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revision 1.1272 by mlosch, Tue May 18 12:26:54 2010 UTC revision 1.1390 by mlosch, Mon Mar 7 09:46:50 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/exf:  o pkg/ctrl/ecco/grdchk:
8      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
9        Fortunately, we do no have any tests for the numerous cpp-flagged
10        option of "obcs as control parameters" so we will never know
11        if this is an improvement (but at least now things compile).
12      - remove an obsolete initialization from ecco_cost_init_barfiles.F
13      - fix some problems within never used ifdefs to make the code compile
14    o pkg/obcs:
15     - Refine Interior mask definition to work with more complex OB (e.g.
16       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
17       read in Interior mask from file. Check if Interior mask is consistent
18       with OB list of indices.
19    o pkg/seaice
20     - beginning code for a seaice tracer package,
21       but currently only used for seaice age: SEAICE_AGE
22       SEAICE_num = 4
23       iTracer = 1: area-weighted ice age
24               = 2: volume-weighted ice age
25               = 3, 4: template for one-year vs. multi-year ice
26       data.seaice has new namelist SEAICE_PARM03 for arrays related to
27       SEAICE_num
28    
29    checkpoint62t (2011/03/05)
30    o pkg/obcs:
31     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
32       then normal component. This ensures that the normal component is set
33       correctly even when it conficts with tangential setting from an other OB.
34       Affects results of test-experiment seaice_obcs: update the output.txt
35    o pkg/obcs:
36     - add code to monitor statistics of dynamical fields at OB.
37     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
38       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
39       - change default: balance the Net inflow through all OB (instead of balancing
40         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
41     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
42       to match Nortern OB inflow (OBCS_balanceFacN=0).
43    o pkg/seaice:
44     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
45    o pkg/seaice (seaice_growth v 1.113):
46     - reverting seaice_growth to v 1.111 in order to have code with exact bit
47       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
48       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
49       runtime flag SEAICEareaFormula is kept but is inactive
50    o model/src:
51     - add new param to scale curvilinear grid distance and area when using
52       a different sphere radius from the grid-files.
53     - test/check multi-threads EXCH applied to local variable (cg2d_x)
54    o adjoint:
55     - enable adjoint of Stevens OB
56     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
57       (a bit delicate because of potentially modified adj. common block structure;
58       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
59    
60    checkpoint62s (2011/02/15)
61    o pkg/seaice (seaice_growth v 1.112):
62     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
63       computing the ice cover tendency from effective thickness tendencies. Include
64       Ian Fenty's formula.
65     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
66       SEAICEareaFormula.
67     - simplify notations for the various d_HEFF/d_AREA terms.
68    o pkg/gmredi:
69     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
70       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
71       add a verification test-run (front_relax.bvp) to test GM_useBVP.
72    o pkg/seaice (seaice_growth v 1.111):
73     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
74     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
75       also melt ice.
76    o pkg/seaice:
77     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
78     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
79    o pkg/cheapaml:
80     - from Nico Wienders: New version of this package.
81    o pkg/flt:
82     - add CPP options to prevent floats to re-enter the opposite side of
83       a periodic domain (default: keep periodicity)
84    o pkg/gmredi:
85     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
86       (needed for multi-dim advection).
87     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
88    o model/src:
89     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
90    o tutorial_tracer_adjsens
91     - extend to NLFS and replace maskC by hFacC
92       (change reference output accordingly)
93    
94    checkpoint62r (2011/01/24)
95    o testreport:
96     - add option -deloutp (-do) to remove output file after successful run
97     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
98       extract exact list of procs from this file ; adjust COMMAND by
99       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
100    o pkg/ecco: replace old ineffective way of penalizing deviations from
101      first guess (of obcs) with code by Matt Mazloff
102    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
103      exf/cal
104      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
105        and handle case of obcs?period == 0
106        Not affected by these changes: There is still an inconsistency in
107        the computation of start/endrec for the obcs variables for ALLOW_CAL
108        defined (see comment by Menemenlis, 7-Mar-2003)
109      - make S/R ctrl_get_gen_rec return something meaningful even if
110        ALLOW_CAL is not defined
111      - ctrl_getobcs?: simplify code so that it does not need to use
112                       S/R exf_swapfields
113    o testreport:
114       allow to test MPI with different number of processors for each experiment:
115       create file "SIZE.h.mpi" in each build dir.
