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revision 1.1258 by mlosch, Wed Apr 28 08:37:41 2010 UTC revision 1.1385 by heimbach, Thu Mar 3 16:57:14 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/obcs:
8     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
9       then normal component. This ensures that the normal component is set
10       correctly even when it conficts with tangential setting from an other OB.
11       Affects results of test-experiment seaice_obcs: update the output.txt
12    o pkg/obcs:
13     - add code to monitor statistics of dynamical fields at OB.
14     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
15       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
16       - change default: balance the Net inflow through all OB (instead of balancing
17         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
18     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
19       to match Nortern OB inflow (OBCS_balanceFacN=0).
20    o pkg/seaice:
21     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
22    o pkg/seaice (seaice_growth v 1.113):
23     - reverting seaice_growth to v 1.111 in order to have code with exact bit
24       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
25       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
26       runtime flag SEAICEareaFormula is kept but is inactive
27    o model/src:
28     - add new param to scale curvilinear grid distance and area when using
29       a different sphere radius from the grid-files.
30     - test/check multi-threads EXCH applied to local variable (cg2d_x)
31    o adjoint:
32     - enable adjoint of Stevens OB
33     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
34       (a bit delicate because of potentially modified adj. common block structure;
35       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
36    
37    checkpoint62s (2011/02/15)
38    o pkg/seaice (seaice_growth v 1.112):
39     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
40       computing the ice cover tendency from effective thickness tendencies. Include
41       Ian Fenty's formula.
42     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
43       SEAICEareaFormula.
44     - simplify notations for the various d_HEFF/d_AREA terms.
45    o pkg/gmredi:
46     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
47       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
48       add a verification test-run (front_relax.bvp) to test GM_useBVP.
49    o pkg/seaice (seaice_growth v 1.111):
50     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
51     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
52       also melt ice.
53    o pkg/seaice:
54     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
55     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
56    o pkg/cheapaml:
57     - from Nico Wienders: New version of this package.
58    o pkg/flt:
59     - add CPP options to prevent floats to re-enter the opposite side of
60       a periodic domain (default: keep periodicity)
61    o pkg/gmredi:
62     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
63       (needed for multi-dim advection).
64     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
65    o model/src:
66     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
67    o tutorial_tracer_adjsens
68     - extend to NLFS and replace maskC by hFacC
69       (change reference output accordingly)
70    
71    checkpoint62r (2011/01/24)
72    o testreport:
73     - add option -deloutp (-do) to remove output file after successful run
74     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
75       extract exact list of procs from this file ; adjust COMMAND by
76       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
77    o pkg/ecco: replace old ineffective way of penalizing deviations from
78      first guess (of obcs) with code by Matt Mazloff
79    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
80      exf/cal
81      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
82        and handle case of obcs?period == 0
83        Not affected by these changes: There is still an inconsistency in
84        the computation of start/endrec for the obcs variables for ALLOW_CAL
85        defined (see comment by Menemenlis, 7-Mar-2003)
86      - make S/R ctrl_get_gen_rec return something meaningful even if
87        ALLOW_CAL is not defined
88      - ctrl_getobcs?: simplify code so that it does not need to use
89                       S/R exf_swapfields
90    o testreport:
91       allow to test MPI with different number of processors for each experiment:
92       create file "SIZE.h.mpi" in each build dir.
93       Note: update of "-command" argument not yet implemented.
94    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
95      alleviate the need for additional 3D tapes when using
96      the non-inear free surface in the adjoint. This is done
97      by adding an 'update' of hfacc etc. to their current
98      value at the beginning of forward_step.F.
99    o pkg/seaice
100      seaice_lsr: move stress-divergence computations out of outer pseudo-
101      timestepping loop
102    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
103      up, so that the calls of the ctrl_* subroutines are really at the end
104      of the routine.
105    o pkg/gmredi:
106      allow to specify a 2-D horizontal map and a 1-D vertical profil
107      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
108    o pkg/seaice:
109      move lsr iterations from seaice_dynsolver to seaice_lsr.
