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revision 1.1267 by mlosch, Tue May 11 15:48:00 2010 UTC revision 1.1384 by jmc, Tue Mar 1 19:19:13 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    
32    checkpoint62s (2011/02/15)
33    o pkg/seaice (seaice_growth v 1.112):
34     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
35       computing the ice cover tendency from effective thickness tendencies. Include
36       Ian Fenty's formula.
37     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
38       SEAICEareaFormula.
39     - simplify notations for the various d_HEFF/d_AREA terms.
40    o pkg/gmredi:
41     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
42       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
43       add a verification test-run (front_relax.bvp) to test GM_useBVP.
44    o pkg/seaice (seaice_growth v 1.111):
45     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
46     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
47       also melt ice.
48    o pkg/seaice:
49     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
50     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
51    o pkg/cheapaml:
52     - from Nico Wienders: New version of this package.
53    o pkg/flt:
54     - add CPP options to prevent floats to re-enter the opposite side of
55       a periodic domain (default: keep periodicity)
56    o pkg/gmredi:
57     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
58       (needed for multi-dim advection).
59     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
60    o model/src:
61     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
62    o tutorial_tracer_adjsens
63     - extend to NLFS and replace maskC by hFacC
64       (change reference output accordingly)
65    
66    checkpoint62r (2011/01/24)
67    o testreport:
68     - add option -deloutp (-do) to remove output file after successful run
69     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
70       extract exact list of procs from this file ; adjust COMMAND by
71       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
72    o pkg/ecco: replace old ineffective way of penalizing deviations from
73      first guess (of obcs) with code by Matt Mazloff
74    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
75      exf/cal
76      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
77        and handle case of obcs?period == 0
78        Not affected by these changes: There is still an inconsistency in
79        the computation of start/endrec for the obcs variables for ALLOW_CAL
80        defined (see comment by Menemenlis, 7-Mar-2003)
81      - make S/R ctrl_get_gen_rec return something meaningful even if
82        ALLOW_CAL is not defined
83      - ctrl_getobcs?: simplify code so that it does not need to use
84                       S/R exf_swapfields
85    o testreport:
86       allow to test MPI with different number of processors for each experiment:
87       create file "SIZE.h.mpi" in each build dir.
88       Note: update of "-command" argument not yet implemented.
89    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
90      alleviate the need for additional 3D tapes when using
91      the non-inear free surface in the adjoint. This is done
92      by adding an 'update' of hfacc etc. to their current
93      value at the beginning of forward_step.F.
94    o pkg/seaice
95      seaice_lsr: move stress-divergence computations out of outer pseudo-
96      timestepping loop
97    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
98      up, so that the calls of the ctrl_* subroutines are really at the end
99      of the routine.
100    o pkg/gmredi:
101      allow to specify a 2-D horizontal map and a 1-D vertical profil
102      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
103    o pkg/seaice:
104      move lsr iterations from seaice_dynsolver to seaice_lsr.
105    o pkg/seaice:
106      reduce memory footprint of seaice mutldim advection tapes,
107      by using a 2D tape independent of the generic_advdiff ones,
108      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
109    
110    checkpoint62q (2010/12/29)
111    o model/src:
112      - check horizontal grid-spacing for unset or zero/negative values.
113      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
114    o pkg/flt:
115      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
116      - precision of input and output files set according to readBinaryPrec
117        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
118      - initial float position from tiled file was not converted to index space
119        (looks like a bug): fixed to make it similar to initial pos. global file.
120    o global_ocean.cs32x15:
121       change SIZE.h of AD set-up to get same tiling as with MPI.
122       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
123    o model/src:
124       add flag to control printing of domain fields (bathymetry, hFac ...) in
125       ini_mask_etc (call to plot_fieds_xy*).
126    o pkg/thsice:
127       if useEXF, some forcing fields are not valid in overlap: fixed by computing
128       over the interior only + apply EXCH at the end (like with SEAICE advection).
129    o pkg/mdsio:
130      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
131        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
132      - change barrier call for safe multi-threads access to 3-D shared buffer.
133      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
134      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
135        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
136    o pkg/flt:
137      - add fourth-order Runge-Kutta integration
138      - add basic exch2 support (only 1 facet supported so far!)
139    o pkg/mdsio+rw:
140      new S/R to read local (or tile independent) vector (read counterpart of
141       mds_writevec_loc, and front-end write_glvec_rl/rs).
