontal map and a 1-D vertical profil
73      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
74    o pkg/seaice:
75      move lsr iterations from seaice_dynsolver to seaice_lsr.
76    o pkg/seaice:
77      reduce memory footprint of seaice mutldim advection tapes,
78      by using a 2D tape independent of the generic_advdiff ones,
79      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
80    
81    checkpoint62q (2010/12/29)
82    o model/src:
83      - check horizontal grid-spacing for unset or zero/negative values.
84      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
85    o pkg/flt:
86      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
87      - precision of input and output files set according to readBinaryPrec
88        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
89      - initial float position from tiled file was not converted to index space
90        (looks like a bug): fixed to make it similar to initial pos. global file.
91    o global_ocean.cs32x15:
92       change SIZE.h of AD set-up to get same tiling as with MPI.
93       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
94    o model/src:
95       add flag to control printing of domain fields (bathymetry, hFac ...) in
96       ini_mask_etc (call to plot_fieds_xy*).
97    o pkg/thsice:
98       if useEXF, some forcing fields are not valid in overlap: fixed by computing
99       over the interior only + apply EXCH at the end (like with SEAICE advection).
100    o pkg/mdsio:
101      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
102        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
103      - change barrier call for safe multi-threads access to 3-D shared buffer.
104      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
105      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
106        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
107    o pkg/flt:
108      - add fourth-order Runge-Kutta integration
109      - add basic exch2 support (only 1 facet supported so far!)
110    o pkg/mdsio+rw:
111      new S/R to read local (or tile independent) vector (read counterpart of
112       mds_writevec_loc, and front-end write_glvec_rl/rs).
113    o global_ocean.cs32x15: additional input_ad.seaice experiment
114        that uses pkg/seaice rather than pkg/thsice.
115        (using multidim advection for seaice)
116    o towards more F95 syntax for array specification in namelist:
117      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
118        of all verification experiments.
119           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
120          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
121      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
122    o global_ocean.cs32x15: additional input.seaice experiment
123        that uses pkg/seaice rather than pkg/thsice.
124    
125    checkpoint62p (2010/12/17)
126    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
127        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
128    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
129        allow for use of multim. advection in seaice adjoint.
130    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
131      - first attempt to close budgets by taking into account the freshwater
132        flux implied by the sublimation of snow and ice. So far only the
133        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
134        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
135    o eesupp/src:
136      new S/R with new option (NML_EXTENDED_F77) to change array specification
137      from F95 standard to commonly accepted extended F77 form.
138      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
139      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
140      for less tolerant f77 compiler (e.g., pgf77, g77).
141    o globalFiles:
142      commented out in parameter file "data" since it's not safe with MPI
143      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
144      in this case); no longer commented out in restart test (tst_2+2).
145    o add adTapeDir to specify a special directory where adjoint tapes are
146      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
147      and cannot be used together with mdsioLocalDir.
148    o nesting pkgs:
149      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
150      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
151      - add parameter files + utils dir + output from short run on beagle.
152    o pkg/seaice:
153        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
154    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
155      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
156    
157    checkpoint62o (2010/11/25)
158    o pkg/exf:
159      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
160    o pkg/seaice:
161      - seaice_ocean_stress: split a loop for better vectorization of the
162        adjoint code
163      - seaice_growth.F: fix bug in conservation of freshwater connected to
164        capping of heff, put contribution into d_HEFFbyNEG
165      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
166        by something more sensible (parameters that are what their name implies)
167      - change some defaults, so that by default exf-parameters are used for
168        things like rhoAir, cpAir,latent/sensible heat parameters, in order
169        to reproduce the old results, many data.seaice now contain funny values
170        for cpAir and latent heat of sublimation
171    o packages_readparms.F: move exf_readparms up in line so that
172        exf-parameters are visible for other packages (e.g. seaice)
173    o debugMode & debugLevel=2:
174      - differentiate between debugMode & debugLevel=2:
175        debugMode: controls printing of debug messages (sequence of S/R calls).
176        debugLevel: controls printing of algorithm intermediate results and stats.
177      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
178        => allows to print debug-stats without all sequence of call messages.
179      - switch control of debug print from debugLevel to debugMode in many S/R.
180    o pkg/obcs (obcs-sponge):
181        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
182        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
183    o pkg/generic_advdiff:
184      - record overlap minimum size for each advection scheme;
185      - refine criteria on overlap minimum size;
186      - check and stop (in gad_check) if overlap size is too small.