110    o pkg/seaice:
111      reduce memory footprint of seaice mutldim advection tapes,
112      by using a 2D tape independent of the generic_advdiff ones,
113      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
114    
115    checkpoint62q (2010/12/29)
116    o model/src:
117      - check horizontal grid-spacing for unset or zero/negative values.
118      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
119    o pkg/flt:
120      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
121      - precision of input and output files set according to readBinaryPrec
122        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
123      - initial float position from tiled file was not converted to index space
124        (looks like a bug): fixed to make it similar to initial pos. global file.
125    o global_ocean.cs32x15:
126       change SIZE.h of AD set-up to get same tiling as with MPI.
127       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
128    o model/src:
129       add flag to control printing of domain fields (bathymetry, hFac ...) in
130       ini_mask_etc (call to plot_fieds_xy*).
131    o pkg/thsice:
132       if useEXF, some forcing fields are not valid in overlap: fixed by computing
133       over the interior only + apply EXCH at the end (like with SEAICE advection).
134    o pkg/mdsio:
135      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
136        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
137      - change barrier call for safe multi-threads access to 3-D shared buffer.
138      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
139      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
140        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
141    o pkg/flt:
142      - add fourth-order Runge-Kutta integration
143      - add basic exch2 support (only 1 facet supported so far!)
144    o pkg/mdsio+rw:
145      new S/R to read local (or tile independent) vector (read counterpart of
146       mds_writevec_loc, and front-end write_glvec_rl/rs).
147    o global_ocean.cs32x15: additional input_ad.seaice experiment
148        that uses pkg/seaice rather than pkg/thsice.
149        (using multidim advection for seaice)
150    o towards more F95 syntax for array specification in namelist:
151      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
152        of all verification experiments.
153           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
154          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
155      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
156    o global_ocean.cs32x15: additional input.seaice experiment
157        that uses pkg/seaice rather than pkg/thsice.
158    
159    checkpoint62p (2010/12/17)
160    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
161        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
162    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
163        allow for use of multim. advection in seaice adjoint.
164    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
165      - first attempt to close budgets by taking into account the freshwater
166        flux implied by the sublimation of snow and ice. So far only the
167        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
168        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
169    o eesupp/src:
170      new S/R with new option (NML_EXTENDED_F77) to change array specification
171      from F95 standard to commonly accepted extended F77 form.
172      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
173      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
174      for less tolerant f77 compiler (e.g., pgf77, g77).
175    o globalFiles:
176      commented out in parameter file "data" since it's not safe with MPI
177      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
178      in this case); no longer commented out in restart test (tst_2+2).
179    o add adTapeDir to specify a special directory where adjoint tapes are
180      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
181      and cannot be used together with mdsioLocalDir.
182    o nesting pkgs:
183      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
184      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
185      - add parameter files + utils dir + output from short run on beagle.
186    o pkg/seaice:
187        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
188    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
189      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
190    
191    checkpoint62o (2010/11/25)
192    o pkg/exf:
193      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
194    o pkg/seaice:
195      - seaice_ocean_stress: split a loop for better vectorization of the
196        adjoint code
197      - seaice_growth.F: fix bug in conservation of freshwater connected to
198        capping of heff, put contribution into d_HEFFbyNEG
199      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
200        by something more sensible (parameters that are what their name implies)
201      - change some defaults, so that by default exf-parameters are used for
202        things like rhoAir, cpAir,latent/sensible heat parameters, in order
203        to reproduce the old results, many data.seaice now contain funny values
204        for cpAir and latent heat of sublimation
205    o packages_readparms.F: move exf_readparms up in line so that
206        exf-parameters are visible for other packages (e.g. seaice)
207    o debugMode & debugLevel=2:
208      - differentiate between debugMode & debugLevel=2:
209        debugMode: controls printing of debug messages (sequence of S/R calls).
210        debugLevel: controls printing of algorithm intermediate results and stats.
211      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
212        => allows to print debug-stats without all sequence of call messages.
213      - switch control of debug print from debugLevel to debugMode in many S/R.
214    o pkg/obcs (obcs-sponge):
215        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
216        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
217    o pkg/generic_advdiff:
218      - record overlap minimum size for each advection scheme;
219      - refine criteria on overlap minimum size;
220      - check and stop (in gad_check) if overlap size is too small.
