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revision 1.1240 by jmc, Wed Mar 24 02:12:51 2010 UTC revision 1.1406 by ifenty, Wed Apr 6 23:54:46 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62v (2011/04/02)
8    o verification/1D_ocean_ice_column added to test Ian Fenty's
9      pkg/seaice_growth.F modifications for improving sea ice code differentiability
10    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
11      (new velocity statistics after changing maskInW & maskInS definition)
12    o pkg/generic_advdiff with OBCS:
13      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
14      equivalent to assumption of no tracer gradient outside the OB region.
15      This will affect the results if using obcs+biharmonic diffusion.
16      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
17    o pkg/obcs:
18      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
19      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
20      in Interior region. No impact on solution but affects Velocity monitor stats.
21    o pkg/ptracers (adjoint)
22      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
23      tape file for each tracer
24    o model/inc/src and pkg/autodiff: add parameters that allow to turn
25      of parts of the adjoint code at run time. For now, there are only
26      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
27      parameters are set in data.pkg.
28      This is the lazy coward's version of doing this, but still useful for
29      debugging. In order to do it right, everything needs to be moved to
30      pkg/autodiff.
31    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
32      the end; this fixes the adjoint balancing code for open boundaries.
33    o pkg/ctrl:
34      - change behavior of xx_${varname}period to be analogous to exf-conventions:
35        xx_${varname}period =   0.,  means time-independent control part
36        xx_${varname}period = -12., means one-year-periodic monthly control part
37      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
38        clean up ctrl_init a little, remove unused variables
39      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
40      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
41    
42    checkpoint62u (2011/03/15)
43    o model/src:
44      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
45        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
46      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
47        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
48    o pkg/ctrl/obcs/ecco:
49      - remove obsolete, unused, and partially broken code:
50        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
51        ALLOW_CTRL_OBCS_BALANCE
52      - put a stop statement into ecco/cost_obcsvol.F, but also add
53        cost_obcsvol to ecco_ad_diff.list
54    o pkg/ecco: fix counting cost function contributions for obcs (code
55      by Matt M.) and diffkr for diagnostics
56    o pkg/ecco, pkg/ctrl, pkg/grdchk:
57      add cost penalty terms for initial uvel, vvel, eta controls
58      and I/O for prior error files
59    o pkg/mdsio:
60       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
61       (new argument) to check for tiled file in mdsioLocalDir : this fix the
62       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
63    o pkg/ctrl:
64     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
65       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
66       unused and superfluous variables
67     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
68    o pkg/ecco
69     - enable adjoint of Stevens OB
70    o pkg/ctrl/ecco/grdchk:
71      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
72        Fortunately, we do not have any tests for the numerous cpp-flagged
73        option of "obcs as control parameters" so we will never know
74        if this is an improvement (but at least now things compile).
75      - remove an obsolete initialization from ecco_cost_init_barfiles.F
76      - fix some problems within never used ifdefs to make the code compile
77    o pkg/obcs:
78     - Refine Interior mask definition to work with more complex OB (e.g.
79       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
80       read in Interior mask from file. Check if Interior mask is consistent
81       with OB list of indices.
82    o pkg/seaice
83     - beginning code for a seaice tracer package,
84       but currently only used for seaice age: SEAICE_AGE
85       SEAICE_num = 4
86       iTracer = 1: area-weighted ice age
87               = 2: volume-weighted ice age
88               = 3, 4: template for one-year vs. multi-year ice
89       data.seaice has new namelist SEAICE_PARM03 for arrays related to
90       SEAICE_num
91    
92    checkpoint62t (2011/03/05)
93    o pkg/obcs:
94     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
95       then normal component. This ensures that the normal component is set
96       correctly even when it conficts with tangential setting from an other OB.
97       Affects results of test-experiment seaice_obcs: update the output.txt
98    o pkg/obcs:
99     - add code to monitor statistics of dynamical fields at OB.
100     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
101       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
102       - change default: balance the Net inflow through all OB (instead of balancing
103         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
104     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
105       to match Nortern OB inflow (OBCS_balanceFacN=0).