187    o pkg/obcs:
188      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
189        once, in ptracers_implicit.F)
190      - with seaice: remove test on empty file name in obcs_apply_seaice (always
191        apply OB values when tile has OB)
192    o model/src, coriolis setting:
193      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
194        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
195        files (selectCoriMap=3) with any grid.
196      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
197    o pkg/seaice/seaice_growth.F:
198        a few cosmetic changes that reduce the number of lines of code
199    o pkg/obcs: add boundary conditions following Stevens (1990)
200      - the code follows old MOM/NAOSIM code
201      - so far it is only implemented for the eastern and western boundaries
202        and NOT for pTracers
203    o pkg/rbcs:
204      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
205        beginning of the first rbcs forcing period.
206      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
207        offline package, i.e., one file per time, labeled by iteration number;
208        deltaTrbcs sets the timestep with which the data was generated;
209        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
210      - rbcsForcingCycle=0 makes forcing non-cyclic.
211      - make arithmetic safe for negative times and odd forcing periods.
212    
213    checkpoint62n (2010/11/09)
214    o pkg/seaice:
215        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
216    o pkg/obcs:
217       New S/R to copy tracer value from the OB location to narrow band region
218        (width = same as overlap) beyond the OB: preserve OB value (needed for
219        high-order scheme) which were overwritten by EXCH call if in overlap
220        region. Applied to theta, salt, ptracer and advected seaice variables.
221       With seaice: use maskInC in similar way as in gad_advection.F,
222        in seaice_advection.F and advect.F.
223       Update output of experiment seaice_obcs and change exp4 to test OBCS with
224        4th order Adv.Scheme. for pasive salt and ptracer.
225    o tools/genmake2:
226      - when looking for an optfile (not specified), only search for Fortran compiler
227        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
228      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
229        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
230      - set default for CPP to "cpp -traditional -P" (was the case without specifying
231        an optfile, but otherwise default was just "cpp".
232      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
233      - when "CC" is not set in the optfile, look for possible C compiler
234        (instead of just setting CC=cc)
235      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
236        => add a ".F" to ".o" rule for source files with no "#include" (such as
237           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
238      - move gfortran before g77 in list of possible Fortran compiler (consistent
239        with reference compiler switch from g77 to gfortran)
240    o pkg/seaice:
241      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
242        seaice_check that stops the model, when the CPP flag is used.
243      o seaice_growth.F: make capping of ice volume conserving by returning the
244        capped ice as freshwater to EmPmR. This does not change the verification
245        experiments but will change runs where the capping is acutally active
246    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
247      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
248         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
249         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
250    o tools/genmake2:
251      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
252      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
253      - clean previous genmake log files before anything else.
254      - change Makefile to remove testreport log files (*.tr_log) and genmake log
255        files only with "CLEAN" target (instead of "Clean");
256    o pkg/generic_advdiff:
257      Change OBCS in multiDim advection (gad_advection.F):
258       Use maskInC to prevent intermediate update of tracer-field in OB regions,
259       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
260       which were applying future time-step OB values.
261      This way, all explicit calculations use current-time-step OB values
262       (simpler and more consistent).
263      Affects results when set-up uses time-varying OBC and multi-dim advection;
264       update output of experiment seaice_obcs.
265    o pkg/seaice:
266      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
267       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
268         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
269      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
270       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
271       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
272    o pkg aim (2010/10/26):
273      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
274        formulation with obliquity, eccentricity, ... as run-time parameters,
275      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
276        upward shortwave radition at the surface (all-sky and clear-sky).
277    o pkg/obcs:
278      - writing sections with globalFiles=T does not work: switch to tiled-files
279        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
280      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
281      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
282    
283    checkpoint62m (2010/10/21)
284    o pkg/seaice: vectorize seaice_solve4temp.F
285      - move iterations loops outside of i/j-loops
286      - requires 2D arrays for TB and effConduct
287      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
288        modified in this routine
289      - a little bit of clean up, adjusting indentation, etc.
290      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
291        performance and '**TWO' by '**2' (because TWO is a float),
292        replaced ONE, ZERO
293    o eesupp/src:
294       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
295    o pkg/seaice/seaice_growth.F
296      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
297      merging process. The merged routine has two branches, and one activates the 'evolution'
298      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
299      In summary, here is what the '10/10 revision' did consist of
300        part 1: seaice_growth.F revisions 1.71 to 1.75
301          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
302            The emphasis here was on improving readability (e.g. by trying to use meaningful
303            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
304        part 1.5:
305          - revising the lab_sea experiment to make it a more useful (i.e. stable
306            and representative of an actual model run). This was done by generating a
307            (winter) pickup to start from, switching back the main experiment dynamic
308            solver from evp to lsr, having one of the experiments use the free drift solution.