221    o pkg/obcs:
222      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
223        once, in ptracers_implicit.F)
224      - with seaice: remove test on empty file name in obcs_apply_seaice (always
225        apply OB values when tile has OB)
226    o model/src, coriolis setting:
227      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
228        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
229        files (selectCoriMap=3) with any grid.
230      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
231    o pkg/seaice/seaice_growth.F:
232        a few cosmetic changes that reduce the number of lines of code
233    o pkg/obcs: add boundary conditions following Stevens (1990)
234      - the code follows old MOM/NAOSIM code
235      - so far it is only implemented for the eastern and western boundaries
236        and NOT for pTracers
237    o pkg/rbcs:
238      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
239        beginning of the first rbcs forcing period.
240      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
241        offline package, i.e., one file per time, labeled by iteration number;
242        deltaTrbcs sets the timestep with which the data was generated;
243        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
244      - rbcsForcingCycle=0 makes forcing non-cyclic.
245      - make arithmetic safe for negative times and odd forcing periods.
246    
247    checkpoint62n (2010/11/09)
248    o pkg/seaice:
249        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
250    o pkg/obcs:
251       New S/R to copy tracer value from the OB location to narrow band region
252        (width = same as overlap) beyond the OB: preserve OB value (needed for
253        high-order scheme) which were overwritten by EXCH call if in overlap
254        region. Applied to theta, salt, ptracer and advected seaice variables.
255       With seaice: use maskInC in similar way as in gad_advection.F,
256        in seaice_advection.F and advect.F.
257       Update output of experiment seaice_obcs and change exp4 to test OBCS with
258        4th order Adv.Scheme. for pasive salt and ptracer.
259    o tools/genmake2:
260      - when looking for an optfile (not specified), only search for Fortran compiler
261        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
262      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
263        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
264      - set default for CPP to "cpp -traditional -P" (was the case without specifying
265        an optfile, but otherwise default was just "cpp".
266      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
267      - when "CC" is not set in the optfile, look for possible C compiler
268        (instead of just setting CC=cc)
269      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
270        => add a ".F" to ".o" rule for source files with no "#include" (such as
271           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
272      - move gfortran before g77 in list of possible Fortran compiler (consistent
273        with reference compiler switch from g77 to gfortran)
274    o pkg/seaice:
275      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
276        seaice_check that stops the model, when the CPP flag is used.
277      o seaice_growth.F: make capping of ice volume conserving by returning the
278        capped ice as freshwater to EmPmR. This does not change the verification
279        experiments but will change runs where the capping is acutally active
280    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
281      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
282         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
283         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
284    o tools/genmake2:
285      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
286      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
287      - clean previous genmake log files before anything else.
288      - change Makefile to remove testreport log files (*.tr_log) and genmake log
289        files only with "CLEAN" target (instead of "Clean");
290    o pkg/generic_advdiff:
291      Change OBCS in multiDim advection (gad_advection.F):
292       Use maskInC to prevent intermediate update of tracer-field in OB regions,
293       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
294       which were applying future time-step OB values.
295      This way, all explicit calculations use current-time-step OB values
296       (simpler and more consistent).
297      Affects results when set-up uses time-varying OBC and multi-dim advection;
298       update output of experiment seaice_obcs.
299    o pkg/seaice:
300      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
301       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
302         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
303      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
304       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
305       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
306    o pkg aim (2010/10/26):
307      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
308        formulation with obliquity, eccentricity, ... as run-time parameters,
309      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
310        upward shortwave radition at the surface (all-sky and clear-sky).
311    o pkg/obcs:
312      - writing sections with globalFiles=T does not work: switch to tiled-files
313        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
314      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
315      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
316    
317    checkpoint62m (2010/10/21)
318    o pkg/seaice: vectorize seaice_solve4temp.F
319      - move iterations loops outside of i/j-loops
320      - requires 2D arrays for TB and effConduct
321      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
322        modified in this routine
323      - a little bit of clean up, adjusting indentation, etc.
