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revision 1.1255 by dimitri, Mon Apr 26 18:50:14 2010 UTC revision 1.1377 by jmc, Fri Feb 11 00:06:10 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/gmredi:
8     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
9       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
10       add a verification test-run (front_relax.bvp) to test GM_useBVP.
11    o pkg/seaice:
12     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
13     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to also melt ice.
14    o pkg/seaice:
15     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
16     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
17    o pkg/cheapaml:
18     - from Nico Wienders: New version of this package.
19    o pkg/flt:
20     - add CPP options to prevent floats to re-enter the opposite side of
21       a periodic domain (default: keep periodicity)
22    o pkg/gmredi:
23     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
24       (needed for multi-dim advection).
25     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
26    o model/src:
27     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
28    o tutorial_tracer_adjsens
29     - extend to NLFS and replace maskC by hFacC
30       (change reference output accordingly)
31    
32    checkpoint62r (2011/01/24)
33    o testreport:
34     - add option -deloutp (-do) to remove output file after successful run
35     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
36       extract exact list of procs from this file ; adjust COMMAND by
37       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
38    o pkg/ecco: replace old ineffective way of penalizing deviations from
39      first guess (of obcs) with code by Matt Mazloff
40    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
41      exf/cal
42      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
43        and handle case of obcs?period == 0
44        Not affected by these changes: There is still an inconsistency in
45        the computation of start/endrec for the obcs variables for ALLOW_CAL
46        defined (see comment by Menemenlis, 7-Mar-2003)
47      - make S/R ctrl_get_gen_rec return something meaningful even if
48        ALLOW_CAL is not defined
49      - ctrl_getobcs?: simplify code so that it does not need to use
50                       S/R exf_swapfields
51    o testreport:
52       allow to test MPI with different number of processors for each experiment:
53       create file "SIZE.h.mpi" in each build dir.
54       Note: update of "-command" argument not yet implemented.
55    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
56      alleviate the need for additional 3D tapes when using
57      the non-inear free surface in the adjoint. This is done
58      by adding an 'update' of hfacc etc. to their current
59      value at the beginning of forward_step.F.
60    o pkg/seaice
61      seaice_lsr: move stress-divergence computations out of outer pseudo-
62      timestepping loop
63    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
64      up, so that the calls of the ctrl_* subroutines are really at the end
65      of the routine.
66    o pkg/gmredi:
67      allow to specify a 2-D horizontal map and a 1-D vertical profil
68      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
69    o pkg/seaice:
70      move lsr iterations from seaice_dynsolver to seaice_lsr.
71    o pkg/seaice:
72      reduce memory footprint of seaice mutldim advection tapes,
73      by using a 2D tape independent of the generic_advdiff ones,
74      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
75    
76    checkpoint62q (2010/12/29)
77    o model/src:
78      - check horizontal grid-spacing for unset or zero/negative values.
79      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
80    o pkg/flt:
81      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
82      - precision of input and output files set according to readBinaryPrec
83        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
84      - initial float position from tiled file was not converted to index space
85        (looks like a bug): fixed to make it similar to initial pos. global file.
86    o global_ocean.cs32x15:
87       change SIZE.h of AD set-up to get same tiling as with MPI.
88       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
89    o model/src:
90       add flag to control printing of domain fields (bathymetry, hFac ...) in
91       ini_mask_etc (call to plot_fieds_xy*).
92    o pkg/thsice:
93       if useEXF, some forcing fields are not valid in overlap: fixed by computing
94       over the interior only + apply EXCH at the end (like with SEAICE advection).
95    o pkg/mdsio:
96      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
97        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
98      - change barrier call for safe multi-threads access to 3-D shared buffer.
99      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
100      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
101        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
102    o pkg/flt:
103      - add fourth-order Runge-Kutta integration
104      - add basic exch2 support (only 1 facet supported so far!)
105    o pkg/mdsio+rw:
106      new S/R to read local (or tile independent) vector (read counterpart of
107       mds_writevec_loc, and front-end write_glvec_rl/rs).
108    o global_ocean.cs32x15: additional input_ad.seaice experiment
109        that uses pkg/seaice rather than pkg/thsice.
110        (using multidim advection for seaice)
111    o towards more F95 syntax for array specification in namelist:
112      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
113        of all verification experiments.
114           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
115          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
116      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
117    o global_ocean.cs32x15: additional input.seaice experiment
118        that uses pkg/seaice rather than pkg/thsice.
119    
120    checkpoint62p (2010/12/17)
121    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
122        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
123    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
124        allow for use of multim. advection in seaice adjoint.