106    o pkg/seaice:
107     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
108    o pkg/seaice (seaice_growth v 1.113):
109     - reverting seaice_growth to v 1.111 in order to have code with exact bit
110       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
111       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
112       runtime flag SEAICEareaFormula is kept but is inactive
113    o model/src:
114     - add new param to scale curvilinear grid distance and area when using
115       a different sphere radius from the grid-files.
116     - test/check multi-threads EXCH applied to local variable (cg2d_x)
117    o adjoint:
118     - enable adjoint of Stevens OB
119     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
120       (a bit delicate because of potentially modified adj. common block structure;
121       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
122    
123    checkpoint62s (2011/02/15)
124    o pkg/seaice (seaice_growth v 1.112):
125     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
126       computing the ice cover tendency from effective thickness tendencies. Include
127       Ian Fenty's formula.
128     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
129       SEAICEareaFormula.
130     - simplify notations for the various d_HEFF/d_AREA terms.
131    o pkg/gmredi:
132     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
133       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
134       add a verification test-run (front_relax.bvp) to test GM_useBVP.
135    o pkg/seaice (seaice_growth v 1.111):
136     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
137     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
138       also melt ice.
139    o pkg/seaice:
140     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
141     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
142    o pkg/cheapaml:
143     - from Nico Wienders: New version of this package.
144    o pkg/flt:
145     - add CPP options to prevent floats to re-enter the opposite side of
146       a periodic domain (default: keep periodicity)
147    o pkg/gmredi:
148     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
149       (needed for multi-dim advection).
150     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
151    o model/src:
152     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
153    o tutorial_tracer_adjsens
154     - extend to NLFS and replace maskC by hFacC
155       (change reference output accordingly)
156    
157    checkpoint62r (2011/01/24)
158    o testreport:
159     - add option -deloutp (-do) to remove output file after successful run
160     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
161       extract exact list of procs from this file ; adjust COMMAND by
162       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
163    o pkg/ecco: replace old ineffective way of penalizing deviations from
164      first guess (of obcs) with code by Matt Mazloff
165    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
166      exf/cal
167      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
168        and handle case of obcs?period == 0
169        Not affected by these changes: There is still an inconsistency in
170        the computation of start/endrec for the obcs variables for ALLOW_CAL
171        defined (see comment by Menemenlis, 7-Mar-2003)
172      - make S/R ctrl_get_gen_rec return something meaningful even if
173        ALLOW_CAL is not defined
174      - ctrl_getobcs?: simplify code so that it does not need to use
175                       S/R exf_swapfields
176    o testreport:
177       allow to test MPI with different number of processors for each experiment:
178       create file "SIZE.h.mpi" in each build dir.
179       Note: update of "-command" argument not yet implemented.
180    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
181      alleviate the need for additional 3D tapes when using
182      the non-inear free surface in the adjoint. This is done
183      by adding an 'update' of hfacc etc. to their current
184      value at the beginning of forward_step.F.
185    o pkg/seaice
186      seaice_lsr: move stress-divergence computations out of outer pseudo-
187      timestepping loop
188    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
189      up, so that the calls of the ctrl_* subroutines are really at the end
190      of the routine.
191    o pkg/gmredi:
192      allow to specify a 2-D horizontal map and a 1-D vertical profil
193      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
194    o pkg/seaice:
195      move lsr iterations from seaice_dynsolver to seaice_lsr.
196    o pkg/seaice:
197      reduce memory footprint of seaice mutldim advection tapes,
198      by using a 2D tape independent of the generic_advdiff ones,
199      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
200    
201    checkpoint62q (2010/12/29)
202    o model/src:
203      - check horizontal grid-spacing for unset or zero/negative values.
204      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
205    o pkg/flt:
206      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
207      - precision of input and output files set according to readBinaryPrec
208        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
209      - initial float position from tiled file was not converted to index space
210        (looks like a bug): fixed to make it similar to initial pos. global file.
211    o global_ocean.cs32x15:
212       change SIZE.h of AD set-up to get same tiling as with MPI.
213       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
214    o model/src:
215       add flag to control printing of domain fields (bathymetry, hFac ...) in
216       ini_mask_etc (call to plot_fieds_xy*).