142    o global_ocean.cs32x15: additional input_ad.seaice experiment
143        that uses pkg/seaice rather than pkg/thsice.
144        (using multidim advection for seaice)
145    o towards more F95 syntax for array specification in namelist:
146      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
147        of all verification experiments.
148           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
149          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
150      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
151    o global_ocean.cs32x15: additional input.seaice experiment
152        that uses pkg/seaice rather than pkg/thsice.
153    
154    checkpoint62p (2010/12/17)
155    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
156        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
157    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
158        allow for use of multim. advection in seaice adjoint.
159    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
160      - first attempt to close budgets by taking into account the freshwater
161        flux implied by the sublimation of snow and ice. So far only the
162        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
163        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
164    o eesupp/src:
165      new S/R with new option (NML_EXTENDED_F77) to change array specification
166      from F95 standard to commonly accepted extended F77 form.
167      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
168      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
169      for less tolerant f77 compiler (e.g., pgf77, g77).
170    o globalFiles:
171      commented out in parameter file "data" since it's not safe with MPI
172      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
173      in this case); no longer commented out in restart test (tst_2+2).
174    o add adTapeDir to specify a special directory where adjoint tapes are
175      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
176      and cannot be used together with mdsioLocalDir.
177    o nesting pkgs:
178      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
179      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
180      - add parameter files + utils dir + output from short run on beagle.
181    o pkg/seaice:
182        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
183    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
184      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
185    
186    checkpoint62o (2010/11/25)
187    o pkg/exf:
188      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
189    o pkg/seaice:
190      - seaice_ocean_stress: split a loop for better vectorization of the
191        adjoint code
192      - seaice_growth.F: fix bug in conservation of freshwater connected to
193        capping of heff, put contribution into d_HEFFbyNEG
194      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
195        by something more sensible (parameters that are what their name implies)
196      - change some defaults, so that by default exf-parameters are used for
197        things like rhoAir, cpAir,latent/sensible heat parameters, in order
198        to reproduce the old results, many data.seaice now contain funny values
199        for cpAir and latent heat of sublimation
200    o packages_readparms.F: move exf_readparms up in line so that
201        exf-parameters are visible for other packages (e.g. seaice)
202    o debugMode & debugLevel=2:
203      - differentiate between debugMode & debugLevel=2:
204        debugMode: controls printing of debug messages (sequence of S/R calls).
205        debugLevel: controls printing of algorithm intermediate results and stats.
206      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
207        => allows to print debug-stats without all sequence of call messages.
208      - switch control of debug print from debugLevel to debugMode in many S/R.
209    o pkg/obcs (obcs-sponge):
210        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
211        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
212    o pkg/generic_advdiff:
213      - record overlap minimum size for each advection scheme;
214      - refine criteria on overlap minimum size;
215      - check and stop (in gad_check) if overlap size is too small.
216    o pkg/obcs:
217      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
218        once, in ptracers_implicit.F)
219      - with seaice: remove test on empty file name in obcs_apply_seaice (always
220        apply OB values when tile has OB)
221    o model/src, coriolis setting:
222      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
223        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
224        files (selectCoriMap=3) with any grid.
225      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
226    o pkg/seaice/seaice_growth.F:
227        a few cosmetic changes that reduce the number of lines of code
228    o pkg/obcs: add boundary conditions following Stevens (1990)
229      - the code follows old MOM/NAOSIM code
230      - so far it is only implemented for the eastern and western boundaries
231        and NOT for pTracers
232    o pkg/rbcs:
233      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
234        beginning of the first rbcs forcing period.
235      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
236        offline package, i.e., one file per time, labeled by iteration number;
237        deltaTrbcs sets the timestep with which the data was generated;
238        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
239      - rbcsForcingCycle=0 makes forcing non-cyclic.
240      - make arithmetic safe for negative times and odd forcing periods.
241    
242    checkpoint62n (2010/11/09)
243    o pkg/seaice:
244        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
245    o pkg/obcs:
246       New S/R to copy tracer value from the OB location to narrow band region
247        (width = same as overlap) beyond the OB: preserve OB value (needed for
248        high-order scheme) which were overwritten by EXCH call if in overlap
249        region. Applied to theta, salt, ptracer and advected seaice variables.
250       With seaice: use maskInC in similar way as in gad_advection.F,
251        in seaice_advection.F and advect.F.