116       Note: update of "-command" argument not yet implemented.
117    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
118      alleviate the need for additional 3D tapes when using
119      the non-inear free surface in the adjoint. This is done
120      by adding an 'update' of hfacc etc. to their current
121      value at the beginning of forward_step.F.
122    o pkg/seaice
123      seaice_lsr: move stress-divergence computations out of outer pseudo-
124      timestepping loop
125    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
126      up, so that the calls of the ctrl_* subroutines are really at the end
127      of the routine.
128    o pkg/gmredi:
129      allow to specify a 2-D horizontal map and a 1-D vertical profil
130      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
131    o pkg/seaice:
132      move lsr iterations from seaice_dynsolver to seaice_lsr.
133    o pkg/seaice:
134      reduce memory footprint of seaice mutldim advection tapes,
135      by using a 2D tape independent of the generic_advdiff ones,
136      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
137    
138    checkpoint62q (2010/12/29)
139    o model/src:
140      - check horizontal grid-spacing for unset or zero/negative values.
141      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
142    o pkg/flt:
143      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
144      - precision of input and output files set according to readBinaryPrec
145        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
146      - initial float position from tiled file was not converted to index space
147        (looks like a bug): fixed to make it similar to initial pos. global file.
148    o global_ocean.cs32x15:
149       change SIZE.h of AD set-up to get same tiling as with MPI.
150       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
151    o model/src:
152       add flag to control printing of domain fields (bathymetry, hFac ...) in
153       ini_mask_etc (call to plot_fieds_xy*).
154    o pkg/thsice:
155       if useEXF, some forcing fields are not valid in overlap: fixed by computing
156       over the interior only + apply EXCH at the end (like with SEAICE advection).
157    o pkg/mdsio:
158      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
159        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
160      - change barrier call for safe multi-threads access to 3-D shared buffer.
161      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
162      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
163        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
164    o pkg/flt:
165      - add fourth-order Runge-Kutta integration
166      - add basic exch2 support (only 1 facet supported so far!)
167    o pkg/mdsio+rw:
168      new S/R to read local (or tile independent) vector (read counterpart of
169       mds_writevec_loc, and front-end write_glvec_rl/rs).
170    o global_ocean.cs32x15: additional input_ad.seaice experiment
171        that uses pkg/seaice rather than pkg/thsice.
172        (using multidim advection for seaice)
173    o towards more F95 syntax for array specification in namelist:
174      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
175        of all verification experiments.
176           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
177          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
178      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
179    o global_ocean.cs32x15: additional input.seaice experiment
180        that uses pkg/seaice rather than pkg/thsice.
181    
182    checkpoint62p (2010/12/17)
183    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
184        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
185    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
186        allow for use of multim. advection in seaice adjoint.
187    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
188      - first attempt to close budgets by taking into account the freshwater
189        flux implied by the sublimation of snow and ice. So far only the
190        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
191        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
192    o eesupp/src:
193      new S/R with new option (NML_EXTENDED_F77) to change array specification
194      from F95 standard to commonly accepted extended F77 form.
195      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
196      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
197      for less tolerant f77 compiler (e.g., pgf77, g77).
198    o globalFiles:
199      commented out in parameter file "data" since it's not safe with MPI
200      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
201      in this case); no longer commented out in restart test (tst_2+2).
202    o add adTapeDir to specify a special directory where adjoint tapes are
203      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
204      and cannot be used together with mdsioLocalDir.
205    o nesting pkgs:
206      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
207      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
208      - add parameter files + utils dir + output from short run on beagle.