217    o pkg/thsice:
218       if useEXF, some forcing fields are not valid in overlap: fixed by computing
219       over the interior only + apply EXCH at the end (like with SEAICE advection).
220    o pkg/mdsio:
221      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
222        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
223      - change barrier call for safe multi-threads access to 3-D shared buffer.
224      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
225      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
226        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
227    o pkg/flt:
228      - add fourth-order Runge-Kutta integration
229      - add basic exch2 support (only 1 facet supported so far!)
230    o pkg/mdsio+rw:
231      new S/R to read local (or tile independent) vector (read counterpart of
232       mds_writevec_loc, and front-end write_glvec_rl/rs).
233    o global_ocean.cs32x15: additional input_ad.seaice experiment
234        that uses pkg/seaice rather than pkg/thsice.
235        (using multidim advection for seaice)
236    o towards more F95 syntax for array specification in namelist:
237      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
238        of all verification experiments.
239           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
240          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
241      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
242    o global_ocean.cs32x15: additional input.seaice experiment
243        that uses pkg/seaice rather than pkg/thsice.
244    
245    checkpoint62p (2010/12/17)
246    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
247        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
248    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
249        allow for use of multim. advection in seaice adjoint.
250    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
251      - first attempt to close budgets by taking into account the freshwater
252        flux implied by the sublimation of snow and ice. So far only the
253        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
254        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
255    o eesupp/src:
256      new S/R with new option (NML_EXTENDED_F77) to change array specification
257      from F95 standard to commonly accepted extended F77 form.
258      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
259      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
260      for less tolerant f77 compiler (e.g., pgf77, g77).
261    o globalFiles:
262      commented out in parameter file "data" since it's not safe with MPI
263      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
264      in this case); no longer commented out in restart test (tst_2+2).
265    o add adTapeDir to specify a special directory where adjoint tapes are
266      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
267      and cannot be used together with mdsioLocalDir.
268    o nesting pkgs:
269      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
270      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
271      - add parameter files + utils dir + output from short run on beagle.
272    o pkg/seaice:
273        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
274    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
275      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
276    
277    checkpoint62o (2010/11/25)
278    o pkg/exf:
279      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
280    o pkg/seaice:
281      - seaice_ocean_stress: split a loop for better vectorization of the
282        adjoint code
283      - seaice_growth.F: fix bug in conservation of freshwater connected to
284        capping of heff, put contribution into d_HEFFbyNEG
285      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
286        by something more sensible (parameters that are what their name implies)
287      - change some defaults, so that by default exf-parameters are used for
288        things like rhoAir, cpAir,latent/sensible heat parameters, in order
289        to reproduce the old results, many data.seaice now contain funny values
290        for cpAir and latent heat of sublimation
291    o packages_readparms.F: move exf_readparms up in line so that
292        exf-parameters are visible for other packages (e.g. seaice)
293    o debugMode & debugLevel=2:
294      - differentiate between debugMode & debugLevel=2:
295        debugMode: controls printing of debug messages (sequence of S/R calls).
296        debugLevel: controls printing of algorithm intermediate results and stats.
297      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
298        => allows to print debug-stats without all sequence of call messages.
299      - switch control of debug print from debugLevel to debugMode in many S/R.
300    o pkg/obcs (obcs-sponge):
301        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
302        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
303    o pkg/generic_advdiff:
304      - record overlap minimum size for each advection scheme;
305      - refine criteria on overlap minimum size;
306      - check and stop (in gad_check) if overlap size is too small.
307    o pkg/obcs:
308      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
309        once, in ptracers_implicit.F)
310      - with seaice: remove test on empty file name in obcs_apply_seaice (always
311        apply OB values when tile has OB)
312    o model/src, coriolis setting:
313      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
314        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
315        files (selectCoriMap=3) with any grid.
316      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
317    o pkg/seaice/seaice_growth.F:
318        a few cosmetic changes that reduce the number of lines of code
319    o pkg/obcs: add boundary conditions following Stevens (1990)
320      - the code follows old MOM/NAOSIM code
321      - so far it is only implemented for the eastern and western boundaries
322        and NOT for pTracers
323    o pkg/rbcs:
324      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
325        beginning of the first rbcs forcing period.
