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revision 1.1273 by jmc, Tue May 18 22:53:25 2010 UTC revision 1.1404 by jmc, Tue Mar 29 20:11:39 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/generic_advdiff with OBCS:
8      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
9      equivalent to assumption of no tracer gradient outside the OB region.
10      This will affect the results if using obcs+biharmonic diffusion.
11      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
12    o pkg/obcs:
13      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
14      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
15      in Interior region. No impact on solution but affects Velocity monitor stats.
16    o pkg/ptracers (adjoint)
17      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
18      tape file for each tracer
19    o model/inc/src and pkg/autodiff: add parameters that allow to turn
20      of parts of the adjoint code at run time. For now, there are only
21      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
22      parameters are set in data.pkg.
23      This is the lazy coward's version of doing this, but still useful for
24      debugging. In order to do it right, everything needs to be moved to
25      pkg/autodiff.
26    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
27      the end; this fixes the adjoint balancing code for open boundaries.
28    o pkg/ctrl:
29      - change behavior of xx_${varname}period to be analogous to exf-conventions:
30        xx_${varname}period =   0.,  means time-independent control part
31        xx_${varname}period = -12., means one-year-periodic monthly control part
32      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
33        clean up ctrl_init a little, remove unused variables
34      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
35      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
36    
37    checkpoint62u (2011/03/15)
38    o model/src:
39      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
40        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
41      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
42        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
43    o pkg/ctrl/obcs/ecco:
44      - remove obsolete, unused, and partially broken code:
45        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
46        ALLOW_CTRL_OBCS_BALANCE
47      - put a stop statement into ecco/cost_obcsvol.F, but also add
48        cost_obcsvol to ecco_ad_diff.list
49    o pkg/ecco: fix counting cost function contributions for obcs (code
50      by Matt M.) and diffkr for diagnostics
51    o pkg/ecco, pkg/ctrl, pkg/grdchk:
52      add cost penalty terms for initial uvel, vvel, eta controls
53      and I/O for prior error files
54    o pkg/mdsio:
55       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
56       (new argument) to check for tiled file in mdsioLocalDir : this fix the
57       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
58    o pkg/ctrl:
59     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
60       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
61       unused and superfluous variables
62     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
63    o pkg/ecco
64     - enable adjoint of Stevens OB
65    o pkg/ctrl/ecco/grdchk:
66      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
67        Fortunately, we do not have any tests for the numerous cpp-flagged
68        option of "obcs as control parameters" so we will never know
69        if this is an improvement (but at least now things compile).
70      - remove an obsolete initialization from ecco_cost_init_barfiles.F
71      - fix some problems within never used ifdefs to make the code compile
72    o pkg/obcs:
73     - Refine Interior mask definition to work with more complex OB (e.g.
74       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
75       read in Interior mask from file. Check if Interior mask is consistent
76       with OB list of indices.
77    o pkg/seaice
78     - beginning code for a seaice tracer package,
79       but currently only used for seaice age: SEAICE_AGE
80       SEAICE_num = 4
81       iTracer = 1: area-weighted ice age
82               = 2: volume-weighted ice age
83               = 3, 4: template for one-year vs. multi-year ice
84       data.seaice has new namelist SEAICE_PARM03 for arrays related to
85       SEAICE_num
86    
87    checkpoint62t (2011/03/05)
88    o pkg/obcs:
89     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
90       then normal component. This ensures that the normal component is set
91       correctly even when it conficts with tangential setting from an other OB.
92       Affects results of test-experiment seaice_obcs: update the output.txt
93    o pkg/obcs:
94     - add code to monitor statistics of dynamical fields at OB.
95     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
96       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
97       - change default: balance the Net inflow through all OB (instead of balancing
98         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
99     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
100       to match Nortern OB inflow (OBCS_balanceFacN=0).
101    o pkg/seaice:
102     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
103    o pkg/seaice (seaice_growth v 1.113):
104     - reverting seaice_growth to v 1.111 in order to have code with exact bit
105       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
106       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
107       runtime flag SEAICEareaFormula is kept but is inactive
108    o model/src:
109     - add new param to scale curvilinear grid distance and area when using
110       a different sphere radius from the grid-files.