209    o pkg/seaice:
210        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
211    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
212      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
213    
214    checkpoint62o (2010/11/25)
215    o pkg/exf:
216      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
217    o pkg/seaice:
218      - seaice_ocean_stress: split a loop for better vectorization of the
219        adjoint code
220      - seaice_growth.F: fix bug in conservation of freshwater connected to
221        capping of heff, put contribution into d_HEFFbyNEG
222      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
223        by something more sensible (parameters that are what their name implies)
224      - change some defaults, so that by default exf-parameters are used for
225        things like rhoAir, cpAir,latent/sensible heat parameters, in order
226        to reproduce the old results, many data.seaice now contain funny values
227        for cpAir and latent heat of sublimation
228    o packages_readparms.F: move exf_readparms up in line so that
229        exf-parameters are visible for other packages (e.g. seaice)
230    o debugMode & debugLevel=2:
231      - differentiate between debugMode & debugLevel=2:
232        debugMode: controls printing of debug messages (sequence of S/R calls).
233        debugLevel: controls printing of algorithm intermediate results and stats.
234      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
235        => allows to print debug-stats without all sequence of call messages.
236      - switch control of debug print from debugLevel to debugMode in many S/R.
237    o pkg/obcs (obcs-sponge):
238        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
239        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
240    o pkg/generic_advdiff:
241      - record overlap minimum size for each advection scheme;
242      - refine criteria on overlap minimum size;
243      - check and stop (in gad_check) if overlap size is too small.
244    o pkg/obcs:
245      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
246        once, in ptracers_implicit.F)
247      - with seaice: remove test on empty file name in obcs_apply_seaice (always
248        apply OB values when tile has OB)
249    o model/src, coriolis setting:
250      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
251        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
252        files (selectCoriMap=3) with any grid.
253      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
254    o pkg/seaice/seaice_growth.F:
255        a few cosmetic changes that reduce the number of lines of code
256    o pkg/obcs: add boundary conditions following Stevens (1990)
257      - the code follows old MOM/NAOSIM code
258      - so far it is only implemented for the eastern and western boundaries
259        and NOT for pTracers
260    o pkg/rbcs:
261      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
262        beginning of the first rbcs forcing period.
263      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
264        offline package, i.e., one file per time, labeled by iteration number;
265        deltaTrbcs sets the timestep with which the data was generated;
266        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
267      - rbcsForcingCycle=0 makes forcing non-cyclic.
268      - make arithmetic safe for negative times and odd forcing periods.
269    
270    checkpoint62n (2010/11/09)
271    o pkg/seaice:
272        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
273    o pkg/obcs:
274       New S/R to copy tracer value from the OB location to narrow band region
275        (width = same as overlap) beyond the OB: preserve OB value (needed for
276        high-order scheme) which were overwritten by EXCH call if in overlap
277        region. Applied to theta, salt, ptracer and advected seaice variables.
278       With seaice: use maskInC in similar way as in gad_advection.F,
279        in seaice_advection.F and advect.F.
280       Update output of experiment seaice_obcs and change exp4 to test OBCS with
281        4th order Adv.Scheme. for pasive salt and ptracer.
282    o tools/genmake2:
283      - when looking for an optfile (not specified), only search for Fortran compiler
284        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
285      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
286        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
287      - set default for CPP to "cpp -traditional -P" (was the case without specifying
288        an optfile, but otherwise default was just "cpp".
289      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
290      - when "CC" is not set in the optfile, look for possible C compiler
291        (instead of just setting CC=cc)
292      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
293        => add a ".F" to ".o" rule for source files with no "#include" (such as
294           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
295      - move gfortran before g77 in list of possible Fortran compiler (consistent
296        with reference compiler switch from g77 to gfortran)
297    o pkg/seaice:
298      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
299        seaice_check that stops the model, when the CPP flag is used.
300      o seaice_growth.F: make capping of ice volume conserving by returning the
301        capped ice as freshwater to EmPmR. This does not change the verification
302        experiments but will change runs where the capping is acutally active
303    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
304      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
305         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
306         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
307    o tools/genmake2:
308      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
309      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
310      - clean previous genmake log files before anything else.
