/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1258 by mlosch, Wed Apr 28 08:37:41 2010 UTC revision 1.1381 by dimitri, Wed Feb 23 21:12:45 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice (seaice_growth v 1.113):
8     - reverting seaice_growth to v 1.111 in order to have code with exact bit
9       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
10       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
11       runtime flag SEAICEareaFormula is kept but is inactive
12    o model/src:
13     - add new param to scale curvilinear grid distance and area when using
14       a different sphere radius from the grid-files.
15     - test/check multi-threads EXCH applied to local variable (cg2d_x)
16    
17    checkpoint62s (2011/02/15)
18    o pkg/seaice (seaice_growth v 1.112):
19     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
20       computing the ice cover tendency from effective thickness tendencies. Include
21       Ian Fenty's formula.
22     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
23       SEAICEareaFormula.
24     - simplify notations for the various d_HEFF/d_AREA terms.
25    o pkg/gmredi:
26     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
27       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
28       add a verification test-run (front_relax.bvp) to test GM_useBVP.
29    o pkg/seaice (seaice_growth v 1.111):
30     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
31     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
32       also melt ice.
33    o pkg/seaice:
34     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
35     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
36    o pkg/cheapaml:
37     - from Nico Wienders: New version of this package.
38    o pkg/flt:
39     - add CPP options to prevent floats to re-enter the opposite side of
40       a periodic domain (default: keep periodicity)
41    o pkg/gmredi:
42     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
43       (needed for multi-dim advection).
44     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
45    o model/src:
46     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
47    o tutorial_tracer_adjsens
48     - extend to NLFS and replace maskC by hFacC
49       (change reference output accordingly)
50    
51    checkpoint62r (2011/01/24)
52    o testreport:
53     - add option -deloutp (-do) to remove output file after successful run
54     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
55       extract exact list of procs from this file ; adjust COMMAND by
56       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
57    o pkg/ecco: replace old ineffective way of penalizing deviations from
58      first guess (of obcs) with code by Matt Mazloff
59    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
60      exf/cal
61      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
62        and handle case of obcs?period == 0
63        Not affected by these changes: There is still an inconsistency in
64        the computation of start/endrec for the obcs variables for ALLOW_CAL
65        defined (see comment by Menemenlis, 7-Mar-2003)
66      - make S/R ctrl_get_gen_rec return something meaningful even if
67        ALLOW_CAL is not defined
68      - ctrl_getobcs?: simplify code so that it does not need to use
69                       S/R exf_swapfields
70    o testreport:
71       allow to test MPI with different number of processors for each experiment:
72       create file "SIZE.h.mpi" in each build dir.
73       Note: update of "-command" argument not yet implemented.
74    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
75      alleviate the need for additional 3D tapes when using
76      the non-inear free surface in the adjoint. This is done
77      by adding an 'update' of hfacc etc. to their current
78      value at the beginning of forward_step.F.
79    o pkg/seaice
80      seaice_lsr: move stress-divergence computations out of outer pseudo-
81      timestepping loop
82    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
83      up, so that the calls of the ctrl_* subroutines are really at the end
84      of the routine.
85    o pkg/gmredi:
86      allow to specify a 2-D horizontal map and a 1-D vertical profil
87      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
88    o pkg/seaice:
89      move lsr iterations from seaice_dynsolver to seaice_lsr.
90    o pkg/seaice:
91      reduce memory footprint of seaice mutldim advection tapes,
92      by using a 2D tape independent of the generic_advdiff ones,
93      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
94    
95    checkpoint62q (2010/12/29)
96    o model/src:
97      - check horizontal grid-spacing for unset or zero/negative values.
98      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
99    o pkg/flt:
100      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
101      - precision of input and output files set according to readBinaryPrec
102        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
103      - initial float position from tiled file was not converted to index space
104        (looks like a bug): fixed to make it similar to initial pos. global file.
105    o global_ocean.cs32x15:
106       change SIZE.h of AD set-up to get same tiling as with MPI.