125    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
126      - first attempt to close budgets by taking into account the freshwater
127        flux implied by the sublimation of snow and ice. So far only the
128        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
129        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
130    o eesupp/src:
131      new S/R with new option (NML_EXTENDED_F77) to change array specification
132      from F95 standard to commonly accepted extended F77 form.
133      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
134      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
135      for less tolerant f77 compiler (e.g., pgf77, g77).
136    o globalFiles:
137      commented out in parameter file "data" since it's not safe with MPI
138      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
139      in this case); no longer commented out in restart test (tst_2+2).
140    o add adTapeDir to specify a special directory where adjoint tapes are
141      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
142      and cannot be used together with mdsioLocalDir.
143    o nesting pkgs:
144      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
145      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
146      - add parameter files + utils dir + output from short run on beagle.
147    o pkg/seaice:
148        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
149    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
150      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
151    
152    checkpoint62o (2010/11/25)
153    o pkg/exf:
154      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
155    o pkg/seaice:
156      - seaice_ocean_stress: split a loop for better vectorization of the
157        adjoint code
158      - seaice_growth.F: fix bug in conservation of freshwater connected to
159        capping of heff, put contribution into d_HEFFbyNEG
160      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
161        by something more sensible (parameters that are what their name implies)
162      - change some defaults, so that by default exf-parameters are used for
163        things like rhoAir, cpAir,latent/sensible heat parameters, in order
164        to reproduce the old results, many data.seaice now contain funny values
165        for cpAir and latent heat of sublimation
166    o packages_readparms.F: move exf_readparms up in line so that
167        exf-parameters are visible for other packages (e.g. seaice)
168    o debugMode & debugLevel=2:
169      - differentiate between debugMode & debugLevel=2:
170        debugMode: controls printing of debug messages (sequence of S/R calls).
171        debugLevel: controls printing of algorithm intermediate results and stats.
172      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
173        => allows to print debug-stats without all sequence of call messages.
174      - switch control of debug print from debugLevel to debugMode in many S/R.
175    o pkg/obcs (obcs-sponge):
176        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
177        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
178    o pkg/generic_advdiff:
179      - record overlap minimum size for each advection scheme;
180      - refine criteria on overlap minimum size;
181      - check and stop (in gad_check) if overlap size is too small.
182    o pkg/obcs:
183      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
184        once, in ptracers_implicit.F)
185      - with seaice: remove test on empty file name in obcs_apply_seaice (always
186        apply OB values when tile has OB)
187    o model/src, coriolis setting:
188      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
189        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
190        files (selectCoriMap=3) with any grid.
191      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
192    o pkg/seaice/seaice_growth.F:
193        a few cosmetic changes that reduce the number of lines of code
194    o pkg/obcs: add boundary conditions following Stevens (1990)
195      - the code follows old MOM/NAOSIM code
196      - so far it is only implemented for the eastern and western boundaries
197        and NOT for pTracers
198    o pkg/rbcs:
199      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
200        beginning of the first rbcs forcing period.
201      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
202        offline package, i.e., one file per time, labeled by iteration number;
203        deltaTrbcs sets the timestep with which the data was generated;
204        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
205      - rbcsForcingCycle=0 makes forcing non-cyclic.
206      - make arithmetic safe for negative times and odd forcing periods.
207    
208    checkpoint62n (2010/11/09)
209    o pkg/seaice:
210        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
211    o pkg/obcs:
212       New S/R to copy tracer value from the OB location to narrow band region
213        (width = same as overlap) beyond the OB: preserve OB value (needed for
214        high-order scheme) which were overwritten by EXCH call if in overlap
215        region. Applied to theta, salt, ptracer and advected seaice variables.
216       With seaice: use maskInC in similar way as in gad_advection.F,
217        in seaice_advection.F and advect.F.
218       Update output of experiment seaice_obcs and change exp4 to test OBCS with
219        4th order Adv.Scheme. for pasive salt and ptracer.
220    o tools/genmake2:
221      - when looking for an optfile (not specified), only search for Fortran compiler
222        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
223      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
224        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
225      - set default for CPP to "cpp -traditional -P" (was the case without specifying
226        an optfile, but otherwise default was just "cpp".
227      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
228      - when "CC" is not set in the optfile, look for possible C compiler
229        (instead of just setting CC=cc)
230      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
231        => add a ".F" to ".o" rule for source files with no "#include" (such as
232           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
233      - move gfortran before g77 in list of possible Fortran compiler (consistent
234        with reference compiler switch from g77 to gfortran)
235    o pkg/seaice:
236      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
237        seaice_check that stops the model, when the CPP flag is used.
