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revision 1.1230 by gforget, Wed Feb 17 00:54:35 2010 UTC revision 1.1389 by mlosch, Mon Mar 7 08:23:57 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/ecco: remove an obsolete initialization from ecco_cost_init_barfiles.F
8    o pkg/obcs:
9     - Refine Interior mask definition to work with more complex OB (e.g.
10       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
11       read in Interior mask from file. Check if Interior mask is consistent
12       with OB list of indices.
13    o pkg/seaice
14     - beginning code for a seaice tracer package,
15       but currently only used for seaice age: SEAICE_AGE
16       SEAICE_num = 4
17       iTracer = 1: area-weighted ice age
18               = 2: volume-weighted ice age
19               = 3, 4: template for one-year vs. multi-year ice
20       data.seaice has new namelist SEAICE_PARM03 for arrays related to
21       SEAICE_num
22    
23    checkpoint62t (2011/03/05)
24    o pkg/obcs:
25     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
26       then normal component. This ensures that the normal component is set
27       correctly even when it conficts with tangential setting from an other OB.
28       Affects results of test-experiment seaice_obcs: update the output.txt
29    o pkg/obcs:
30     - add code to monitor statistics of dynamical fields at OB.
31     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
32       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
33       - change default: balance the Net inflow through all OB (instead of balancing
34         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
35     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
36       to match Nortern OB inflow (OBCS_balanceFacN=0).
37    o pkg/seaice:
38     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
39    o pkg/seaice (seaice_growth v 1.113):
40     - reverting seaice_growth to v 1.111 in order to have code with exact bit
41       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
42       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
43       runtime flag SEAICEareaFormula is kept but is inactive
44    o model/src:
45     - add new param to scale curvilinear grid distance and area when using
46       a different sphere radius from the grid-files.
47     - test/check multi-threads EXCH applied to local variable (cg2d_x)
48    o adjoint:
49     - enable adjoint of Stevens OB
50     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
51       (a bit delicate because of potentially modified adj. common block structure;
52       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
53    
54    checkpoint62s (2011/02/15)
55    o pkg/seaice (seaice_growth v 1.112):
56     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
57       computing the ice cover tendency from effective thickness tendencies. Include
58       Ian Fenty's formula.
59     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
60       SEAICEareaFormula.
61     - simplify notations for the various d_HEFF/d_AREA terms.
62    o pkg/gmredi:
63     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
64       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
65       add a verification test-run (front_relax.bvp) to test GM_useBVP.
66    o pkg/seaice (seaice_growth v 1.111):
67     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
68     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
69       also melt ice.
70    o pkg/seaice:
71     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
72     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
73    o pkg/cheapaml:
74     - from Nico Wienders: New version of this package.
75    o pkg/flt:
76     - add CPP options to prevent floats to re-enter the opposite side of
77       a periodic domain (default: keep periodicity)
78    o pkg/gmredi:
79     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
80       (needed for multi-dim advection).
81     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
82    o model/src:
83     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
84    o tutorial_tracer_adjsens
85     - extend to NLFS and replace maskC by hFacC
86       (change reference output accordingly)
87    
88    checkpoint62r (2011/01/24)
89    o testreport:
90     - add option -deloutp (-do) to remove output file after successful run
91     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
92       extract exact list of procs from this file ; adjust COMMAND by
93       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
94    o pkg/ecco: replace old ineffective way of penalizing deviations from
95      first guess (of obcs) with code by Matt Mazloff
96    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
97      exf/cal
98      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
99        and handle case of obcs?period == 0
100        Not affected by these changes: There is still an inconsistency in
101        the computation of start/endrec for the obcs variables for ALLOW_CAL
102        defined (see comment by Menemenlis, 7-Mar-2003)
103      - make S/R ctrl_get_gen_rec return something meaningful even if
104        ALLOW_CAL is not defined
105      - ctrl_getobcs?: simplify code so that it does not need to use
106                       S/R exf_swapfields
107    o testreport:
108       allow to test MPI with different number of processors for each experiment:
109       create file "SIZE.h.mpi" in each build dir.