107       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
108    o model/src:
109       add flag to control printing of domain fields (bathymetry, hFac ...) in
110       ini_mask_etc (call to plot_fieds_xy*).
111    o pkg/thsice:
112       if useEXF, some forcing fields are not valid in overlap: fixed by computing
113       over the interior only + apply EXCH at the end (like with SEAICE advection).
114    o pkg/mdsio:
115      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
116        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
117      - change barrier call for safe multi-threads access to 3-D shared buffer.
118      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
119      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
120        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
121    o pkg/flt:
122      - add fourth-order Runge-Kutta integration
123      - add basic exch2 support (only 1 facet supported so far!)
124    o pkg/mdsio+rw:
125      new S/R to read local (or tile independent) vector (read counterpart of
126       mds_writevec_loc, and front-end write_glvec_rl/rs).
127    o global_ocean.cs32x15: additional input_ad.seaice experiment
128        that uses pkg/seaice rather than pkg/thsice.
129        (using multidim advection for seaice)
130    o towards more F95 syntax for array specification in namelist:
131      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
132        of all verification experiments.
133           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
134          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
135      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
136    o global_ocean.cs32x15: additional input.seaice experiment
137        that uses pkg/seaice rather than pkg/thsice.
138    
139    checkpoint62p (2010/12/17)
140    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
141        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
142    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
143        allow for use of multim. advection in seaice adjoint.
144    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
145      - first attempt to close budgets by taking into account the freshwater
146        flux implied by the sublimation of snow and ice. So far only the
147        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
148        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
149    o eesupp/src:
150      new S/R with new option (NML_EXTENDED_F77) to change array specification
151      from F95 standard to commonly accepted extended F77 form.
152      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
153      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
154      for less tolerant f77 compiler (e.g., pgf77, g77).
155    o globalFiles:
156      commented out in parameter file "data" since it's not safe with MPI
157      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
158      in this case); no longer commented out in restart test (tst_2+2).
159    o add adTapeDir to specify a special directory where adjoint tapes are
160      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
161      and cannot be used together with mdsioLocalDir.
162    o nesting pkgs:
163      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
164      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
165      - add parameter files + utils dir + output from short run on beagle.
166    o pkg/seaice:
167        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
168    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
169      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
170    
171    checkpoint62o (2010/11/25)
172    o pkg/exf:
173      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
174    o pkg/seaice:
175      - seaice_ocean_stress: split a loop for better vectorization of the
176        adjoint code
177      - seaice_growth.F: fix bug in conservation of freshwater connected to
178        capping of heff, put contribution into d_HEFFbyNEG
179      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
180        by something more sensible (parameters that are what their name implies)
181      - change some defaults, so that by default exf-parameters are used for
182        things like rhoAir, cpAir,latent/sensible heat parameters, in order
183        to reproduce the old results, many data.seaice now contain funny values
184        for cpAir and latent heat of sublimation
185    o packages_readparms.F: move exf_readparms up in line so that
186        exf-parameters are visible for other packages (e.g. seaice)
187    o debugMode & debugLevel=2:
188      - differentiate between debugMode & debugLevel=2:
189        debugMode: controls printing of debug messages (sequence of S/R calls).
190        debugLevel: controls printing of algorithm intermediate results and stats.
191      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
192        => allows to print debug-stats without all sequence of call messages.
193      - switch control of debug print from debugLevel to debugMode in many S/R.
194    o pkg/obcs (obcs-sponge):
195        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
196        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
197    o pkg/generic_advdiff:
198      - record overlap minimum size for each advection scheme;
199      - refine criteria on overlap minimum size;
200      - check and stop (in gad_check) if overlap size is too small.
201    o pkg/obcs:
202      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
203        once, in ptracers_implicit.F)
204      - with seaice: remove test on empty file name in obcs_apply_seaice (always
205        apply OB values when tile has OB)
206    o model/src, coriolis setting:
207      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
208        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
209        files (selectCoriMap=3) with any grid.