324      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
325        performance and '**TWO' by '**2' (because TWO is a float),
326        replaced ONE, ZERO
327    o eesupp/src:
328       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
329    o pkg/seaice/seaice_growth.F
330      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
331      merging process. The merged routine has two branches, and one activates the 'evolution'
332      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
333      In summary, here is what the '10/10 revision' did consist of
334        part 1: seaice_growth.F revisions 1.71 to 1.75
335          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
336            The emphasis here was on improving readability (e.g. by trying to use meaningful
337            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
338        part 1.5:
339          - revising the lab_sea experiment to make it a more useful (i.e. stable
340            and representative of an actual model run). This was done by generating a
341            (winter) pickup to start from, switching back the main experiment dynamic
342            solver from evp to lsr, having one of the experiments use the free drift solution.
343        part 2: seaice_growth.F revisions 1.76 to 1.85
344          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
345          - Sorting out the various fields units and sign (set early on and reset at the end)
346            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
347            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
348          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
349            and simplifying logical expressions to further improve readibility.
350        part 3: seaice_growth.F revisions 1.86 to 1.89
351          - Re-organize the blocks of code more logically.
352          - Merging the '_if.F' pieces that add something new.
353    o pkg/thsice:
354      - vectorize thsice_solve4temp and thsice_get_exf.
355        Problem: thsice_solve4temp has an unvectorizable statement that
356        might also be problematic for TAF
357      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
358        does not change the verifcation experiment, but will change all
359        experiments that have this flag undefined (not tested in verification);
360        a little reorganization to save a few 2D fields and recomputations
361      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
362      - 2nd step:  fix some store dirs
363        o seems to work somewhat, i.e. using ifort but not g77
364        o likely cause are incomplete init. or recomputation
365        o start verification/global_ocean.cs32x15/input_ad.thsice
366    o pkg/obcs: add support for exch2
367      - the position of the boundary and prescribed values are specified using
368        a global domain with exch2 facets stacked
369        - in x for N,S boundaries (like W2_mapIO=-1)
370        - in y for E,W boundaries (so E,W boundaries do not overlap)
371    o pkg/mdsio: add support for writing global sections with exch2
372        file layout is as for obcs described above:
373        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
374        - for y-z sections, facets are stacked in y
375    o pkg/thsice:
376       - change a few routines for better vectorization: thsice_albedo.F,
377         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
378         not affected, but in particular the latter routine has changed
379         dramatically (not necessarily easier to read now).
380       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
381       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
382    o verification/lab_sea:
383      - overhaul of the forward model experiments. The main motivation
384        for this revision is that lab_sea has proven quite fragile (when
385        changing the sea-ice code, and switching platforms) to a point
386        when failures were very hard to attribute to specific code problems.
387      - the suspected reason for this fragility is noise amplification by evp so,
388        to start with, we decided to replace evp with lsr in the main experiment.
389      - the input.lsr experiment thus became obsolete and was removed.
390      - it was replaced with the input.fd experiment that uses an
391        analytical "free drift" solution as the ice velocity field.
392      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
393        will hopefully allow us to discriminate problems due to dynamic solvers
394        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
395        us to test additional options, along with the salt plume package.
396      - Finally a pickup was generated (at the end of a one year run) to
397        make the tests more representative of an actual model run. Previously
398        the tests starting point was a 1m thickness of ice everywhere.
399    o pkg/seaice:
400      - introducing S\R seaice_freedrift.F that compute the
401        analytical solution to an approximate ice momentum
402        equation (i.e. the simple stress/coriolis balance).
403      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
404        of the free drift velocity field, and enable its use.
405        To actually use the free drift solution as the model ice
406        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
407    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
408    
409    checkpoint62l (2010/10/04)
410    o pkg/seaice:
411      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
412      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
413       version (with USE_ORIGINAL_SBI undef);
414    o add hooks for new packages OASIS, the package will follow
415      (hooks exclude the seaice pkg for now)
416    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
417      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
418      rather than mdsio_readvector.F/mdsio_writevector.F, within
419      adread_adwrite.F to read/write adjoint-related tapes to disk.