110       Note: update of "-command" argument not yet implemented.
111    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
112      alleviate the need for additional 3D tapes when using
113      the non-inear free surface in the adjoint. This is done
114      by adding an 'update' of hfacc etc. to their current
115      value at the beginning of forward_step.F.
116    o pkg/seaice
117      seaice_lsr: move stress-divergence computations out of outer pseudo-
118      timestepping loop
119    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
120      up, so that the calls of the ctrl_* subroutines are really at the end
121      of the routine.
122    o pkg/gmredi:
123      allow to specify a 2-D horizontal map and a 1-D vertical profil
124      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
125    o pkg/seaice:
126      move lsr iterations from seaice_dynsolver to seaice_lsr.
127    o pkg/seaice:
128      reduce memory footprint of seaice mutldim advection tapes,
129      by using a 2D tape independent of the generic_advdiff ones,
130      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
131    
132    checkpoint62q (2010/12/29)
133    o model/src:
134      - check horizontal grid-spacing for unset or zero/negative values.
135      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
136    o pkg/flt:
137      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
138      - precision of input and output files set according to readBinaryPrec
139        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
140      - initial float position from tiled file was not converted to index space
141        (looks like a bug): fixed to make it similar to initial pos. global file.
142    o global_ocean.cs32x15:
143       change SIZE.h of AD set-up to get same tiling as with MPI.
144       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
145    o model/src:
146       add flag to control printing of domain fields (bathymetry, hFac ...) in
147       ini_mask_etc (call to plot_fieds_xy*).
148    o pkg/thsice:
149       if useEXF, some forcing fields are not valid in overlap: fixed by computing
150       over the interior only + apply EXCH at the end (like with SEAICE advection).
151    o pkg/mdsio:
152      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
153        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
154      - change barrier call for safe multi-threads access to 3-D shared buffer.
155      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
156      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
157        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
158    o pkg/flt:
159      - add fourth-order Runge-Kutta integration
160      - add basic exch2 support (only 1 facet supported so far!)
161    o pkg/mdsio+rw:
162      new S/R to read local (or tile independent) vector (read counterpart of
163       mds_writevec_loc, and front-end write_glvec_rl/rs).
164    o global_ocean.cs32x15: additional input_ad.seaice experiment
165        that uses pkg/seaice rather than pkg/thsice.
166        (using multidim advection for seaice)
167    o towards more F95 syntax for array specification in namelist:
168      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
169        of all verification experiments.
170           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
171          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
172      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
173    o global_ocean.cs32x15: additional input.seaice experiment
174        that uses pkg/seaice rather than pkg/thsice.
175    
176    checkpoint62p (2010/12/17)
177    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
178        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
179    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
180        allow for use of multim. advection in seaice adjoint.
181    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
182      - first attempt to close budgets by taking into account the freshwater
183        flux implied by the sublimation of snow and ice. So far only the
184        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
185        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
186    o eesupp/src:
187      new S/R with new option (NML_EXTENDED_F77) to change array specification
188      from F95 standard to commonly accepted extended F77 form.
189      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
190      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
191      for less tolerant f77 compiler (e.g., pgf77, g77).
192    o globalFiles:
193      commented out in parameter file "data" since it's not safe with MPI
194      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
195      in this case); no longer commented out in restart test (tst_2+2).
196    o add adTapeDir to specify a special directory where adjoint tapes are
197      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
198      and cannot be used together with mdsioLocalDir.
199    o nesting pkgs:
200      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
201      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
202      - add parameter files + utils dir + output from short run on beagle.