210      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
211    o pkg/seaice/seaice_growth.F:
212        a few cosmetic changes that reduce the number of lines of code
213    o pkg/obcs: add boundary conditions following Stevens (1990)
214      - the code follows old MOM/NAOSIM code
215      - so far it is only implemented for the eastern and western boundaries
216        and NOT for pTracers
217    o pkg/rbcs:
218      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
219        beginning of the first rbcs forcing period.
220      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
221        offline package, i.e., one file per time, labeled by iteration number;
222        deltaTrbcs sets the timestep with which the data was generated;
223        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
224      - rbcsForcingCycle=0 makes forcing non-cyclic.
225      - make arithmetic safe for negative times and odd forcing periods.
226    
227    checkpoint62n (2010/11/09)
228    o pkg/seaice:
229        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
230    o pkg/obcs:
231       New S/R to copy tracer value from the OB location to narrow band region
232        (width = same as overlap) beyond the OB: preserve OB value (needed for
233        high-order scheme) which were overwritten by EXCH call if in overlap
234        region. Applied to theta, salt, ptracer and advected seaice variables.
235       With seaice: use maskInC in similar way as in gad_advection.F,
236        in seaice_advection.F and advect.F.
237       Update output of experiment seaice_obcs and change exp4 to test OBCS with
238        4th order Adv.Scheme. for pasive salt and ptracer.
239    o tools/genmake2:
240      - when looking for an optfile (not specified), only search for Fortran compiler
241        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
242      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
243        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
244      - set default for CPP to "cpp -traditional -P" (was the case without specifying
245        an optfile, but otherwise default was just "cpp".
246      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
247      - when "CC" is not set in the optfile, look for possible C compiler
248        (instead of just setting CC=cc)
249      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
250        => add a ".F" to ".o" rule for source files with no "#include" (such as
251           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
252      - move gfortran before g77 in list of possible Fortran compiler (consistent
253        with reference compiler switch from g77 to gfortran)
254    o pkg/seaice:
255      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
256        seaice_check that stops the model, when the CPP flag is used.
257      o seaice_growth.F: make capping of ice volume conserving by returning the
258        capped ice as freshwater to EmPmR. This does not change the verification
259        experiments but will change runs where the capping is acutally active
260    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
261      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
262         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
263         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
264    o tools/genmake2:
265      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
266      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
267      - clean previous genmake log files before anything else.
268      - change Makefile to remove testreport log files (*.tr_log) and genmake log
269        files only with "CLEAN" target (instead of "Clean");
270    o pkg/generic_advdiff:
271      Change OBCS in multiDim advection (gad_advection.F):
272       Use maskInC to prevent intermediate update of tracer-field in OB regions,
273       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
274       which were applying future time-step OB values.
275      This way, all explicit calculations use current-time-step OB values
276       (simpler and more consistent).
277      Affects results when set-up uses time-varying OBC and multi-dim advection;
278       update output of experiment seaice_obcs.
279    o pkg/seaice:
280      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
281       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
282         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
283      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
284       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
285       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
286    o pkg aim (2010/10/26):
287      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
288        formulation with obliquity, eccentricity, ... as run-time parameters,
289      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
290        upward shortwave radition at the surface (all-sky and clear-sky).
291    o pkg/obcs:
292      - writing sections with globalFiles=T does not work: switch to tiled-files
293        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
294      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
295      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
296    
297    checkpoint62m (2010/10/21)
298    o pkg/seaice: vectorize seaice_solve4temp.F
299      - move iterations loops outside of i/j-loops
300      - requires 2D arrays for TB and effConduct
301      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
302        modified in this routine
303      - a little bit of clean up, adjusting indentation, etc.
304      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
305        performance and '**TWO' by '**2' (because TWO is a float),
306        replaced ONE, ZERO
307    o eesupp/src:
308       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
309    o pkg/seaice/seaice_growth.F
310      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
311      merging process. The merged routine has two branches, and one activates the 'evolution'
312      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
313      In summary, here is what the '10/10 revision' did consist of
314        part 1: seaice_growth.F revisions 1.71 to 1.75
315          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
316            The emphasis here was on improving readability (e.g. by trying to use meaningful
317            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
318        part 1.5:
319          - revising the lab_sea experiment to make it a more useful (i.e. stable
320            and representative of an actual model run). This was done by generating a
321            (winter) pickup to start from, switching back the main experiment dynamic
322            solver from evp to lsr, having one of the experiments use the free drift solution.