311      - change Makefile to remove testreport log files (*.tr_log) and genmake log
312        files only with "CLEAN" target (instead of "Clean");
313    o pkg/generic_advdiff:
314      Change OBCS in multiDim advection (gad_advection.F):
315       Use maskInC to prevent intermediate update of tracer-field in OB regions,
316       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
317       which were applying future time-step OB values.
318      This way, all explicit calculations use current-time-step OB values
319       (simpler and more consistent).
320      Affects results when set-up uses time-varying OBC and multi-dim advection;
321       update output of experiment seaice_obcs.
322    o pkg/seaice:
323      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
324       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
325         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
326      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
327       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
328       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
329    o pkg aim (2010/10/26):
330      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
331        formulation with obliquity, eccentricity, ... as run-time parameters,
332      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
333        upward shortwave radition at the surface (all-sky and clear-sky).
334    o pkg/obcs:
335      - writing sections with globalFiles=T does not work: switch to tiled-files
336        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
337      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
338      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
339    
340    checkpoint62m (2010/10/21)
341    o pkg/seaice: vectorize seaice_solve4temp.F
342      - move iterations loops outside of i/j-loops
343      - requires 2D arrays for TB and effConduct
344      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
345        modified in this routine
346      - a little bit of clean up, adjusting indentation, etc.
347      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
348        performance and '**TWO' by '**2' (because TWO is a float),
349        replaced ONE, ZERO
350    o eesupp/src:
351       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
352    o pkg/seaice/seaice_growth.F
353      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
354      merging process. The merged routine has two branches, and one activates the 'evolution'
355      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
356      In summary, here is what the '10/10 revision' did consist of
357        part 1: seaice_growth.F revisions 1.71 to 1.75
358          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
359            The emphasis here was on improving readability (e.g. by trying to use meaningful
360            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
361        part 1.5:
362          - revising the lab_sea experiment to make it a more useful (i.e. stable
363            and representative of an actual model run). This was done by generating a
364            (winter) pickup to start from, switching back the main experiment dynamic
365            solver from evp to lsr, having one of the experiments use the free drift solution.
366        part 2: seaice_growth.F revisions 1.76 to 1.85
367          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
368          - Sorting out the various fields units and sign (set early on and reset at the end)
369            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
370            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
371          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
372            and simplifying logical expressions to further improve readibility.
373        part 3: seaice_growth.F revisions 1.86 to 1.89
374          - Re-organize the blocks of code more logically.
375          - Merging the '_if.F' pieces that add something new.
376    o pkg/thsice:
377      - vectorize thsice_solve4temp and thsice_get_exf.
378        Problem: thsice_solve4temp has an unvectorizable statement that
379        might also be problematic for TAF
380      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
381        does not change the verifcation experiment, but will change all
382        experiments that have this flag undefined (not tested in verification);
383        a little reorganization to save a few 2D fields and recomputations
384      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
385      - 2nd step:  fix some store dirs
386        o seems to work somewhat, i.e. using ifort but not g77
387        o likely cause are incomplete init. or recomputation
388        o start verification/global_ocean.cs32x15/input_ad.thsice
389    o pkg/obcs: add support for exch2
390      - the position of the boundary and prescribed values are specified using
391        a global domain with exch2 facets stacked
392        - in x for N,S boundaries (like W2_mapIO=-1)
393        - in y for E,W boundaries (so E,W boundaries do not overlap)
394    o pkg/mdsio: add support for writing global sections with exch2
395        file layout is as for obcs described above:
396        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
397        - for y-z sections, facets are stacked in y
398    o pkg/thsice:
399       - change a few routines for better vectorization: thsice_albedo.F,
400         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
401         not affected, but in particular the latter routine has changed
402         dramatically (not necessarily easier to read now).