203    o pkg/seaice:
204        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
205    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
206      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
207    
208    checkpoint62o (2010/11/25)
209    o pkg/exf:
210      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
211    o pkg/seaice:
212      - seaice_ocean_stress: split a loop for better vectorization of the
213        adjoint code
214      - seaice_growth.F: fix bug in conservation of freshwater connected to
215        capping of heff, put contribution into d_HEFFbyNEG
216      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
217        by something more sensible (parameters that are what their name implies)
218      - change some defaults, so that by default exf-parameters are used for
219        things like rhoAir, cpAir,latent/sensible heat parameters, in order
220        to reproduce the old results, many data.seaice now contain funny values
221        for cpAir and latent heat of sublimation
222    o packages_readparms.F: move exf_readparms up in line so that
223        exf-parameters are visible for other packages (e.g. seaice)
224    o debugMode & debugLevel=2:
225      - differentiate between debugMode & debugLevel=2:
226        debugMode: controls printing of debug messages (sequence of S/R calls).
227        debugLevel: controls printing of algorithm intermediate results and stats.
228      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
229        => allows to print debug-stats without all sequence of call messages.
230      - switch control of debug print from debugLevel to debugMode in many S/R.
231    o pkg/obcs (obcs-sponge):
232        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
233        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
234    o pkg/generic_advdiff:
235      - record overlap minimum size for each advection scheme;
236      - refine criteria on overlap minimum size;
237      - check and stop (in gad_check) if overlap size is too small.
238    o pkg/obcs:
239      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
240        once, in ptracers_implicit.F)
241      - with seaice: remove test on empty file name in obcs_apply_seaice (always
242        apply OB values when tile has OB)
243    o model/src, coriolis setting:
244      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
245        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
246        files (selectCoriMap=3) with any grid.
247      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
248    o pkg/seaice/seaice_growth.F:
249        a few cosmetic changes that reduce the number of lines of code
250    o pkg/obcs: add boundary conditions following Stevens (1990)
251      - the code follows old MOM/NAOSIM code
252      - so far it is only implemented for the eastern and western boundaries
253        and NOT for pTracers
254    o pkg/rbcs:
255      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
256        beginning of the first rbcs forcing period.
257      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
258        offline package, i.e., one file per time, labeled by iteration number;
259        deltaTrbcs sets the timestep with which the data was generated;
260        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
261      - rbcsForcingCycle=0 makes forcing non-cyclic.
262      - make arithmetic safe for negative times and odd forcing periods.
263    
264    checkpoint62n (2010/11/09)
265    o pkg/seaice:
266        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
267    o pkg/obcs:
268       New S/R to copy tracer value from the OB location to narrow band region
269        (width = same as overlap) beyond the OB: preserve OB value (needed for
270        high-order scheme) which were overwritten by EXCH call if in overlap
271        region. Applied to theta, salt, ptracer and advected seaice variables.
272       With seaice: use maskInC in similar way as in gad_advection.F,
273        in seaice_advection.F and advect.F.
274       Update output of experiment seaice_obcs and change exp4 to test OBCS with
275        4th order Adv.Scheme. for pasive salt and ptracer.
276    o tools/genmake2:
277      - when looking for an optfile (not specified), only search for Fortran compiler
278        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
279      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
280        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
281      - set default for CPP to "cpp -traditional -P" (was the case without specifying
282        an optfile, but otherwise default was just "cpp".
283      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
284      - when "CC" is not set in the optfile, look for possible C compiler
285        (instead of just setting CC=cc)
286      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
287        => add a ".F" to ".o" rule for source files with no "#include" (such as
288           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
289      - move gfortran before g77 in list of possible Fortran compiler (consistent
290        with reference compiler switch from g77 to gfortran)
291    o pkg/seaice:
292      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
293        seaice_check that stops the model, when the CPP flag is used.
294      o seaice_growth.F: make capping of ice volume conserving by returning the
295        capped ice as freshwater to EmPmR. This does not change the verification
296        experiments but will change runs where the capping is acutally active
297    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
298      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
299         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
300         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
301    o tools/genmake2:
302      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
303      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
304      - clean previous genmake log files before anything else.
305      - change Makefile to remove testreport log files (*.tr_log) and genmake log
306        files only with "CLEAN" target (instead of "Clean");
307    o pkg/generic_advdiff:
308      Change OBCS in multiDim advection (gad_advection.F):
309       Use maskInC to prevent intermediate update of tracer-field in OB regions,
310       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
311       which were applying future time-step OB values.