111     - test/check multi-threads EXCH applied to local variable (cg2d_x)
112    o adjoint:
113     - enable adjoint of Stevens OB
114     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
115       (a bit delicate because of potentially modified adj. common block structure;
116       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
117    
118    checkpoint62s (2011/02/15)
119    o pkg/seaice (seaice_growth v 1.112):
120     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
121       computing the ice cover tendency from effective thickness tendencies. Include
122       Ian Fenty's formula.
123     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
124       SEAICEareaFormula.
125     - simplify notations for the various d_HEFF/d_AREA terms.
126    o pkg/gmredi:
127     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
128       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
129       add a verification test-run (front_relax.bvp) to test GM_useBVP.
130    o pkg/seaice (seaice_growth v 1.111):
131     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
132     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
133       also melt ice.
134    o pkg/seaice:
135     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
136     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
137    o pkg/cheapaml:
138     - from Nico Wienders: New version of this package.
139    o pkg/flt:
140     - add CPP options to prevent floats to re-enter the opposite side of
141       a periodic domain (default: keep periodicity)
142    o pkg/gmredi:
143     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
144       (needed for multi-dim advection).
145     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
146    o model/src:
147     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
148    o tutorial_tracer_adjsens
149     - extend to NLFS and replace maskC by hFacC
150       (change reference output accordingly)
151    
152    checkpoint62r (2011/01/24)
153    o testreport:
154     - add option -deloutp (-do) to remove output file after successful run
155     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
156       extract exact list of procs from this file ; adjust COMMAND by
157       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
158    o pkg/ecco: replace old ineffective way of penalizing deviations from
159      first guess (of obcs) with code by Matt Mazloff
160    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
161      exf/cal
162      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
163        and handle case of obcs?period == 0
164        Not affected by these changes: There is still an inconsistency in
165        the computation of start/endrec for the obcs variables for ALLOW_CAL
166        defined (see comment by Menemenlis, 7-Mar-2003)
167      - make S/R ctrl_get_gen_rec return something meaningful even if
168        ALLOW_CAL is not defined
169      - ctrl_getobcs?: simplify code so that it does not need to use
170                       S/R exf_swapfields
171    o testreport:
172       allow to test MPI with different number of processors for each experiment:
173       create file "SIZE.h.mpi" in each build dir.
174       Note: update of "-command" argument not yet implemented.
175    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
176      alleviate the need for additional 3D tapes when using
177      the non-inear free surface in the adjoint. This is done
178      by adding an 'update' of hfacc etc. to their current
179      value at the beginning of forward_step.F.
180    o pkg/seaice
181      seaice_lsr: move stress-divergence computations out of outer pseudo-
182      timestepping loop
183    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
184      up, so that the calls of the ctrl_* subroutines are really at the end
185      of the routine.
186    o pkg/gmredi:
187      allow to specify a 2-D horizontal map and a 1-D vertical profil
188      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
189    o pkg/seaice:
190      move lsr iterations from seaice_dynsolver to seaice_lsr.
191    o pkg/seaice:
192      reduce memory footprint of seaice mutldim advection tapes,
193      by using a 2D tape independent of the generic_advdiff ones,
194      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
195    
196    checkpoint62q (2010/12/29)
197    o model/src:
198      - check horizontal grid-spacing for unset or zero/negative values.
199      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
200    o pkg/flt:
201      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
202      - precision of input and output files set according to readBinaryPrec
203        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
204      - initial float position from tiled file was not converted to index space
205        (looks like a bug): fixed to make it similar to initial pos. global file.
206    o global_ocean.cs32x15:
207       change SIZE.h of AD set-up to get same tiling as with MPI.
208       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
209    o model/src:
210       add flag to control printing of domain fields (bathymetry, hFac ...) in
211       ini_mask_etc (call to plot_fieds_xy*).
212    o pkg/thsice:
213       if useEXF, some forcing fields are not valid in overlap: fixed by computing
214       over the interior only + apply EXCH at the end (like with SEAICE advection).
215    o pkg/mdsio:
216      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
217        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
218      - change barrier call for safe multi-threads access to 3-D shared buffer.
219      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
220      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
221        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
222    o pkg/flt:
223      - add fourth-order Runge-Kutta integration
224      - add basic exch2 support (only 1 facet supported so far!)