252       Update output of experiment seaice_obcs and change exp4 to test OBCS with
253        4th order Adv.Scheme. for pasive salt and ptracer.
254    o tools/genmake2:
255      - when looking for an optfile (not specified), only search for Fortran compiler
256        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
257      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
258        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
259      - set default for CPP to "cpp -traditional -P" (was the case without specifying
260        an optfile, but otherwise default was just "cpp".
261      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
262      - when "CC" is not set in the optfile, look for possible C compiler
263        (instead of just setting CC=cc)
264      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
265        => add a ".F" to ".o" rule for source files with no "#include" (such as
266           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
267      - move gfortran before g77 in list of possible Fortran compiler (consistent
268        with reference compiler switch from g77 to gfortran)
269    o pkg/seaice:
270      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
271        seaice_check that stops the model, when the CPP flag is used.
272      o seaice_growth.F: make capping of ice volume conserving by returning the
273        capped ice as freshwater to EmPmR. This does not change the verification
274        experiments but will change runs where the capping is acutally active
275    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
276      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
277         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
278         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
279    o tools/genmake2:
280      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
281      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
282      - clean previous genmake log files before anything else.
283      - change Makefile to remove testreport log files (*.tr_log) and genmake log
284        files only with "CLEAN" target (instead of "Clean");
285    o pkg/generic_advdiff:
286      Change OBCS in multiDim advection (gad_advection.F):
287       Use maskInC to prevent intermediate update of tracer-field in OB regions,
288       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
289       which were applying future time-step OB values.
290      This way, all explicit calculations use current-time-step OB values
291       (simpler and more consistent).
292      Affects results when set-up uses time-varying OBC and multi-dim advection;
293       update output of experiment seaice_obcs.
294    o pkg/seaice:
295      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
296       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
297         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
298      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
299       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
300       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
301    o pkg aim (2010/10/26):
302      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
303        formulation with obliquity, eccentricity, ... as run-time parameters,
304      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
305        upward shortwave radition at the surface (all-sky and clear-sky).
306    o pkg/obcs:
307      - writing sections with globalFiles=T does not work: switch to tiled-files
308        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
309      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
310      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
311    
312    checkpoint62m (2010/10/21)
313    o pkg/seaice: vectorize seaice_solve4temp.F
314      - move iterations loops outside of i/j-loops
315      - requires 2D arrays for TB and effConduct
316      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
317        modified in this routine
318      - a little bit of clean up, adjusting indentation, etc.
319      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
320        performance and '**TWO' by '**2' (because TWO is a float),
321        replaced ONE, ZERO
322    o eesupp/src:
323       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
324    o pkg/seaice/seaice_growth.F
325      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
326      merging process. The merged routine has two branches, and one activates the 'evolution'
327      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
328      In summary, here is what the '10/10 revision' did consist of
329        part 1: seaice_growth.F revisions 1.71 to 1.75
330          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
331            The emphasis here was on improving readability (e.g. by trying to use meaningful
332            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
333        part 1.5:
334          - revising the lab_sea experiment to make it a more useful (i.e. stable
335            and representative of an actual model run). This was done by generating a
336            (winter) pickup to start from, switching back the main experiment dynamic
337            solver from evp to lsr, having one of the experiments use the free drift solution.
338        part 2: seaice_growth.F revisions 1.76 to 1.85
339          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
340          - Sorting out the various fields units and sign (set early on and reset at the end)
341            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
342            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
343          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
344            and simplifying logical expressions to further improve readibility.
345        part 3: seaice_growth.F revisions 1.86 to 1.89
346          - Re-organize the blocks of code more logically.
347          - Merging the '_if.F' pieces that add something new.
348    o pkg/thsice:
349      - vectorize thsice_solve4temp and thsice_get_exf.
350        Problem: thsice_solve4temp has an unvectorizable statement that
351        might also be problematic for TAF
352      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
353        does not change the verifcation experiment, but will change all
354        experiments that have this flag undefined (not tested in verification);
355        a little reorganization to save a few 2D fields and recomputations
356      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
357      - 2nd step:  fix some store dirs
358        o seems to work somewhat, i.e. using ifort but not g77
359        o likely cause are incomplete init. or recomputation
360        o start verification/global_ocean.cs32x15/input_ad.thsice
361    o pkg/obcs: add support for exch2
362      - the position of the boundary and prescribed values are specified using
363        a global domain with exch2 facets stacked
364        - in x for N,S boundaries (like W2_mapIO=-1)
365        - in y for E,W boundaries (so E,W boundaries do not overlap)
366    o pkg/mdsio: add support for writing global sections with exch2
367        file layout is as for obcs described above:
368        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
369        - for y-z sections, facets are stacked in y
370    o pkg/thsice:
371       - change a few routines for better vectorization: thsice_albedo.F,
372         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
373         not affected, but in particular the latter routine has changed
374         dramatically (not necessarily easier to read now).