323        part 2: seaice_growth.F revisions 1.76 to 1.85
324          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
325          - Sorting out the various fields units and sign (set early on and reset at the end)
326            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
327            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
328          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
329            and simplifying logical expressions to further improve readibility.
330        part 3: seaice_growth.F revisions 1.86 to 1.89
331          - Re-organize the blocks of code more logically.
332          - Merging the '_if.F' pieces that add something new.
333    o pkg/thsice:
334      - vectorize thsice_solve4temp and thsice_get_exf.
335        Problem: thsice_solve4temp has an unvectorizable statement that
336        might also be problematic for TAF
337      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
338        does not change the verifcation experiment, but will change all
339        experiments that have this flag undefined (not tested in verification);
340        a little reorganization to save a few 2D fields and recomputations
341      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
342      - 2nd step:  fix some store dirs
343        o seems to work somewhat, i.e. using ifort but not g77
344        o likely cause are incomplete init. or recomputation
345        o start verification/global_ocean.cs32x15/input_ad.thsice
346    o pkg/obcs: add support for exch2
347      - the position of the boundary and prescribed values are specified using
348        a global domain with exch2 facets stacked
349        - in x for N,S boundaries (like W2_mapIO=-1)
350        - in y for E,W boundaries (so E,W boundaries do not overlap)
351    o pkg/mdsio: add support for writing global sections with exch2
352        file layout is as for obcs described above:
353        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
354        - for y-z sections, facets are stacked in y
355    o pkg/thsice:
356       - change a few routines for better vectorization: thsice_albedo.F,
357         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
358         not affected, but in particular the latter routine has changed
359         dramatically (not necessarily easier to read now).
360       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
361       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
362    o verification/lab_sea:
363      - overhaul of the forward model experiments. The main motivation
364        for this revision is that lab_sea has proven quite fragile (when
365        changing the sea-ice code, and switching platforms) to a point
366        when failures were very hard to attribute to specific code problems.
367      - the suspected reason for this fragility is noise amplification by evp so,
368        to start with, we decided to replace evp with lsr in the main experiment.
369      - the input.lsr experiment thus became obsolete and was removed.
370      - it was replaced with the input.fd experiment that uses an
371        analytical "free drift" solution as the ice velocity field.
372      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
373        will hopefully allow us to discriminate problems due to dynamic solvers
374        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
375        us to test additional options, along with the salt plume package.
376      - Finally a pickup was generated (at the end of a one year run) to
377        make the tests more representative of an actual model run. Previously
378        the tests starting point was a 1m thickness of ice everywhere.
379    o pkg/seaice:
380      - introducing S\R seaice_freedrift.F that compute the
381        analytical solution to an approximate ice momentum
382        equation (i.e. the simple stress/coriolis balance).
383      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
384        of the free drift velocity field, and enable its use.
385        To actually use the free drift solution as the model ice
386        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
387    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
388    
389    checkpoint62l (2010/10/04)
390    o pkg/seaice:
391      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
392      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
393       version (with USE_ORIGINAL_SBI undef);
394    o add hooks for new packages OASIS, the package will follow
395      (hooks exclude the seaice pkg for now)
396    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
397      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
398      rather than mdsio_readvector.F/mdsio_writevector.F, within
399      adread_adwrite.F to read/write adjoint-related tapes to disk.
400    o eesupp and pkg/mdsio: ALLOW_WHIO
401      Option to write/read 2D fields to files including tiles halos.
402      The main purpose is for adjoint related "tape I/O".
403      The secondary purpose is for debugging phases.
404      A word on those rather specifically intended purposes.
405      The code was meant to be stripped down to the bare minimum.
406      Typically, there is a unique and basic mapping to the global
407      buffer (tile by tile, then proc by proc, then level by level), and
408      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
409      meant to generate user friendly outputs of various shapes and forms.