225    o pkg/mdsio+rw:
226      new S/R to read local (or tile independent) vector (read counterpart of
227       mds_writevec_loc, and front-end write_glvec_rl/rs).
228    o global_ocean.cs32x15: additional input_ad.seaice experiment
229        that uses pkg/seaice rather than pkg/thsice.
230        (using multidim advection for seaice)
231    o towards more F95 syntax for array specification in namelist:
232      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
233        of all verification experiments.
234           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
235          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
236      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
237    o global_ocean.cs32x15: additional input.seaice experiment
238        that uses pkg/seaice rather than pkg/thsice.
239    
240    checkpoint62p (2010/12/17)
241    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
242        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
243    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
244        allow for use of multim. advection in seaice adjoint.
245    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
246      - first attempt to close budgets by taking into account the freshwater
247        flux implied by the sublimation of snow and ice. So far only the
248        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
249        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
250    o eesupp/src:
251      new S/R with new option (NML_EXTENDED_F77) to change array specification
252      from F95 standard to commonly accepted extended F77 form.
253      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
254      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
255      for less tolerant f77 compiler (e.g., pgf77, g77).
256    o globalFiles:
257      commented out in parameter file "data" since it's not safe with MPI
258      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
259      in this case); no longer commented out in restart test (tst_2+2).
260    o add adTapeDir to specify a special directory where adjoint tapes are
261      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
262      and cannot be used together with mdsioLocalDir.
263    o nesting pkgs:
264      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
265      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
266      - add parameter files + utils dir + output from short run on beagle.
267    o pkg/seaice:
268        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
269    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
270      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
271    
272    checkpoint62o (2010/11/25)
273    o pkg/exf:
274      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
275    o pkg/seaice:
276      - seaice_ocean_stress: split a loop for better vectorization of the
277        adjoint code
278      - seaice_growth.F: fix bug in conservation of freshwater connected to
279        capping of heff, put contribution into d_HEFFbyNEG
280      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
281        by something more sensible (parameters that are what their name implies)
282      - change some defaults, so that by default exf-parameters are used for
283        things like rhoAir, cpAir,latent/sensible heat parameters, in order
284        to reproduce the old results, many data.seaice now contain funny values
285        for cpAir and latent heat of sublimation
286    o packages_readparms.F: move exf_readparms up in line so that
287        exf-parameters are visible for other packages (e.g. seaice)
288    o debugMode & debugLevel=2:
289      - differentiate between debugMode & debugLevel=2:
290        debugMode: controls printing of debug messages (sequence of S/R calls).
291        debugLevel: controls printing of algorithm intermediate results and stats.
292      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
293        => allows to print debug-stats without all sequence of call messages.
294      - switch control of debug print from debugLevel to debugMode in many S/R.
295    o pkg/obcs (obcs-sponge):
296        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
297        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
298    o pkg/generic_advdiff:
299      - record overlap minimum size for each advection scheme;
300      - refine criteria on overlap minimum size;
301      - check and stop (in gad_check) if overlap size is too small.
302    o pkg/obcs:
303      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
304        once, in ptracers_implicit.F)
305      - with seaice: remove test on empty file name in obcs_apply_seaice (always
306        apply OB values when tile has OB)
307    o model/src, coriolis setting:
308      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
309        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
310        files (selectCoriMap=3) with any grid.
311      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
312    o pkg/seaice/seaice_growth.F:
313        a few cosmetic changes that reduce the number of lines of code
314    o pkg/obcs: add boundary conditions following Stevens (1990)
315      - the code follows old MOM/NAOSIM code
316      - so far it is only implemented for the eastern and western boundaries
317        and NOT for pTracers
318    o pkg/rbcs:
319      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
320        beginning of the first rbcs forcing period.
321      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
322        offline package, i.e., one file per time, labeled by iteration number;
323        deltaTrbcs sets the timestep with which the data was generated;
324        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
325      - rbcsForcingCycle=0 makes forcing non-cyclic.
326      - make arithmetic safe for negative times and odd forcing periods.
327    
328    checkpoint62n (2010/11/09)
329    o pkg/seaice:
330        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
331    o pkg/obcs:
332       New S/R to copy tracer value from the OB location to narrow band region
333        (width = same as overlap) beyond the OB: preserve OB value (needed for
334        high-order scheme) which were overwritten by EXCH call if in overlap
335        region. Applied to theta, salt, ptracer and advected seaice variables.