375       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
376       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
377    o verification/lab_sea:
378      - overhaul of the forward model experiments. The main motivation
379        for this revision is that lab_sea has proven quite fragile (when
380        changing the sea-ice code, and switching platforms) to a point
381        when failures were very hard to attribute to specific code problems.
382      - the suspected reason for this fragility is noise amplification by evp so,
383        to start with, we decided to replace evp with lsr in the main experiment.
384      - the input.lsr experiment thus became obsolete and was removed.
385      - it was replaced with the input.fd experiment that uses an
386        analytical "free drift" solution as the ice velocity field.
387      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
388        will hopefully allow us to discriminate problems due to dynamic solvers
389        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
390        us to test additional options, along with the salt plume package.
391      - Finally a pickup was generated (at the end of a one year run) to
392        make the tests more representative of an actual model run. Previously
393        the tests starting point was a 1m thickness of ice everywhere.
394    o pkg/seaice:
395      - introducing S\R seaice_freedrift.F that compute the
396        analytical solution to an approximate ice momentum
397        equation (i.e. the simple stress/coriolis balance).
398      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
399        of the free drift velocity field, and enable its use.
400        To actually use the free drift solution as the model ice
401        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
402    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
403    
404    checkpoint62l (2010/10/04)
405    o pkg/seaice:
406      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
407      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
408       version (with USE_ORIGINAL_SBI undef);
409    o add hooks for new packages OASIS, the package will follow
410      (hooks exclude the seaice pkg for now)
411    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
412      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
413      rather than mdsio_readvector.F/mdsio_writevector.F, within
414      adread_adwrite.F to read/write adjoint-related tapes to disk.
415    o eesupp and pkg/mdsio: ALLOW_WHIO
416      Option to write/read 2D fields to files including tiles halos.
417      The main purpose is for adjoint related "tape I/O".
418      The secondary purpose is for debugging phases.
419      A word on those rather specifically intended purposes.
420      The code was meant to be stripped down to the bare minimum.
421      Typically, there is a unique and basic mapping to the global
422      buffer (tile by tile, then proc by proc, then level by level), and
423      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
424      meant to generate user friendly outputs of various shapes and forms.
425      Rather it is intended, for the knowledgeabale developers,
426      to be largely independent of the many mdsio options, to allow
427      outputs of tiles+halos in debugging phases and in adjoint runs,
428      and to allow some flexibility in tuning (adoint) I/O depending on each
429      file system behavior. With regard to tuning, most of the potential knobs
430      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
431      to specify directories, to specify the typical size of I/O calls, etc.)
432      are not yet included, and will be added if they prove useful.
433    o pkg/seaice:
434       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
435    o pkg/seaice:
436       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
437       code (seaice_budget_ice_if.F) which enable to recover old standard
438       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
439       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
440    o model/src (rStar):
441       use simple average (not area weighted) of rStarFac at U,V point when using
442       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
443       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
444    
445    checkpoint62k (2010/09/17)
446    o adjoint
447       * changed verification/global_ocean.cs32x15 ; adjoint now tests
448         Adams-Bashforth 3 + NLFS + RSTAR
449       * some more modifs required for ECCO-GODAE v4
450    o pkg/seaice
451       add SEAICE_AGE_VOL option to use volume instead of area for
452       integrating SEAICE_AGE
453    o model/src:
454       first check-in of sigma & hybrid-sigma coordinate code ; also includes
455       non-linear free-surface parts ; but pressure-gradient not yet coded.
456    o pkg/ptracers:
457       option for ptracer to convert Salt Relax into additional EmP.