312      This way, all explicit calculations use current-time-step OB values
313       (simpler and more consistent).
314      Affects results when set-up uses time-varying OBC and multi-dim advection;
315       update output of experiment seaice_obcs.
316    o pkg/seaice:
317      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
318       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
319         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
320      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
321       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
322       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
323    o pkg aim (2010/10/26):
324      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
325        formulation with obliquity, eccentricity, ... as run-time parameters,
326      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
327        upward shortwave radition at the surface (all-sky and clear-sky).
328    o pkg/obcs:
329      - writing sections with globalFiles=T does not work: switch to tiled-files
330        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
331      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
332      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
333    
334    checkpoint62m (2010/10/21)
335    o pkg/seaice: vectorize seaice_solve4temp.F
336      - move iterations loops outside of i/j-loops
337      - requires 2D arrays for TB and effConduct
338      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
339        modified in this routine
340      - a little bit of clean up, adjusting indentation, etc.
341      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
342        performance and '**TWO' by '**2' (because TWO is a float),
343        replaced ONE, ZERO
344    o eesupp/src:
345       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
346    o pkg/seaice/seaice_growth.F
347      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
348      merging process. The merged routine has two branches, and one activates the 'evolution'
349      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
350      In summary, here is what the '10/10 revision' did consist of
351        part 1: seaice_growth.F revisions 1.71 to 1.75
352          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
353            The emphasis here was on improving readability (e.g. by trying to use meaningful
354            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
355        part 1.5:
356          - revising the lab_sea experiment to make it a more useful (i.e. stable
357            and representative of an actual model run). This was done by generating a
358            (winter) pickup to start from, switching back the main experiment dynamic
359            solver from evp to lsr, having one of the experiments use the free drift solution.
360        part 2: seaice_growth.F revisions 1.76 to 1.85
361          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
362          - Sorting out the various fields units and sign (set early on and reset at the end)
363            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
364            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
365          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
366            and simplifying logical expressions to further improve readibility.
367        part 3: seaice_growth.F revisions 1.86 to 1.89
368          - Re-organize the blocks of code more logically.
369          - Merging the '_if.F' pieces that add something new.
370    o pkg/thsice:
371      - vectorize thsice_solve4temp and thsice_get_exf.
372        Problem: thsice_solve4temp has an unvectorizable statement that
373        might also be problematic for TAF
374      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
375        does not change the verifcation experiment, but will change all
376        experiments that have this flag undefined (not tested in verification);
377        a little reorganization to save a few 2D fields and recomputations
378      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
379      - 2nd step:  fix some store dirs
380        o seems to work somewhat, i.e. using ifort but not g77
381        o likely cause are incomplete init. or recomputation
382        o start verification/global_ocean.cs32x15/input_ad.thsice
383    o pkg/obcs: add support for exch2
384      - the position of the boundary and prescribed values are specified using
385        a global domain with exch2 facets stacked
386        - in x for N,S boundaries (like W2_mapIO=-1)
387        - in y for E,W boundaries (so E,W boundaries do not overlap)
388    o pkg/mdsio: add support for writing global sections with exch2
389        file layout is as for obcs described above:
390        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
391        - for y-z sections, facets are stacked in y
392    o pkg/thsice:
393       - change a few routines for better vectorization: thsice_albedo.F,
394         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
395         not affected, but in particular the latter routine has changed
396         dramatically (not necessarily easier to read now).
397       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
398       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
399    o verification/lab_sea:
400      - overhaul of the forward model experiments. The main motivation
401        for this revision is that lab_sea has proven quite fragile (when
402        changing the sea-ice code, and switching platforms) to a point
403        when failures were very hard to attribute to specific code problems.
404      - the suspected reason for this fragility is noise amplification by evp so,
405        to start with, we decided to replace evp with lsr in the main experiment.
406      - the input.lsr experiment thus became obsolete and was removed.
407      - it was replaced with the input.fd experiment that uses an
408        analytical "free drift" solution as the ice velocity field.