238      o seaice_growth.F: make capping of ice volume conserving by returning the
239        capped ice as freshwater to EmPmR. This does not change the verification
240        experiments but will change runs where the capping is acutally active
241    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
242      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
243         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
244         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
245    o tools/genmake2:
246      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
247      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
248      - clean previous genmake log files before anything else.
249      - change Makefile to remove testreport log files (*.tr_log) and genmake log
250        files only with "CLEAN" target (instead of "Clean");
251    o pkg/generic_advdiff:
252      Change OBCS in multiDim advection (gad_advection.F):
253       Use maskInC to prevent intermediate update of tracer-field in OB regions,
254       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
255       which were applying future time-step OB values.
256      This way, all explicit calculations use current-time-step OB values
257       (simpler and more consistent).
258      Affects results when set-up uses time-varying OBC and multi-dim advection;
259       update output of experiment seaice_obcs.
260    o pkg/seaice:
261      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
262       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
263         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
264      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
265       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
266       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
267    o pkg aim (2010/10/26):
268      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
269        formulation with obliquity, eccentricity, ... as run-time parameters,
270      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
271        upward shortwave radition at the surface (all-sky and clear-sky).
272    o pkg/obcs:
273      - writing sections with globalFiles=T does not work: switch to tiled-files
274        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
275      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
276      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
277    
278    checkpoint62m (2010/10/21)
279    o pkg/seaice: vectorize seaice_solve4temp.F
280      - move iterations loops outside of i/j-loops
281      - requires 2D arrays for TB and effConduct
282      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
283        modified in this routine
284      - a little bit of clean up, adjusting indentation, etc.
285      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
286        performance and '**TWO' by '**2' (because TWO is a float),
287        replaced ONE, ZERO
288    o eesupp/src:
289       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
290    o pkg/seaice/seaice_growth.F
291      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
292      merging process. The merged routine has two branches, and one activates the 'evolution'
293      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
294      In summary, here is what the '10/10 revision' did consist of
295        part 1: seaice_growth.F revisions 1.71 to 1.75
296          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
297            The emphasis here was on improving readability (e.g. by trying to use meaningful
298            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
299        part 1.5:
300          - revising the lab_sea experiment to make it a more useful (i.e. stable
301            and representative of an actual model run). This was done by generating a
302            (winter) pickup to start from, switching back the main experiment dynamic
303            solver from evp to lsr, having one of the experiments use the free drift solution.
304        part 2: seaice_growth.F revisions 1.76 to 1.85
305          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
306          - Sorting out the various fields units and sign (set early on and reset at the end)
307            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
308            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
309          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
310            and simplifying logical expressions to further improve readibility.
311        part 3: seaice_growth.F revisions 1.86 to 1.89
312          - Re-organize the blocks of code more logically.
313          - Merging the '_if.F' pieces that add something new.
314    o pkg/thsice:
315      - vectorize thsice_solve4temp and thsice_get_exf.
316        Problem: thsice_solve4temp has an unvectorizable statement that
317        might also be problematic for TAF
318      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
319        does not change the verifcation experiment, but will change all
320        experiments that have this flag undefined (not tested in verification);
321        a little reorganization to save a few 2D fields and recomputations
322      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
323      - 2nd step:  fix some store dirs
324        o seems to work somewhat, i.e. using ifort but not g77
325        o likely cause are incomplete init. or recomputation
326        o start verification/global_ocean.cs32x15/input_ad.thsice
327    o pkg/obcs: add support for exch2
328      - the position of the boundary and prescribed values are specified using
329        a global domain with exch2 facets stacked
330        - in x for N,S boundaries (like W2_mapIO=-1)
331        - in y for E,W boundaries (so E,W boundaries do not overlap)
332    o pkg/mdsio: add support for writing global sections with exch2
333        file layout is as for obcs described above:
334        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
335        - for y-z sections, facets are stacked in y
336    o pkg/thsice:
337       - change a few routines for better vectorization: thsice_albedo.F,
338         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
339         not affected, but in particular the latter routine has changed
340         dramatically (not necessarily easier to read now).
341       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
342       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
343    o verification/lab_sea:
344      - overhaul of the forward model experiments. The main motivation
345        for this revision is that lab_sea has proven quite fragile (when
346        changing the sea-ice code, and switching platforms) to a point
347        when failures were very hard to attribute to specific code problems.
348      - the suspected reason for this fragility is noise amplification by evp so,
349        to start with, we decided to replace evp with lsr in the main experiment.
350      - the input.lsr experiment thus became obsolete and was removed.
351      - it was replaced with the input.fd experiment that uses an
352        analytical "free drift" solution as the ice velocity field.