410      Rather it is intended, for the knowledgeabale developers,
411      to be largely independent of the many mdsio options, to allow
412      outputs of tiles+halos in debugging phases and in adjoint runs,
413      and to allow some flexibility in tuning (adoint) I/O depending on each
414      file system behavior. With regard to tuning, most of the potential knobs
415      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
416      to specify directories, to specify the typical size of I/O calls, etc.)
417      are not yet included, and will be added if they prove useful.
418    o pkg/seaice:
419       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
420    o pkg/seaice:
421       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
422       code (seaice_budget_ice_if.F) which enable to recover old standard
423       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
424       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
425    o model/src (rStar):
426       use simple average (not area weighted) of rStarFac at U,V point when using
427       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
428       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
429    
430    checkpoint62k (2010/09/17)
431    o adjoint
432       * changed verification/global_ocean.cs32x15 ; adjoint now tests
433         Adams-Bashforth 3 + NLFS + RSTAR
434       * some more modifs required for ECCO-GODAE v4
435    o pkg/seaice
436       add SEAICE_AGE_VOL option to use volume instead of area for
437       integrating SEAICE_AGE
438    o model/src:
439       first check-in of sigma & hybrid-sigma coordinate code ; also includes
440       non-linear free-surface parts ; but pressure-gradient not yet coded.
441    o pkg/ptracers:
442       option for ptracer to convert Salt Relax into additional EmP.
443        tested in exp. global_ocean.90x40x15.dwnslp (update output)
444    
445    checkpoint62j (2010/08/25)
446    o pkg/ggl90:
447       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
448    o pkg/dic: car_flux.F, phos_flux.F
449      - reduce number of exp-calls in order to improve performance
450      - clean up a little (replace fields by their macros, etc., fix
451        typo in CPP-flag)
452    o pkg/ggl90: minor changes
453      - GGL90diffKrS was removed --> always use GGL90diffKr
454      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
455      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
456        (commented out for now)
457      - change in max/min operations to ensure that smoothing is ok
458      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
459      - always use diffKrNrT as background profile (i.e. never use diffKr field)
460    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
461    o pkg/dic:
462      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
463        vectorization
464      - small bug fix in insol for the unlikely case of a cartesian grid
465      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
466        + now vectorize, which also removes adjoint recomputations;
467        + replace integer maksp1 by _RL maskp1
468        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
469    
470    checkpoint62i (2010/07/21)
471    o pkg/flt:
472      - with OBCS: stop floats which enter the OB region
473    o model/src:
474      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
475        for implicit vertical advection.
476    o pkg/seaice:
477     - account for melting in seaice age evolution.
478     - remove double counting of seaice ridging effect on seaice age.
479    
480    checkpoint62h (2010/06/18)
481    o pkg/exch2:
482     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
483    o tools/genmake2
484      - remove "-pdefault" option: redundant with the use of "packages.conf";
485      - remove file pkg/pkg_default : set the default as a pkg group
486        ("default_pkg_list") defined in pkg/pkg_groups;
487      - fix for case pkg/pkg_depend is missing (was hanging before);
488      - add option "-pgroups" to specify a different pkg_groups than the default.
489    o verification/adjustment.cs-32x32x1:
490       add a "minimal" set-up test (code_min & input_min) which only compiles
491       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
492    o tools/genmake2
493      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
494      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
495    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
496      files are nearly the same anyway.
497      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
498       - redefinition of tau(i,i) (by a factor of ustar)
499       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
500       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
501       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
502       - replace
503         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
504         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
505         by
506         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
507         (changes results)
508       -> exf_bulkformulae v1.22,
509          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
510          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
511                    output.txt 1.63
512           offline_exf_seaice: output.seaicetd.txt 1.7
513           seaice_obcs: output.txt 1.10)
514      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
515       -> exf_bulkformulae v1.23,
516          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
517          and global_ocean.cs32x15.icedyn (only 11 matching digits)
518      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
519    o adjoint of exch-1:
520     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
521       (note: was already like this when using EXCH-2) and remove flow dir
522       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
523     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
524     - update pkg/exch2 diff list.