326      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
327        offline package, i.e., one file per time, labeled by iteration number;
328        deltaTrbcs sets the timestep with which the data was generated;
329        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
330      - rbcsForcingCycle=0 makes forcing non-cyclic.
331      - make arithmetic safe for negative times and odd forcing periods.
332    
333    checkpoint62n (2010/11/09)
334    o pkg/seaice:
335        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
336    o pkg/obcs:
337       New S/R to copy tracer value from the OB location to narrow band region
338        (width = same as overlap) beyond the OB: preserve OB value (needed for
339        high-order scheme) which were overwritten by EXCH call if in overlap
340        region. Applied to theta, salt, ptracer and advected seaice variables.
341       With seaice: use maskInC in similar way as in gad_advection.F,
342        in seaice_advection.F and advect.F.
343       Update output of experiment seaice_obcs and change exp4 to test OBCS with
344        4th order Adv.Scheme. for pasive salt and ptracer.
345    o tools/genmake2:
346      - when looking for an optfile (not specified), only search for Fortran compiler
347        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
348      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
349        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
350      - set default for CPP to "cpp -traditional -P" (was the case without specifying
351        an optfile, but otherwise default was just "cpp".
352      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
353      - when "CC" is not set in the optfile, look for possible C compiler
354        (instead of just setting CC=cc)
355      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
356        => add a ".F" to ".o" rule for source files with no "#include" (such as
357           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
358      - move gfortran before g77 in list of possible Fortran compiler (consistent
359        with reference compiler switch from g77 to gfortran)
360    o pkg/seaice:
361      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
362        seaice_check that stops the model, when the CPP flag is used.
363      o seaice_growth.F: make capping of ice volume conserving by returning the
364        capped ice as freshwater to EmPmR. This does not change the verification
365        experiments but will change runs where the capping is acutally active
366    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
367      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
368         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
369         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
370    o tools/genmake2:
371      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
372      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
373      - clean previous genmake log files before anything else.
374      - change Makefile to remove testreport log files (*.tr_log) and genmake log
375        files only with "CLEAN" target (instead of "Clean");
376    o pkg/generic_advdiff:
377      Change OBCS in multiDim advection (gad_advection.F):
378       Use maskInC to prevent intermediate update of tracer-field in OB regions,
379       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
380       which were applying future time-step OB values.
381      This way, all explicit calculations use current-time-step OB values
382       (simpler and more consistent).
383      Affects results when set-up uses time-varying OBC and multi-dim advection;
384       update output of experiment seaice_obcs.
385    o pkg/seaice:
386      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
387       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
388         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
389      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
390       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
391       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
392    o pkg aim (2010/10/26):
393      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
394        formulation with obliquity, eccentricity, ... as run-time parameters,
395      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
396        upward shortwave radition at the surface (all-sky and clear-sky).
397    o pkg/obcs:
398      - writing sections with globalFiles=T does not work: switch to tiled-files
399        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
400      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
401      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
402    
403    checkpoint62m (2010/10/21)
404    o pkg/seaice: vectorize seaice_solve4temp.F
405      - move iterations loops outside of i/j-loops
406      - requires 2D arrays for TB and effConduct
407      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
408        modified in this routine
409      - a little bit of clean up, adjusting indentation, etc.
410      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
411        performance and '**TWO' by '**2' (because TWO is a float),
412        replaced ONE, ZERO
413    o eesupp/src:
414       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
415    o pkg/seaice/seaice_growth.F
416      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
417      merging process. The merged routine has two branches, and one activates the 'evolution'
418      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
419      In summary, here is what the '10/10 revision' did consist of
420        part 1: seaice_growth.F revisions 1.71 to 1.75
421          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
422            The emphasis here was on improving readability (e.g. by trying to use meaningful
423            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
424        part 1.5:
425          - revising the lab_sea experiment to make it a more useful (i.e. stable
426            and representative of an actual model run). This was done by generating a
427            (winter) pickup to start from, switching back the main experiment dynamic
428            solver from evp to lsr, having one of the experiments use the free drift solution.