336       With seaice: use maskInC in similar way as in gad_advection.F,
337        in seaice_advection.F and advect.F.
338       Update output of experiment seaice_obcs and change exp4 to test OBCS with
339        4th order Adv.Scheme. for pasive salt and ptracer.
340    o tools/genmake2:
341      - when looking for an optfile (not specified), only search for Fortran compiler
342        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
343      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
344        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
345      - set default for CPP to "cpp -traditional -P" (was the case without specifying
346        an optfile, but otherwise default was just "cpp".
347      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
348      - when "CC" is not set in the optfile, look for possible C compiler
349        (instead of just setting CC=cc)
350      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
351        => add a ".F" to ".o" rule for source files with no "#include" (such as
352           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
353      - move gfortran before g77 in list of possible Fortran compiler (consistent
354        with reference compiler switch from g77 to gfortran)
355    o pkg/seaice:
356      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
357        seaice_check that stops the model, when the CPP flag is used.
358      o seaice_growth.F: make capping of ice volume conserving by returning the
359        capped ice as freshwater to EmPmR. This does not change the verification
360        experiments but will change runs where the capping is acutally active
361    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
362      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
363         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
364         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
365    o tools/genmake2:
366      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
367      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
368      - clean previous genmake log files before anything else.
369      - change Makefile to remove testreport log files (*.tr_log) and genmake log
370        files only with "CLEAN" target (instead of "Clean");
371    o pkg/generic_advdiff:
372      Change OBCS in multiDim advection (gad_advection.F):
373       Use maskInC to prevent intermediate update of tracer-field in OB regions,
374       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
375       which were applying future time-step OB values.
376      This way, all explicit calculations use current-time-step OB values
377       (simpler and more consistent).
378      Affects results when set-up uses time-varying OBC and multi-dim advection;
379       update output of experiment seaice_obcs.
380    o pkg/seaice:
381      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
382       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
383         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
384      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
385       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
386       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
387    o pkg aim (2010/10/26):
388      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
389        formulation with obliquity, eccentricity, ... as run-time parameters,
390      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
391        upward shortwave radition at the surface (all-sky and clear-sky).
392    o pkg/obcs:
393      - writing sections with globalFiles=T does not work: switch to tiled-files
394        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
395      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
396      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
397    
398    checkpoint62m (2010/10/21)
399    o pkg/seaice: vectorize seaice_solve4temp.F
400      - move iterations loops outside of i/j-loops
401      - requires 2D arrays for TB and effConduct
402      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
403        modified in this routine
404      - a little bit of clean up, adjusting indentation, etc.
405      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
406        performance and '**TWO' by '**2' (because TWO is a float),
407        replaced ONE, ZERO
408    o eesupp/src:
409       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
410    o pkg/seaice/seaice_growth.F
411      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
412      merging process. The merged routine has two branches, and one activates the 'evolution'
413      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
414      In summary, here is what the '10/10 revision' did consist of
415        part 1: seaice_growth.F revisions 1.71 to 1.75
416          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
417            The emphasis here was on improving readability (e.g. by trying to use meaningful
418            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
419        part 1.5:
420          - revising the lab_sea experiment to make it a more useful (i.e. stable
421            and representative of an actual model run). This was done by generating a
422            (winter) pickup to start from, switching back the main experiment dynamic
423            solver from evp to lsr, having one of the experiments use the free drift solution.
424        part 2: seaice_growth.F revisions 1.76 to 1.85
425          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
426          - Sorting out the various fields units and sign (set early on and reset at the end)
427            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
428            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
429          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
430            and simplifying logical expressions to further improve readibility.
431        part 3: seaice_growth.F revisions 1.86 to 1.89
432          - Re-organize the blocks of code more logically.
433          - Merging the '_if.F' pieces that add something new.
434    o pkg/thsice:
435      - vectorize thsice_solve4temp and thsice_get_exf.