420    o eesupp and pkg/mdsio: ALLOW_WHIO
421      Option to write/read 2D fields to files including tiles halos.
422      The main purpose is for adjoint related "tape I/O".
423      The secondary purpose is for debugging phases.
424      A word on those rather specifically intended purposes.
425      The code was meant to be stripped down to the bare minimum.
426      Typically, there is a unique and basic mapping to the global
427      buffer (tile by tile, then proc by proc, then level by level), and
428      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
429      meant to generate user friendly outputs of various shapes and forms.
430      Rather it is intended, for the knowledgeabale developers,
431      to be largely independent of the many mdsio options, to allow
432      outputs of tiles+halos in debugging phases and in adjoint runs,
433      and to allow some flexibility in tuning (adoint) I/O depending on each
434      file system behavior. With regard to tuning, most of the potential knobs
435      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
436      to specify directories, to specify the typical size of I/O calls, etc.)
437      are not yet included, and will be added if they prove useful.
438    o pkg/seaice:
439       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
440    o pkg/seaice:
441       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
442       code (seaice_budget_ice_if.F) which enable to recover old standard
443       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
444       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
445    o model/src (rStar):
446       use simple average (not area weighted) of rStarFac at U,V point when using
447       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
448       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
449    
450    checkpoint62k (2010/09/17)
451    o adjoint
452       * changed verification/global_ocean.cs32x15 ; adjoint now tests
453         Adams-Bashforth 3 + NLFS + RSTAR
454       * some more modifs required for ECCO-GODAE v4
455    o pkg/seaice
456       add SEAICE_AGE_VOL option to use volume instead of area for
457       integrating SEAICE_AGE
458    o model/src:
459       first check-in of sigma & hybrid-sigma coordinate code ; also includes
460       non-linear free-surface parts ; but pressure-gradient not yet coded.
461    o pkg/ptracers:
462       option for ptracer to convert Salt Relax into additional EmP.
463        tested in exp. global_ocean.90x40x15.dwnslp (update output)
464    
465    checkpoint62j (2010/08/25)
466    o pkg/ggl90:
467       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
468    o pkg/dic: car_flux.F, phos_flux.F
469      - reduce number of exp-calls in order to improve performance
470      - clean up a little (replace fields by their macros, etc., fix
471        typo in CPP-flag)
472    o pkg/ggl90: minor changes
473      - GGL90diffKrS was removed --> always use GGL90diffKr
474      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
475      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
476        (commented out for now)
477      - change in max/min operations to ensure that smoothing is ok
478      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
479      - always use diffKrNrT as background profile (i.e. never use diffKr field)
480    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
481    o pkg/dic:
482      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
483        vectorization
484      - small bug fix in insol for the unlikely case of a cartesian grid
485      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
486        + now vectorize, which also removes adjoint recomputations;
487        + replace integer maksp1 by _RL maskp1
488        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
489    
490    checkpoint62i (2010/07/21)
491    o pkg/flt:
492      - with OBCS: stop floats which enter the OB region
493    o model/src:
494      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
495        for implicit vertical advection.
496    o pkg/seaice:
497     - account for melting in seaice age evolution.
498     - remove double counting of seaice ridging effect on seaice age.
499    
500    checkpoint62h (2010/06/18)
501    o pkg/exch2:
502     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
503    o tools/genmake2
504      - remove "-pdefault" option: redundant with the use of "packages.conf";
505      - remove file pkg/pkg_default : set the default as a pkg group
506        ("default_pkg_list") defined in pkg/pkg_groups;
507      - fix for case pkg/pkg_depend is missing (was hanging before);
508      - add option "-pgroups" to specify a different pkg_groups than the default.
509    o verification/adjustment.cs-32x32x1:
510       add a "minimal" set-up test (code_min & input_min) which only compiles
511       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
512    o tools/genmake2
513      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
514      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
515    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
516      files are nearly the same anyway.