403       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
404       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
405    o verification/lab_sea:
406      - overhaul of the forward model experiments. The main motivation
407        for this revision is that lab_sea has proven quite fragile (when
408        changing the sea-ice code, and switching platforms) to a point
409        when failures were very hard to attribute to specific code problems.
410      - the suspected reason for this fragility is noise amplification by evp so,
411        to start with, we decided to replace evp with lsr in the main experiment.
412      - the input.lsr experiment thus became obsolete and was removed.
413      - it was replaced with the input.fd experiment that uses an
414        analytical "free drift" solution as the ice velocity field.
415      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
416        will hopefully allow us to discriminate problems due to dynamic solvers
417        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
418        us to test additional options, along with the salt plume package.
419      - Finally a pickup was generated (at the end of a one year run) to
420        make the tests more representative of an actual model run. Previously
421        the tests starting point was a 1m thickness of ice everywhere.
422    o pkg/seaice:
423      - introducing S\R seaice_freedrift.F that compute the
424        analytical solution to an approximate ice momentum
425        equation (i.e. the simple stress/coriolis balance).
426      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
427        of the free drift velocity field, and enable its use.
428        To actually use the free drift solution as the model ice
429        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
430    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
431    
432    checkpoint62l (2010/10/04)
433    o pkg/seaice:
434      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
435      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
436       version (with USE_ORIGINAL_SBI undef);
437    o add hooks for new packages OASIS, the package will follow
438      (hooks exclude the seaice pkg for now)
439    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
440      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
441      rather than mdsio_readvector.F/mdsio_writevector.F, within
442      adread_adwrite.F to read/write adjoint-related tapes to disk.
443    o eesupp and pkg/mdsio: ALLOW_WHIO
444      Option to write/read 2D fields to files including tiles halos.
445      The main purpose is for adjoint related "tape I/O".
446      The secondary purpose is for debugging phases.
447      A word on those rather specifically intended purposes.
448      The code was meant to be stripped down to the bare minimum.
449      Typically, there is a unique and basic mapping to the global
450      buffer (tile by tile, then proc by proc, then level by level), and
451      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
452      meant to generate user friendly outputs of various shapes and forms.
453      Rather it is intended, for the knowledgeabale developers,
454      to be largely independent of the many mdsio options, to allow
455      outputs of tiles+halos in debugging phases and in adjoint runs,
456      and to allow some flexibility in tuning (adoint) I/O depending on each
457      file system behavior. With regard to tuning, most of the potential knobs
458      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
459      to specify directories, to specify the typical size of I/O calls, etc.)
460      are not yet included, and will be added if they prove useful.
461    o pkg/seaice:
462       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
463    o pkg/seaice:
464       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
465       code (seaice_budget_ice_if.F) which enable to recover old standard
466       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
467       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
468    o model/src (rStar):
469       use simple average (not area weighted) of rStarFac at U,V point when using
470       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
471       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
472    
473    checkpoint62k (2010/09/17)
474    o adjoint
475       * changed verification/global_ocean.cs32x15 ; adjoint now tests
476         Adams-Bashforth 3 + NLFS + RSTAR
477       * some more modifs required for ECCO-GODAE v4
478    o pkg/seaice
479       add SEAICE_AGE_VOL option to use volume instead of area for
480       integrating SEAICE_AGE
481    o model/src:
482       first check-in of sigma & hybrid-sigma coordinate code ; also includes
483       non-linear free-surface parts ; but pressure-gradient not yet coded.
484    o pkg/ptracers:
485       option for ptracer to convert Salt Relax into additional EmP.