353      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
354        will hopefully allow us to discriminate problems due to dynamic solvers
355        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
356        us to test additional options, along with the salt plume package.
357      - Finally a pickup was generated (at the end of a one year run) to
358        make the tests more representative of an actual model run. Previously
359        the tests starting point was a 1m thickness of ice everywhere.
360    o pkg/seaice:
361      - introducing S\R seaice_freedrift.F that compute the
362        analytical solution to an approximate ice momentum
363        equation (i.e. the simple stress/coriolis balance).
364      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
365        of the free drift velocity field, and enable its use.
366        To actually use the free drift solution as the model ice
367        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
368    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
369    
370    checkpoint62l (2010/10/04)
371    o pkg/seaice:
372      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
373      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
374       version (with USE_ORIGINAL_SBI undef);
375    o add hooks for new packages OASIS, the package will follow
376      (hooks exclude the seaice pkg for now)
377    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
378      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
379      rather than mdsio_readvector.F/mdsio_writevector.F, within
380      adread_adwrite.F to read/write adjoint-related tapes to disk.
381    o eesupp and pkg/mdsio: ALLOW_WHIO
382      Option to write/read 2D fields to files including tiles halos.
383      The main purpose is for adjoint related "tape I/O".
384      The secondary purpose is for debugging phases.
385      A word on those rather specifically intended purposes.
386      The code was meant to be stripped down to the bare minimum.
387      Typically, there is a unique and basic mapping to the global
388      buffer (tile by tile, then proc by proc, then level by level), and
389      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
390      meant to generate user friendly outputs of various shapes and forms.
391      Rather it is intended, for the knowledgeabale developers,
392      to be largely independent of the many mdsio options, to allow
393      outputs of tiles+halos in debugging phases and in adjoint runs,
394      and to allow some flexibility in tuning (adoint) I/O depending on each
395      file system behavior. With regard to tuning, most of the potential knobs
396      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
397      to specify directories, to specify the typical size of I/O calls, etc.)
398      are not yet included, and will be added if they prove useful.
399    o pkg/seaice:
400       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
401    o pkg/seaice:
402       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
403       code (seaice_budget_ice_if.F) which enable to recover old standard
404       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
405       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
406    o model/src (rStar):
407       use simple average (not area weighted) of rStarFac at U,V point when using
408       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
409       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
410    
411    checkpoint62k (2010/09/17)
412    o adjoint
413       * changed verification/global_ocean.cs32x15 ; adjoint now tests
414         Adams-Bashforth 3 + NLFS + RSTAR
415       * some more modifs required for ECCO-GODAE v4
416    o pkg/seaice
417       add SEAICE_AGE_VOL option to use volume instead of area for
418       integrating SEAICE_AGE
419    o model/src:
420       first check-in of sigma & hybrid-sigma coordinate code ; also includes
421       non-linear free-surface parts ; but pressure-gradient not yet coded.
422    o pkg/ptracers:
423       option for ptracer to convert Salt Relax into additional EmP.
424        tested in exp. global_ocean.90x40x15.dwnslp (update output)
425    
426    checkpoint62j (2010/08/25)
427    o pkg/ggl90:
428       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
429    o pkg/dic: car_flux.F, phos_flux.F
430      - reduce number of exp-calls in order to improve performance
431      - clean up a little (replace fields by their macros, etc., fix
432        typo in CPP-flag)
433    o pkg/ggl90: minor changes
434      - GGL90diffKrS was removed --> always use GGL90diffKr
435      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
436      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
437        (commented out for now)
438      - change in max/min operations to ensure that smoothing is ok
439      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
440      - always use diffKrNrT as background profile (i.e. never use diffKr field)
441    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
442    o pkg/dic:
443      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
444        vectorization
445      - small bug fix in insol for the unlikely case of a cartesian grid
446      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
447        + now vectorize, which also removes adjoint recomputations;
448        + replace integer maksp1 by _RL maskp1
449        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
450    
451    checkpoint62i (2010/07/21)
452    o pkg/flt:
453      - with OBCS: stop floats which enter the OB region
454    o model/src:
455      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
456        for implicit vertical advection.
457    o pkg/seaice:
458     - account for melting in seaice age evolution.
459     - remove double counting of seaice ridging effect on seaice age.
460    
461    checkpoint62h (2010/06/18)
462    o pkg/exch2:
463     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
464    o tools/genmake2
465      - remove "-pdefault" option: redundant with the use of "packages.conf";
466      - remove file pkg/pkg_default : set the default as a pkg group
467        ("default_pkg_list") defined in pkg/pkg_groups;
468      - fix for case pkg/pkg_depend is missing (was hanging before);
469      - add option "-pgroups" to specify a different pkg_groups than the default.