517      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
518       - redefinition of tau(i,i) (by a factor of ustar)
519       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
520       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
521       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
522       - replace
523         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
524         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
525         by
526         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
527         (changes results)
528       -> exf_bulkformulae v1.22,
529          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
530          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
531                    output.txt 1.63
532           offline_exf_seaice: output.seaicetd.txt 1.7
533           seaice_obcs: output.txt 1.10)
534      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
535       -> exf_bulkformulae v1.23,
536          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
537          and global_ocean.cs32x15.icedyn (only 11 matching digits)
538      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
539    o adjoint of exch-1:
540     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
541       (note: was already like this when using EXCH-2) and remove flow dir
542       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
543     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
544     - update pkg/exch2 diff list.
545    
546    checkpoint62g (2010/05/19)
547    o eesupp/src (exch-1):
548     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
549       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
550       (renamed to exch1_*rx_cube.F).
551     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
552       to call new exch1 S/R ; update Makefile and .cvsignore.
553     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
554       exch2_xy_rx later)
555      Note: after updating your code, need to run "make clean" in eesupp/src
556    o test experiment bottom_ctrl_5x5:
557       new output_adm.txt with fewer grdchk & less monitor output.
558    o model/src:
559      remove the call to ini_cori in initialise_varia.F (just keep the usual one
560       in initialise_fixed.F). More consistent with coriolis & horizontal grid
561       beeing treated in the same way (ini_grid is not called a 2nd time).
562    o pkg/exf:
563      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
564      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
565      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
566      - cosmetic changes to exf_bulkformulae.F to make it look more like
567        exf_bulk_largeyeager04.F
568    o eesupp/src (exch-1):
569      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
570      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
571        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
572        (even without using MPI).
573      - Message mode: move RecvAck setting (indicator of buffer being ready)
574        from send_put to recv_get S/R (was useless before, but not sure if
575        it's much more useful now);
576      - Switch the order of sync: MPI-proc 1rst and then threads;
577      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
578      - fix AD code for communication mode ='get' (but not used).
579    o model/src:
580      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
581      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
582    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
583    o pkg/ctrl: require a specific set of control variables and exf-flags for
584      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
585    o model/src:
586     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
587       1rst forward sweep, to avoid over-writing output files during recomputations
588       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
589     b) 2nd version:
590      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
591      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
592         writePickupAtEnd) + seaice & ptracers output;
593      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
594    o model/src:
595      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
596    o pkg/exch2:
597      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
598      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
599    o pkg/autodiff & exch2:
600      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
601      (for now, only if ALLOW_EXCH2 is defined).
602    o pkg/autodiff:
603      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
604        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
605       + clean-up comments (_RS is not always real*4)
606      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
607      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
608        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
609    o testreport (AD-tests):
610      no longer link files from dir "../input" (1rst link files from
611      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
612    
613    checkpoint62f (2010/04/29)
614  o model/src/the_main_loop.F:  o model/src/the_main_loop.F:
615    adjust store directives for seaice evp and multicategory according to    adjust store directives for seaice evp and multicategory according to
616    pkg/ecco/the_main_loop.F    pkg/ecco/the_main_loop.F
617  o adjoint:  o adjoint:
618    global_sum_ad was incomplete (noted many times by many people ;)    global_sum_ad was incomplete (noted many times by many people ;)
619    nice description by Jean U. as follows:    nice description by Jean U. as follows:
620    * allreduce(var) in global_sum.F can be interpreted as    * allreduce(var) in global_sum.F can be interpreted as
621      reduce(sum) followed by broadcast of sum.        reduce(sum) followed by broadcast of sum.
622    * The adjoint of that is    * The adjoint of that is
623      sum(adjoint) followed by broadcast(summed adjoint value)      sum(adjoint) followed by broadcast(summed adjoint value)
624      or in other words, allreduce(sum, adjoint vars)      or in other words, allreduce(sum, adjoint vars)
625    We were missing the sum(adjoint)!    We were missing the sum(adjoint)!
626    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
# Line 117  o tools/build_options: Line 724  o tools/build_options:
724      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
725  o pkg/ecco  o pkg/ecco
726    - allow user defined cost function contributions    - allow user defined cost function contributions
727          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
728          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
729    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
730        the two options are complementary.        the two options are complementary.
731  o pkg/smooth  o pkg/smooth
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