409      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
410        will hopefully allow us to discriminate problems due to dynamic solvers
411        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
412        us to test additional options, along with the salt plume package.
413      - Finally a pickup was generated (at the end of a one year run) to
414        make the tests more representative of an actual model run. Previously
415        the tests starting point was a 1m thickness of ice everywhere.
416    o pkg/seaice:
417      - introducing S\R seaice_freedrift.F that compute the
418        analytical solution to an approximate ice momentum
419        equation (i.e. the simple stress/coriolis balance).
420      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
421        of the free drift velocity field, and enable its use.
422        To actually use the free drift solution as the model ice
423        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
424    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
425    
426    checkpoint62l (2010/10/04)
427    o pkg/seaice:
428      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
429      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
430       version (with USE_ORIGINAL_SBI undef);
431    o add hooks for new packages OASIS, the package will follow
432      (hooks exclude the seaice pkg for now)
433    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
434      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
435      rather than mdsio_readvector.F/mdsio_writevector.F, within
436      adread_adwrite.F to read/write adjoint-related tapes to disk.
437    o eesupp and pkg/mdsio: ALLOW_WHIO
438      Option to write/read 2D fields to files including tiles halos.
439      The main purpose is for adjoint related "tape I/O".
440      The secondary purpose is for debugging phases.
441      A word on those rather specifically intended purposes.
442      The code was meant to be stripped down to the bare minimum.
443      Typically, there is a unique and basic mapping to the global
444      buffer (tile by tile, then proc by proc, then level by level), and
445      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
446      meant to generate user friendly outputs of various shapes and forms.
447      Rather it is intended, for the knowledgeabale developers,
448      to be largely independent of the many mdsio options, to allow
449      outputs of tiles+halos in debugging phases and in adjoint runs,
450      and to allow some flexibility in tuning (adoint) I/O depending on each
451      file system behavior. With regard to tuning, most of the potential knobs
452      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
453      to specify directories, to specify the typical size of I/O calls, etc.)
454      are not yet included, and will be added if they prove useful.
455    o pkg/seaice:
456       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
457    o pkg/seaice:
458       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
459       code (seaice_budget_ice_if.F) which enable to recover old standard
460       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
461       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
462    o model/src (rStar):
463       use simple average (not area weighted) of rStarFac at U,V point when using
464       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
465       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
466    
467    checkpoint62k (2010/09/17)
468    o adjoint
469       * changed verification/global_ocean.cs32x15 ; adjoint now tests
470         Adams-Bashforth 3 + NLFS + RSTAR
471       * some more modifs required for ECCO-GODAE v4
472    o pkg/seaice
473       add SEAICE_AGE_VOL option to use volume instead of area for
474       integrating SEAICE_AGE
475    o model/src:
476       first check-in of sigma & hybrid-sigma coordinate code ; also includes
477       non-linear free-surface parts ; but pressure-gradient not yet coded.
478    o pkg/ptracers:
479       option for ptracer to convert Salt Relax into additional EmP.
480        tested in exp. global_ocean.90x40x15.dwnslp (update output)
481    
482    checkpoint62j (2010/08/25)
483    o pkg/ggl90:
484       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
485    o pkg/dic: car_flux.F, phos_flux.F
486      - reduce number of exp-calls in order to improve performance
487      - clean up a little (replace fields by their macros, etc., fix
488        typo in CPP-flag)
489    o pkg/ggl90: minor changes
490      - GGL90diffKrS was removed --> always use GGL90diffKr
491      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
492      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
493        (commented out for now)
494      - change in max/min operations to ensure that smoothing is ok
495      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
496      - always use diffKrNrT as background profile (i.e. never use diffKr field)
497    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
498    o pkg/dic:
499      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
500        vectorization
501      - small bug fix in insol for the unlikely case of a cartesian grid
502      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
503        + now vectorize, which also removes adjoint recomputations;
504        + replace integer maksp1 by _RL maskp1
505        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
506    
507    checkpoint62i (2010/07/21)
508    o pkg/flt:
509      - with OBCS: stop floats which enter the OB region
510    o model/src:
511      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
512        for implicit vertical advection.