309        part 2: seaice_growth.F revisions 1.76 to 1.85
310          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
311          - Sorting out the various fields units and sign (set early on and reset at the end)
312            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
313            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
314          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
315            and simplifying logical expressions to further improve readibility.
316        part 3: seaice_growth.F revisions 1.86 to 1.89
317          - Re-organize the blocks of code more logically.
318          - Merging the '_if.F' pieces that add something new.
319    o pkg/thsice:
320      - vectorize thsice_solve4temp and thsice_get_exf.
321        Problem: thsice_solve4temp has an unvectorizable statement that
322        might also be problematic for TAF
323      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
324        does not change the verifcation experiment, but will change all
325        experiments that have this flag undefined (not tested in verification);
326        a little reorganization to save a few 2D fields and recomputations
327      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
328      - 2nd step:  fix some store dirs
329        o seems to work somewhat, i.e. using ifort but not g77
330        o likely cause are incomplete init. or recomputation
331        o start verification/global_ocean.cs32x15/input_ad.thsice
332    o pkg/obcs: add support for exch2
333      - the position of the boundary and prescribed values are specified using
334        a global domain with exch2 facets stacked
335        - in x for N,S boundaries (like W2_mapIO=-1)
336        - in y for E,W boundaries (so E,W boundaries do not overlap)
337    o pkg/mdsio: add support for writing global sections with exch2
338        file layout is as for obcs described above:
339        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
340        - for y-z sections, facets are stacked in y
341    o pkg/thsice:
342       - change a few routines for better vectorization: thsice_albedo.F,
343         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
344         not affected, but in particular the latter routine has changed
345         dramatically (not necessarily easier to read now).
346       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
347       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
348    o verification/lab_sea:
349      - overhaul of the forward model experiments. The main motivation
350        for this revision is that lab_sea has proven quite fragile (when
351        changing the sea-ice code, and switching platforms) to a point
352        when failures were very hard to attribute to specific code problems.
353      - the suspected reason for this fragility is noise amplification by evp so,
354        to start with, we decided to replace evp with lsr in the main experiment.
355      - the input.lsr experiment thus became obsolete and was removed.
356      - it was replaced with the input.fd experiment that uses an
357        analytical "free drift" solution as the ice velocity field.
358      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
359        will hopefully allow us to discriminate problems due to dynamic solvers
360        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
361        us to test additional options, along with the salt plume package.
362      - Finally a pickup was generated (at the end of a one year run) to
363        make the tests more representative of an actual model run. Previously
364        the tests starting point was a 1m thickness of ice everywhere.
365    o pkg/seaice:
366      - introducing S\R seaice_freedrift.F that compute the
367        analytical solution to an approximate ice momentum
368        equation (i.e. the simple stress/coriolis balance).
369      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
370        of the free drift velocity field, and enable its use.
371        To actually use the free drift solution as the model ice
372        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
373    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
374    
375    checkpoint62l (2010/10/04)
376    o pkg/seaice:
377      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
378      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
379       version (with USE_ORIGINAL_SBI undef);
380    o add hooks for new packages OASIS, the package will follow
381      (hooks exclude the seaice pkg for now)
382    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
383      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
384      rather than mdsio_readvector.F/mdsio_writevector.F, within
385      adread_adwrite.F to read/write adjoint-related tapes to disk.
386    o eesupp and pkg/mdsio: ALLOW_WHIO
387      Option to write/read 2D fields to files including tiles halos.
388      The main purpose is for adjoint related "tape I/O".
389      The secondary purpose is for debugging phases.
390      A word on those rather specifically intended purposes.
391      The code was meant to be stripped down to the bare minimum.
392      Typically, there is a unique and basic mapping to the global
393      buffer (tile by tile, then proc by proc, then level by level), and
394      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
395      meant to generate user friendly outputs of various shapes and forms.
396      Rather it is intended, for the knowledgeabale developers,
397      to be largely independent of the many mdsio options, to allow
398      outputs of tiles+halos in debugging phases and in adjoint runs,
399      and to allow some flexibility in tuning (adoint) I/O depending on each
400      file system behavior. With regard to tuning, most of the potential knobs
401      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
402      to specify directories, to specify the typical size of I/O calls, etc.)