436        Problem: thsice_solve4temp has an unvectorizable statement that
437        might also be problematic for TAF
438      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
439        does not change the verifcation experiment, but will change all
440        experiments that have this flag undefined (not tested in verification);
441        a little reorganization to save a few 2D fields and recomputations
442      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
443      - 2nd step:  fix some store dirs
444        o seems to work somewhat, i.e. using ifort but not g77
445        o likely cause are incomplete init. or recomputation
446        o start verification/global_ocean.cs32x15/input_ad.thsice
447    o pkg/obcs: add support for exch2
448      - the position of the boundary and prescribed values are specified using
449        a global domain with exch2 facets stacked
450        - in x for N,S boundaries (like W2_mapIO=-1)
451        - in y for E,W boundaries (so E,W boundaries do not overlap)
452    o pkg/mdsio: add support for writing global sections with exch2
453        file layout is as for obcs described above:
454        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
455        - for y-z sections, facets are stacked in y
456    o pkg/thsice:
457       - change a few routines for better vectorization: thsice_albedo.F,
458         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
459         not affected, but in particular the latter routine has changed
460         dramatically (not necessarily easier to read now).
461       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
462       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
463    o verification/lab_sea:
464      - overhaul of the forward model experiments. The main motivation
465        for this revision is that lab_sea has proven quite fragile (when
466        changing the sea-ice code, and switching platforms) to a point
467        when failures were very hard to attribute to specific code problems.
468      - the suspected reason for this fragility is noise amplification by evp so,
469        to start with, we decided to replace evp with lsr in the main experiment.
470      - the input.lsr experiment thus became obsolete and was removed.
471      - it was replaced with the input.fd experiment that uses an
472        analytical "free drift" solution as the ice velocity field.
473      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
474        will hopefully allow us to discriminate problems due to dynamic solvers
475        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
476        us to test additional options, along with the salt plume package.
477      - Finally a pickup was generated (at the end of a one year run) to
478        make the tests more representative of an actual model run. Previously
479        the tests starting point was a 1m thickness of ice everywhere.
480    o pkg/seaice:
481      - introducing S\R seaice_freedrift.F that compute the
482        analytical solution to an approximate ice momentum
483        equation (i.e. the simple stress/coriolis balance).
484      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
485        of the free drift velocity field, and enable its use.
486        To actually use the free drift solution as the model ice
487        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
488    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
489    
490    checkpoint62l (2010/10/04)
491    o pkg/seaice:
492      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
493      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
494       version (with USE_ORIGINAL_SBI undef);
495    o add hooks for new packages OASIS, the package will follow
496      (hooks exclude the seaice pkg for now)
497    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
498      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
499      rather than mdsio_readvector.F/mdsio_writevector.F, within
500      adread_adwrite.F to read/write adjoint-related tapes to disk.
501    o eesupp and pkg/mdsio: ALLOW_WHIO
502      Option to write/read 2D fields to files including tiles halos.
503      The main purpose is for adjoint related "tape I/O".
504      The secondary purpose is for debugging phases.
505      A word on those rather specifically intended purposes.
506      The code was meant to be stripped down to the bare minimum.
507      Typically, there is a unique and basic mapping to the global
508      buffer (tile by tile, then proc by proc, then level by level), and
509      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
510      meant to generate user friendly outputs of various shapes and forms.
511      Rather it is intended, for the knowledgeabale developers,
512      to be largely independent of the many mdsio options, to allow
513      outputs of tiles+halos in debugging phases and in adjoint runs,
514      and to allow some flexibility in tuning (adoint) I/O depending on each
515      file system behavior. With regard to tuning, most of the potential knobs
516      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
517      to specify directories, to specify the typical size of I/O calls, etc.)
518      are not yet included, and will be added if they prove useful.
519    o pkg/seaice:
520       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
521    o pkg/seaice:
522       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
523       code (seaice_budget_ice_if.F) which enable to recover old standard
524       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
525       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
526    o model/src (rStar):
527       use simple average (not area weighted) of rStarFac at U,V point when using
528       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
529       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
530    
531    checkpoint62k (2010/09/17)
532    o adjoint
533       * changed verification/global_ocean.cs32x15 ; adjoint now tests
534         Adams-Bashforth 3 + NLFS + RSTAR
535       * some more modifs required for ECCO-GODAE v4
536    o pkg/seaice
537       add SEAICE_AGE_VOL option to use volume instead of area for
538       integrating SEAICE_AGE
539    o model/src:
540       first check-in of sigma & hybrid-sigma coordinate code ; also includes
541       non-linear free-surface parts ; but pressure-gradient not yet coded.