486        tested in exp. global_ocean.90x40x15.dwnslp (update output)
487    
488    checkpoint62j (2010/08/25)
489    o pkg/ggl90:
490       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
491    o pkg/dic: car_flux.F, phos_flux.F
492      - reduce number of exp-calls in order to improve performance
493      - clean up a little (replace fields by their macros, etc., fix
494        typo in CPP-flag)
495    o pkg/ggl90: minor changes
496      - GGL90diffKrS was removed --> always use GGL90diffKr
497      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
498      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
499        (commented out for now)
500      - change in max/min operations to ensure that smoothing is ok
501      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
502      - always use diffKrNrT as background profile (i.e. never use diffKr field)
503    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
504    o pkg/dic:
505      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
506        vectorization
507      - small bug fix in insol for the unlikely case of a cartesian grid
508      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
509        + now vectorize, which also removes adjoint recomputations;
510        + replace integer maksp1 by _RL maskp1
511        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
512    
513    checkpoint62i (2010/07/21)
514    o pkg/flt:
515      - with OBCS: stop floats which enter the OB region
516    o model/src:
517      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
518        for implicit vertical advection.
519    o pkg/seaice:
520     - account for melting in seaice age evolution.
521     - remove double counting of seaice ridging effect on seaice age.
522    
523    checkpoint62h (2010/06/18)
524    o pkg/exch2:
525     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
526    o tools/genmake2
527      - remove "-pdefault" option: redundant with the use of "packages.conf";
528      - remove file pkg/pkg_default : set the default as a pkg group
529        ("default_pkg_list") defined in pkg/pkg_groups;
530      - fix for case pkg/pkg_depend is missing (was hanging before);
531      - add option "-pgroups" to specify a different pkg_groups than the default.
532    o verification/adjustment.cs-32x32x1:
533       add a "minimal" set-up test (code_min & input_min) which only compiles
534       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
535    o tools/genmake2
536      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
537      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
538    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
539      files are nearly the same anyway.
540      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
541       - redefinition of tau(i,i) (by a factor of ustar)
542       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
543       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
544       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
545       - replace
546         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
547         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
548         by
549         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
550         (changes results)
551       -> exf_bulkformulae v1.22,
552          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
553          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
554                    output.txt 1.63
555           offline_exf_seaice: output.seaicetd.txt 1.7
556           seaice_obcs: output.txt 1.10)
557      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
558       -> exf_bulkformulae v1.23,
559          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
560          and global_ocean.cs32x15.icedyn (only 11 matching digits)
561      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
562    o adjoint of exch-1:
563     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
564       (note: was already like this when using EXCH-2) and remove flow dir
565       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
566     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
567     - update pkg/exch2 diff list.
568    
569    checkpoint62g (2010/05/19)
570    o eesupp/src (exch-1):
571     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
572       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
573       (renamed to exch1_*rx_cube.F).
574     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
575       to call new exch1 S/R ; update Makefile and .cvsignore.
576     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
577       exch2_xy_rx later)
578      Note: after updating your code, need to run "make clean" in eesupp/src
579    o test experiment bottom_ctrl_5x5:
580       new output_adm.txt with fewer grdchk & less monitor output.
581    o model/src:
582      remove the call to ini_cori in initialise_varia.F (just keep the usual one
583       in initialise_fixed.F). More consistent with coriolis & horizontal grid
584       beeing treated in the same way (ini_grid is not called a 2nd time).
585    o pkg/exf:
586    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
587    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
588    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
# Line 18  o eesupp/src (exch-1): Line 596  o eesupp/src (exch-1):
596    - Message mode: move RecvAck setting (indicator of buffer being ready)    - Message mode: move RecvAck setting (indicator of buffer being ready)
597      from send_put to recv_get S/R (was useless before, but not sure if      from send_put to recv_get S/R (was useless before, but not sure if
598      it's much more useful now);      it's much more useful now);
599    - switch the order of sync: MPI-proc 1rst and then threads;    - Switch the order of sync: MPI-proc 1rst and then threads;
600    - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.    - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
601      - fix AD code for communication mode ='get' (but not used).
602  o model/src:  o model/src:
603    initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does    initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
604    not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).    not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
# Line 168  o tools/build_options: Line 747  o tools/build_options:
747      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
748  o pkg/ecco  o pkg/ecco
749    - allow user defined cost function contributions    - allow user defined cost function contributions
750          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
751          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
752    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
753        the two options are complementary.        the two options are complementary.
754  o pkg/smooth  o pkg/smooth
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