403      are not yet included, and will be added if they prove useful.
404    o pkg/seaice:
405       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
406    o pkg/seaice:
407       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
408       code (seaice_budget_ice_if.F) which enable to recover old standard
409       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
410       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
411    o model/src (rStar):
412       use simple average (not area weighted) of rStarFac at U,V point when using
413       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
414       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
415    
416    checkpoint62k (2010/09/17)
417    o adjoint
418       * changed verification/global_ocean.cs32x15 ; adjoint now tests
419         Adams-Bashforth 3 + NLFS + RSTAR
420       * some more modifs required for ECCO-GODAE v4
421    o pkg/seaice
422       add SEAICE_AGE_VOL option to use volume instead of area for
423       integrating SEAICE_AGE
424    o model/src:
425       first check-in of sigma & hybrid-sigma coordinate code ; also includes
426       non-linear free-surface parts ; but pressure-gradient not yet coded.
427    o pkg/ptracers:
428       option for ptracer to convert Salt Relax into additional EmP.
429        tested in exp. global_ocean.90x40x15.dwnslp (update output)
430    
431    checkpoint62j (2010/08/25)
432    o pkg/ggl90:
433       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
434    o pkg/dic: car_flux.F, phos_flux.F
435      - reduce number of exp-calls in order to improve performance
436      - clean up a little (replace fields by their macros, etc., fix
437        typo in CPP-flag)
438    o pkg/ggl90: minor changes
439      - GGL90diffKrS was removed --> always use GGL90diffKr
440      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
441      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
442        (commented out for now)
443      - change in max/min operations to ensure that smoothing is ok
444      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
445      - always use diffKrNrT as background profile (i.e. never use diffKr field)
446    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
447    o pkg/dic:
448      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
449        vectorization
450      - small bug fix in insol for the unlikely case of a cartesian grid
451      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
452        + now vectorize, which also removes adjoint recomputations;
453        + replace integer maksp1 by _RL maskp1
454        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
455    
456    checkpoint62i (2010/07/21)
457    o pkg/flt:
458      - with OBCS: stop floats which enter the OB region
459    o model/src:
460      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
461        for implicit vertical advection.
462    o pkg/seaice:
463     - account for melting in seaice age evolution.
464     - remove double counting of seaice ridging effect on seaice age.
465    
466    checkpoint62h (2010/06/18)
467    o pkg/exch2:
468     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
469    o tools/genmake2
470      - remove "-pdefault" option: redundant with the use of "packages.conf";
471      - remove file pkg/pkg_default : set the default as a pkg group
472        ("default_pkg_list") defined in pkg/pkg_groups;
473      - fix for case pkg/pkg_depend is missing (was hanging before);
474      - add option "-pgroups" to specify a different pkg_groups than the default.
475    o verification/adjustment.cs-32x32x1:
476       add a "minimal" set-up test (code_min & input_min) which only compiles
477       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
478    o tools/genmake2
479      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
480      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
481    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
482      files are nearly the same anyway.
483      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
484       - redefinition of tau(i,i) (by a factor of ustar)
485       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
486       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
487       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
488       - replace
489         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
490         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
491         by
492         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
493         (changes results)
494       -> exf_bulkformulae v1.22,
495          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
496          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
497                    output.txt 1.63
498           offline_exf_seaice: output.seaicetd.txt 1.7
499           seaice_obcs: output.txt 1.10)
500      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
501       -> exf_bulkformulae v1.23,
502          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
503          and global_ocean.cs32x15.icedyn (only 11 matching digits)
504      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
505    o adjoint of exch-1:
506     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
507       (note: was already like this when using EXCH-2) and remove flow dir
508       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
509     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
510     - update pkg/exch2 diff list.
511    
512    checkpoint62g (2010/05/19)
513    o eesupp/src (exch-1):
514     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
515       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
516       (renamed to exch1_*rx_cube.F).
517     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
518       to call new exch1 S/R ; update Makefile and .cvsignore.
519     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
520       exch2_xy_rx later)
521      Note: after updating your code, need to run "make clean" in eesupp/src
522    o test experiment bottom_ctrl_5x5:
523       new output_adm.txt with fewer grdchk & less monitor output.
524    o model/src:
525      remove the call to ini_cori in initialise_varia.F (just keep the usual one
526       in initialise_fixed.F). More consistent with coriolis & horizontal grid
527       beeing treated in the same way (ini_grid is not called a 2nd time).