542    o pkg/ptracers:
543       option for ptracer to convert Salt Relax into additional EmP.
544        tested in exp. global_ocean.90x40x15.dwnslp (update output)
545    
546    checkpoint62j (2010/08/25)
547    o pkg/ggl90:
548       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
549    o pkg/dic: car_flux.F, phos_flux.F
550      - reduce number of exp-calls in order to improve performance
551      - clean up a little (replace fields by their macros, etc., fix
552        typo in CPP-flag)
553    o pkg/ggl90: minor changes
554      - GGL90diffKrS was removed --> always use GGL90diffKr
555      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
556      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
557        (commented out for now)
558      - change in max/min operations to ensure that smoothing is ok
559      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
560      - always use diffKrNrT as background profile (i.e. never use diffKr field)
561    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
562    o pkg/dic:
563      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
564        vectorization
565      - small bug fix in insol for the unlikely case of a cartesian grid
566      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
567        + now vectorize, which also removes adjoint recomputations;
568        + replace integer maksp1 by _RL maskp1
569        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
570    
571    checkpoint62i (2010/07/21)
572    o pkg/flt:
573      - with OBCS: stop floats which enter the OB region
574    o model/src:
575      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
576        for implicit vertical advection.
577    o pkg/seaice:
578     - account for melting in seaice age evolution.
579     - remove double counting of seaice ridging effect on seaice age.
580    
581    checkpoint62h (2010/06/18)
582    o pkg/exch2:
583     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
584    o tools/genmake2
585      - remove "-pdefault" option: redundant with the use of "packages.conf";
586      - remove file pkg/pkg_default : set the default as a pkg group
587        ("default_pkg_list") defined in pkg/pkg_groups;
588      - fix for case pkg/pkg_depend is missing (was hanging before);
589      - add option "-pgroups" to specify a different pkg_groups than the default.
590    o verification/adjustment.cs-32x32x1:
591       add a "minimal" set-up test (code_min & input_min) which only compiles
592       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
593    o tools/genmake2
594      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
595      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
596    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
597      files are nearly the same anyway.
598      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
599       - redefinition of tau(i,i) (by a factor of ustar)
600       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
601       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
602       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
603       - replace
604         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
605         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
606         by
607         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
608         (changes results)
609       -> exf_bulkformulae v1.22,
610          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
611          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
612                    output.txt 1.63
613           offline_exf_seaice: output.seaicetd.txt 1.7
614           seaice_obcs: output.txt 1.10)
615      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
616       -> exf_bulkformulae v1.23,
617          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
618          and global_ocean.cs32x15.icedyn (only 11 matching digits)
619      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
620    o adjoint of exch-1:
621     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
622       (note: was already like this when using EXCH-2) and remove flow dir
623       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
624     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
625     - update pkg/exch2 diff list.
626    
627    checkpoint62g (2010/05/19)
628    o eesupp/src (exch-1):
629     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
630       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
631       (renamed to exch1_*rx_cube.F).
632     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
633       to call new exch1 S/R ; update Makefile and .cvsignore.
634     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
635       exch2_xy_rx later)
636      Note: after updating your code, need to run "make clean" in eesupp/src
637  o test experiment bottom_ctrl_5x5:  o test experiment bottom_ctrl_5x5:
638     new output_adm.txt with fewer grdchk & less monitor output.     new output_adm.txt with fewer grdchk & less monitor output.
639  o model/src:  o model/src:
640    remove the call to ini_cori in initialise_varia.F (just keep the usual one    remove the call to ini_cori in initialise_varia.F (just keep the usual one
641     in initialise_fixed.F). More consistent with coriolis & horizontal grid     in initialise_fixed.F). More consistent with coriolis & horizontal grid
642     beeing treated in the same way (ini_grid is not called a 2nd time).     beeing treated in the same way (ini_grid is not called a 2nd time).
643  o pkg/exf:  o pkg/exf:
644    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
645    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
646    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
# Line 175  o tools/build_options: Line 805  o tools/build_options:
805      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
806  o pkg/ecco  o pkg/ecco
807    - allow user defined cost function contributions    - allow user defined cost function contributions
808          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
809          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
810    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
811        the two options are complementary.        the two options are complementary.
812  o pkg/smooth  o pkg/smooth
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