513    o pkg/seaice:
514     - account for melting in seaice age evolution.
515     - remove double counting of seaice ridging effect on seaice age.
516    
517    checkpoint62h (2010/06/18)
518    o pkg/exch2:
519     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
520    o tools/genmake2
521      - remove "-pdefault" option: redundant with the use of "packages.conf";
522      - remove file pkg/pkg_default : set the default as a pkg group
523        ("default_pkg_list") defined in pkg/pkg_groups;
524      - fix for case pkg/pkg_depend is missing (was hanging before);
525      - add option "-pgroups" to specify a different pkg_groups than the default.
526    o verification/adjustment.cs-32x32x1:
527       add a "minimal" set-up test (code_min & input_min) which only compiles
528       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
529    o tools/genmake2
530      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
531      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
532    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
533      files are nearly the same anyway.
534      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
535       - redefinition of tau(i,i) (by a factor of ustar)
536       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
537       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
538       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
539       - replace
540         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
541         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
542         by
543         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
544         (changes results)
545       -> exf_bulkformulae v1.22,
546          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
547          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
548                    output.txt 1.63
549           offline_exf_seaice: output.seaicetd.txt 1.7
550           seaice_obcs: output.txt 1.10)
551      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
552       -> exf_bulkformulae v1.23,
553          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
554          and global_ocean.cs32x15.icedyn (only 11 matching digits)
555      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
556    o adjoint of exch-1:
557     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
558       (note: was already like this when using EXCH-2) and remove flow dir
559       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
560     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
561     - update pkg/exch2 diff list.
562    
563    checkpoint62g (2010/05/19)
564    o eesupp/src (exch-1):
565     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
566       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
567       (renamed to exch1_*rx_cube.F).
568     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
569       to call new exch1 S/R ; update Makefile and .cvsignore.
570     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
571       exch2_xy_rx later)
572      Note: after updating your code, need to run "make clean" in eesupp/src
573    o test experiment bottom_ctrl_5x5:
574       new output_adm.txt with fewer grdchk & less monitor output.
575    o model/src:
576      remove the call to ini_cori in initialise_varia.F (just keep the usual one
577       in initialise_fixed.F). More consistent with coriolis & horizontal grid
578       beeing treated in the same way (ini_grid is not called a 2nd time).
579    o pkg/exf:
580      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
581      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
582      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
583      - cosmetic changes to exf_bulkformulae.F to make it look more like
584        exf_bulk_largeyeager04.F
585    o eesupp/src (exch-1):
586      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
587      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
588        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
589        (even without using MPI).
590      - Message mode: move RecvAck setting (indicator of buffer being ready)
591        from send_put to recv_get S/R (was useless before, but not sure if
592        it's much more useful now);
593      - Switch the order of sync: MPI-proc 1rst and then threads;
594      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
595      - fix AD code for communication mode ='get' (but not used).
596    o model/src:
597      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
598      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
599    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
600    o pkg/ctrl: require a specific set of control variables and exf-flags for
601      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
602    o model/src:
603     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
604       1rst forward sweep, to avoid over-writing output files during recomputations
605       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
606     b) 2nd version:
607      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
608      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
609         writePickupAtEnd) + seaice & ptracers output;
610      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
611    o model/src:
612      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
613    o pkg/exch2:
614      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
615      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
616    o pkg/autodiff & exch2:
617      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
618      (for now, only if ALLOW_EXCH2 is defined).
619    o pkg/autodiff:
620      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
621        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
622       + clean-up comments (_RS is not always real*4)
623      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
624      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
625        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
626    o testreport (AD-tests):
627      no longer link files from dir "../input" (1rst link files from
628      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
629    
630    checkpoint62f (2010/04/29)
631    o model/src/the_main_loop.F:
632      adjust store directives for seaice evp and multicategory according to
633      pkg/ecco/the_main_loop.F
634    o adjoint:
635      global_sum_ad was incomplete (noted many times by many people ;)
636      nice description by Jean U. as follows:
637      * allreduce(var) in global_sum.F can be interpreted as
638        reduce(sum) followed by broadcast of sum.