528    o pkg/exf:
529      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
530      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
531      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
532      - cosmetic changes to exf_bulkformulae.F to make it look more like
533        exf_bulk_largeyeager04.F
534    o eesupp/src (exch-1):
535      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
536      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
537        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
538        (even without using MPI).
539      - Message mode: move RecvAck setting (indicator of buffer being ready)
540        from send_put to recv_get S/R (was useless before, but not sure if
541        it's much more useful now);
542      - Switch the order of sync: MPI-proc 1rst and then threads;
543      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
544      - fix AD code for communication mode ='get' (but not used).
545    o model/src:
546      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
547      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
548    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
549    o pkg/ctrl: require a specific set of control variables and exf-flags for
550      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
551    o model/src:
552     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
553       1rst forward sweep, to avoid over-writing output files during recomputations
554       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
555     b) 2nd version:
556      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
557      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
558         writePickupAtEnd) + seaice & ptracers output;
559      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
560    o model/src:
561      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
562    o pkg/exch2:
563      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
564      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
565    o pkg/autodiff & exch2:
566      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
567      (for now, only if ALLOW_EXCH2 is defined).
568    o pkg/autodiff:
569      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
570        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
571       + clean-up comments (_RS is not always real*4)
572      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
573      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
574        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
575    o testreport (AD-tests):
576      no longer link files from dir "../input" (1rst link files from
577      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
578    
579    checkpoint62f (2010/04/29)
580    o model/src/the_main_loop.F:
581      adjust store directives for seaice evp and multicategory according to
582      pkg/ecco/the_main_loop.F
583    o adjoint:
584      global_sum_ad was incomplete (noted many times by many people ;)
585      nice description by Jean U. as follows:
586      * allreduce(var) in global_sum.F can be interpreted as
587        reduce(sum) followed by broadcast of sum.
588      * The adjoint of that is
589        sum(adjoint) followed by broadcast(summed adjoint value)
590        or in other words, allreduce(sum, adjoint vars)
591      We were missing the sum(adjoint)!
592      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
593      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
594      The fix should produce 16-digit accuracy between
595      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
596      multi-CPU single-tile (e.g. nSx=1, nPx-2)
597      We'll probably change this yet again shortly
598    o eesupp/src:
599      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
600    o pkg/icefront
601      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
602        specification of addmass array based on a 2D field, which is added
603        at bottommost wet level at each horizontal location.
604    o model/src:
605     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
606     layout; (not always compatible with delX,delY setting; commented out for now).
607    o pkg/exch2:
608     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
609     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
610    
611    checkpoint62e (2010/04/15)
612    o pkg/obcs:
613      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
614    o pkg/dic:
615      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
616        (note: not presently tested in any forward verification exp.)
617       update tutorial_global_oce_biogeo AD output file.
618    o pkg/exf:
619      - account for the variation of albedo as a function of zenith angle
620        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
621    o build_options:
622     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
623    o pkg/dic:
624      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
625      - use binary pickup file for restart;
626      - initialise atmos-CO2 box from dic_pCO2 parameter;
627      - fix multi-threaded.
628    o pkg/rbcs:
629     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
630       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
631     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
632       and update output.txt
633    o pkg/kpp:
634     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
635     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
636       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
637       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
638     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
639       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
640    o pkg/offline:
641      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
642      (bug was added in version 1.10 on 2007-08-23).
643    o pkg/offline:
644      - no need to specify periodicExternalForcing, etc ... to use offline pack
645      - offline input files no longer just single prec --> parameter offlineLoadPrec
646    o verification/lab_sea:
647      change AD test to multi-tile setup and update all 4 AD output.
648      NOTE: while cost function values remain very similar,
649      gradients are very different, although gradient checks are self-consistent
650      Should try to get to the bottom of this (cost function summation order?)
651    o pkg/dic:
652      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
653      a weakness of TAF that drops part of double precision in log10 derivative.
654      <= changes removed since problem has been fixed in current TAF version 1.9.71
655      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
656  o pkg/ecco:  o pkg/ecco:
657    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
658    update all 4 lab_sea AD output.    update all 4 lab_sea AD output.
# Line 41  o tools/build_options: Line 690  o tools/build_options:
690      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
691  o pkg/ecco  o pkg/ecco
692    - allow user defined cost function contributions    - allow user defined cost function contributions
693          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
694          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
695    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
696        the two options are complementary.        the two options are complementary.
697  o pkg/smooth  o pkg/smooth
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