470    o verification/adjustment.cs-32x32x1:
471       add a "minimal" set-up test (code_min & input_min) which only compiles
472       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
473    o tools/genmake2
474      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
475      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
476    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
477      files are nearly the same anyway.
478      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
479       - redefinition of tau(i,i) (by a factor of ustar)
480       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
481       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
482       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
483       - replace
484         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
485         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
486         by
487         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
488         (changes results)
489       -> exf_bulkformulae v1.22,
490          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
491          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
492                    output.txt 1.63
493           offline_exf_seaice: output.seaicetd.txt 1.7
494           seaice_obcs: output.txt 1.10)
495      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
496       -> exf_bulkformulae v1.23,
497          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
498          and global_ocean.cs32x15.icedyn (only 11 matching digits)
499      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
500    o adjoint of exch-1:
501     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
502       (note: was already like this when using EXCH-2) and remove flow dir
503       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
504     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
505     - update pkg/exch2 diff list.
506    
507    checkpoint62g (2010/05/19)
508    o eesupp/src (exch-1):
509     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
510       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
511       (renamed to exch1_*rx_cube.F).
512     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
513       to call new exch1 S/R ; update Makefile and .cvsignore.
514     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
515       exch2_xy_rx later)
516      Note: after updating your code, need to run "make clean" in eesupp/src
517    o test experiment bottom_ctrl_5x5:
518       new output_adm.txt with fewer grdchk & less monitor output.
519    o model/src:
520      remove the call to ini_cori in initialise_varia.F (just keep the usual one
521       in initialise_fixed.F). More consistent with coriolis & horizontal grid
522       beeing treated in the same way (ini_grid is not called a 2nd time).
523    o pkg/exf:
524      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
525      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
526      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
527      - cosmetic changes to exf_bulkformulae.F to make it look more like
528        exf_bulk_largeyeager04.F
529    o eesupp/src (exch-1):
530      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
531      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
532        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
533        (even without using MPI).
534      - Message mode: move RecvAck setting (indicator of buffer being ready)
535        from send_put to recv_get S/R (was useless before, but not sure if
536        it's much more useful now);
537      - Switch the order of sync: MPI-proc 1rst and then threads;
538      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
539      - fix AD code for communication mode ='get' (but not used).
540    o model/src:
541      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
542      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
543    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
544    o pkg/ctrl: require a specific set of control variables and exf-flags for
545      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
546    o model/src:
547     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
548       1rst forward sweep, to avoid over-writing output files during recomputations
549       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
550     b) 2nd version:
551      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
552      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
553         writePickupAtEnd) + seaice & ptracers output;
554      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
555    o model/src:
556      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
557    o pkg/exch2:
558      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
559      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
560    o pkg/autodiff & exch2:
561      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
562      (for now, only if ALLOW_EXCH2 is defined).
563    o pkg/autodiff:
564      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
565        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
566       + clean-up comments (_RS is not always real*4)
567      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
568      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
569        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
570    o testreport (AD-tests):
571      no longer link files from dir "../input" (1rst link files from
572      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
573    
574    checkpoint62f (2010/04/29)
575    o model/src/the_main_loop.F:
576      adjust store directives for seaice evp and multicategory according to
577      pkg/ecco/the_main_loop.F
578    o adjoint:
579      global_sum_ad was incomplete (noted many times by many people ;)
580      nice description by Jean U. as follows:
581      * allreduce(var) in global_sum.F can be interpreted as
582        reduce(sum) followed by broadcast of sum.
583      * The adjoint of that is
584        sum(adjoint) followed by broadcast(summed adjoint value)
585        or in other words, allreduce(sum, adjoint vars)
586      We were missing the sum(adjoint)!
587      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
588      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
589      The fix should produce 16-digit accuracy between
590      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
591      multi-CPU single-tile (e.g. nSx=1, nPx-2)
592      We'll probably change this yet again shortly
593    o eesupp/src:
594      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
595  o pkg/icefront  o pkg/icefront
596    - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving    - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
597      specification of addmass array based on a 2D field, which is added      specification of addmass array based on a 2D field, which is added
# Line 97  o tools/build_options: Line 685  o tools/build_options:
685      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
686  o pkg/ecco  o pkg/ecco
687    - allow user defined cost function contributions    - allow user defined cost function contributions
688          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
689          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
690    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
691        the two options are complementary.        the two options are complementary.
692  o pkg/smooth  o pkg/smooth
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