525    
526    checkpoint62g (2010/05/19)
527    o eesupp/src (exch-1):
528     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
529       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
530       (renamed to exch1_*rx_cube.F).
531     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
532       to call new exch1 S/R ; update Makefile and .cvsignore.
533     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
534       exch2_xy_rx later)
535      Note: after updating your code, need to run "make clean" in eesupp/src
536    o test experiment bottom_ctrl_5x5:
537       new output_adm.txt with fewer grdchk & less monitor output.
538    o model/src:
539      remove the call to ini_cori in initialise_varia.F (just keep the usual one
540       in initialise_fixed.F). More consistent with coriolis & horizontal grid
541       beeing treated in the same way (ini_grid is not called a 2nd time).
542    o pkg/exf:
543      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
544      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
545      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
546      - cosmetic changes to exf_bulkformulae.F to make it look more like
547        exf_bulk_largeyeager04.F
548    o eesupp/src (exch-1):
549      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
550      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
551        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
552        (even without using MPI).
553      - Message mode: move RecvAck setting (indicator of buffer being ready)
554        from send_put to recv_get S/R (was useless before, but not sure if
555        it's much more useful now);
556      - Switch the order of sync: MPI-proc 1rst and then threads;
557      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
558      - fix AD code for communication mode ='get' (but not used).
559    o model/src:
560      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
561      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
562    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
563    o pkg/ctrl: require a specific set of control variables and exf-flags for
564      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
565    o model/src:
566     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
567       1rst forward sweep, to avoid over-writing output files during recomputations
568       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
569     b) 2nd version:
570      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
571      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
572         writePickupAtEnd) + seaice & ptracers output;
573      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
574    o model/src:
575      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
576    o pkg/exch2:
577      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
578      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
579    o pkg/autodiff & exch2:
580      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
581      (for now, only if ALLOW_EXCH2 is defined).
582    o pkg/autodiff:
583      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
584        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
585       + clean-up comments (_RS is not always real*4)
586      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
587      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
588        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
589    o testreport (AD-tests):
590      no longer link files from dir "../input" (1rst link files from
591      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
592    
593    checkpoint62f (2010/04/29)
594  o model/src/the_main_loop.F:  o model/src/the_main_loop.F:
595    adjust store directives for seaice evp and multicategory according to    adjust store directives for seaice evp and multicategory according to
596    pkg/ecco/the_main_loop.F    pkg/ecco/the_main_loop.F
597  o adjoint:  o adjoint:
598    global_sum_ad was incomplete (noted many times by many people ;)    global_sum_ad was incomplete (noted many times by many people ;)
599    nice description by Jean U. as follows:    nice description by Jean U. as follows:
600    * allreduce(var) in global_sum.F can be interpreted as    * allreduce(var) in global_sum.F can be interpreted as
601      reduce(sum) followed by broadcast of sum.        reduce(sum) followed by broadcast of sum.
602    * The adjoint of that is    * The adjoint of that is
603      sum(adjoint) followed by broadcast(summed adjoint value)      sum(adjoint) followed by broadcast(summed adjoint value)
604      or in other words, allreduce(sum, adjoint vars)      or in other words, allreduce(sum, adjoint vars)
605    We were missing the sum(adjoint)!    We were missing the sum(adjoint)!
606    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 704  o tools/build_options:
704      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
705  o pkg/ecco  o pkg/ecco
706    - allow user defined cost function contributions    - allow user defined cost function contributions
707          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
708          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
709    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
710        the two options are complementary.        the two options are complementary.
711  o pkg/smooth  o pkg/smooth
Legend:
Removed from v.1.1258  
changed lines
  Added in v.1.1381
  ViewVC Help
Powered by ViewVC 1.1.22