458        tested in exp. global_ocean.90x40x15.dwnslp (update output)
459    
460    checkpoint62j (2010/08/25)
461    o pkg/ggl90:
462       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
463    o pkg/dic: car_flux.F, phos_flux.F
464      - reduce number of exp-calls in order to improve performance
465      - clean up a little (replace fields by their macros, etc., fix
466        typo in CPP-flag)
467    o pkg/ggl90: minor changes
468      - GGL90diffKrS was removed --> always use GGL90diffKr
469      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
470      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
471        (commented out for now)
472      - change in max/min operations to ensure that smoothing is ok
473      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
474      - always use diffKrNrT as background profile (i.e. never use diffKr field)
475    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
476    o pkg/dic:
477      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
478        vectorization
479      - small bug fix in insol for the unlikely case of a cartesian grid
480      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
481        + now vectorize, which also removes adjoint recomputations;
482        + replace integer maksp1 by _RL maskp1
483        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
484    
485    checkpoint62i (2010/07/21)
486    o pkg/flt:
487      - with OBCS: stop floats which enter the OB region
488    o model/src:
489      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
490        for implicit vertical advection.
491    o pkg/seaice:
492     - account for melting in seaice age evolution.
493     - remove double counting of seaice ridging effect on seaice age.
494    
495    checkpoint62h (2010/06/18)
496    o pkg/exch2:
497     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
498    o tools/genmake2
499      - remove "-pdefault" option: redundant with the use of "packages.conf";
500      - remove file pkg/pkg_default : set the default as a pkg group
501        ("default_pkg_list") defined in pkg/pkg_groups;
502      - fix for case pkg/pkg_depend is missing (was hanging before);
503      - add option "-pgroups" to specify a different pkg_groups than the default.
504    o verification/adjustment.cs-32x32x1:
505       add a "minimal" set-up test (code_min & input_min) which only compiles
506       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
507    o tools/genmake2
508      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
509      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
510    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
511      files are nearly the same anyway.
512      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
513       - redefinition of tau(i,i) (by a factor of ustar)
514       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
515       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
516       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
517       - replace
518         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
519         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
520         by
521         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
522         (changes results)
523       -> exf_bulkformulae v1.22,
524          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
525          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
526                    output.txt 1.63
527           offline_exf_seaice: output.seaicetd.txt 1.7
528           seaice_obcs: output.txt 1.10)
529      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
530       -> exf_bulkformulae v1.23,
531          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
532          and global_ocean.cs32x15.icedyn (only 11 matching digits)
533      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
534    o adjoint of exch-1:
535     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
536       (note: was already like this when using EXCH-2) and remove flow dir
537       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
538     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
539     - update pkg/exch2 diff list.
540    
541    checkpoint62g (2010/05/19)
542    o eesupp/src (exch-1):
543     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
544       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
545       (renamed to exch1_*rx_cube.F).
546     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
547       to call new exch1 S/R ; update Makefile and .cvsignore.
548     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
549       exch2_xy_rx later)
550      Note: after updating your code, need to run "make clean" in eesupp/src
551    o test experiment bottom_ctrl_5x5:
552       new output_adm.txt with fewer grdchk & less monitor output.
553    o model/src:
554      remove the call to ini_cori in initialise_varia.F (just keep the usual one
555       in initialise_fixed.F). More consistent with coriolis & horizontal grid
556       beeing treated in the same way (ini_grid is not called a 2nd time).
557    o pkg/exf:
558      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
559      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
560      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
561      - cosmetic changes to exf_bulkformulae.F to make it look more like
562        exf_bulk_largeyeager04.F
563    o eesupp/src (exch-1):
564      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
565      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
566        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
567        (even without using MPI).
568      - Message mode: move RecvAck setting (indicator of buffer being ready)
569        from send_put to recv_get S/R (was useless before, but not sure if
570        it's much more useful now);
571      - Switch the order of sync: MPI-proc 1rst and then threads;
572      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
573      - fix AD code for communication mode ='get' (but not used).
574    o model/src:
575      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
576      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
577    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
578  o pkg/ctrl: require a specific set of control variables and exf-flags for  o pkg/ctrl: require a specific set of control variables and exf-flags for
579    adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)    adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
580  o model/src:  o model/src:
# Line 148  o tools/build_options: Line 719  o tools/build_options:
719      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
720  o pkg/ecco  o pkg/ecco
721    - allow user defined cost function contributions    - allow user defined cost function contributions
722          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
723          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
724    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
725        the two options are complementary.        the two options are complementary.
726  o pkg/smooth  o pkg/smooth
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