639      * The adjoint of that is
640        sum(adjoint) followed by broadcast(summed adjoint value)
641        or in other words, allreduce(sum, adjoint vars)
642      We were missing the sum(adjoint)!
643      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
644      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
645      The fix should produce 16-digit accuracy between
646      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
647      multi-CPU single-tile (e.g. nSx=1, nPx-2)
648      We'll probably change this yet again shortly
649    o eesupp/src:
650      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
651    o pkg/icefront
652      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
653        specification of addmass array based on a 2D field, which is added
654        at bottommost wet level at each horizontal location.
655    o model/src:
656     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
657     layout; (not always compatible with delX,delY setting; commented out for now).
658    o pkg/exch2:
659     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
660     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
661    
662    checkpoint62e (2010/04/15)
663    o pkg/obcs:
664      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
665    o pkg/dic:
666      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
667        (note: not presently tested in any forward verification exp.)
668       update tutorial_global_oce_biogeo AD output file.
669    o pkg/exf:
670      - account for the variation of albedo as a function of zenith angle
671        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
672    o build_options:
673     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
674    o pkg/dic:
675      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
676      - use binary pickup file for restart;
677      - initialise atmos-CO2 box from dic_pCO2 parameter;
678      - fix multi-threaded.
679    o pkg/rbcs:
680     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
681       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
682     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
683       and update output.txt
684    o pkg/kpp:
685     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
686     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
687       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
688       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
689     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
690       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
691    o pkg/offline:
692      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
693      (bug was added in version 1.10 on 2007-08-23).
694    o pkg/offline:
695      - no need to specify periodicExternalForcing, etc ... to use offline pack
696      - offline input files no longer just single prec --> parameter offlineLoadPrec
697    o verification/lab_sea:
698      change AD test to multi-tile setup and update all 4 AD output.
699      NOTE: while cost function values remain very similar,
700      gradients are very different, although gradient checks are self-consistent
701      Should try to get to the bottom of this (cost function summation order?)
702    o pkg/dic:
703      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
704      a weakness of TAF that drops part of double precision in log10 derivative.
705      <= changes removed since problem has been fixed in current TAF version 1.9.71
706      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
707    o pkg/ecco:
708      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
709      update all 4 lab_sea AD output.
710    
711    checkpoint62d (2010/03/22)
712    o build_options:
713      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
714    o remove unbalanced quote (single or double) in commented line of source code
715      (may cause some warning with some preprocessor/makedepend versions).
716    o pkg/seaice:
717      fix seaice_model.F for adjoint (gael) and update AD results of experiments
718       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
719    o testreport:
720      add option '-runonly' (short: '-ro') to just do the run part (without make).
721    o eesupp: remove JAM communication code (obsolete).
722    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
723      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
724      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
725      (update also the output).
726    
727    checkpoint62c (2010/03/02)
728    o tools/build_options :
729       move (some) old optfiles from build_options/ to build_options/unsupported/
730    o model/src and pkg/exf
731       surface relaxation -- separating data and data.exf options
732       The point is to ensure that we specify the surface relaxation
733       either in data or in data.exf (but not half and half) and to
734       avoid an accidental relaxation to 0 (which happened if a time
735       scale was specified but the file name was left empty)
736  o model/src model/inc and pkg/mom_common  o model/src model/inc and pkg/mom_common
737     ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity     ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
738     => addition to the viscosity field as computed by others schemes     => addition to the viscosity field as computed by others schemes
# Line 12  o tools/build_options: Line 741  o tools/build_options:
741      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
742  o pkg/ecco  o pkg/ecco
743    - allow user defined cost function contributions    - allow user defined cost function contributions
744          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
745          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
746    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
747        the two options are complementary.        the two options are complementary.
748  o pkg/smooth  o pkg/smooth
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