429        part 2: seaice_growth.F revisions 1.76 to 1.85
430          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
431          - Sorting out the various fields units and sign (set early on and reset at the end)
432            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
433            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
434          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
435            and simplifying logical expressions to further improve readibility.
436        part 3: seaice_growth.F revisions 1.86 to 1.89
437          - Re-organize the blocks of code more logically.
438          - Merging the '_if.F' pieces that add something new.
439    o pkg/thsice:
440      - vectorize thsice_solve4temp and thsice_get_exf.
441        Problem: thsice_solve4temp has an unvectorizable statement that
442        might also be problematic for TAF
443      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
444        does not change the verifcation experiment, but will change all
445        experiments that have this flag undefined (not tested in verification);
446        a little reorganization to save a few 2D fields and recomputations
447      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
448      - 2nd step:  fix some store dirs
449        o seems to work somewhat, i.e. using ifort but not g77
450        o likely cause are incomplete init. or recomputation
451        o start verification/global_ocean.cs32x15/input_ad.thsice
452    o pkg/obcs: add support for exch2
453      - the position of the boundary and prescribed values are specified using
454        a global domain with exch2 facets stacked
455        - in x for N,S boundaries (like W2_mapIO=-1)
456        - in y for E,W boundaries (so E,W boundaries do not overlap)
457    o pkg/mdsio: add support for writing global sections with exch2
458        file layout is as for obcs described above:
459        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
460        - for y-z sections, facets are stacked in y
461    o pkg/thsice:
462       - change a few routines for better vectorization: thsice_albedo.F,
463         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
464         not affected, but in particular the latter routine has changed
465         dramatically (not necessarily easier to read now).
466       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
467       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
468    o verification/lab_sea:
469      - overhaul of the forward model experiments. The main motivation
470        for this revision is that lab_sea has proven quite fragile (when
471        changing the sea-ice code, and switching platforms) to a point
472        when failures were very hard to attribute to specific code problems.
473      - the suspected reason for this fragility is noise amplification by evp so,
474        to start with, we decided to replace evp with lsr in the main experiment.
475      - the input.lsr experiment thus became obsolete and was removed.
476      - it was replaced with the input.fd experiment that uses an
477        analytical "free drift" solution as the ice velocity field.
478      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
479        will hopefully allow us to discriminate problems due to dynamic solvers
480        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
481        us to test additional options, along with the salt plume package.
482      - Finally a pickup was generated (at the end of a one year run) to
483        make the tests more representative of an actual model run. Previously
484        the tests starting point was a 1m thickness of ice everywhere.
485    o pkg/seaice:
486      - introducing S\R seaice_freedrift.F that compute the
487        analytical solution to an approximate ice momentum
488        equation (i.e. the simple stress/coriolis balance).
489      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
490        of the free drift velocity field, and enable its use.
491        To actually use the free drift solution as the model ice
492        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
493    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
494    
495    checkpoint62l (2010/10/04)
496    o pkg/seaice:
497      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
498      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
499       version (with USE_ORIGINAL_SBI undef);
500    o add hooks for new packages OASIS, the package will follow
501      (hooks exclude the seaice pkg for now)
502    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
503      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
504      rather than mdsio_readvector.F/mdsio_writevector.F, within
505      adread_adwrite.F to read/write adjoint-related tapes to disk.
506    o eesupp and pkg/mdsio: ALLOW_WHIO
507      Option to write/read 2D fields to files including tiles halos.
508      The main purpose is for adjoint related "tape I/O".
509      The secondary purpose is for debugging phases.
510      A word on those rather specifically intended purposes.
511      The code was meant to be stripped down to the bare minimum.
512      Typically, there is a unique and basic mapping to the global
513      buffer (tile by tile, then proc by proc, then level by level), and
514      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
515      meant to generate user friendly outputs of various shapes and forms.
516      Rather it is intended, for the knowledgeabale developers,
517      to be largely independent of the many mdsio options, to allow
518      outputs of tiles+halos in debugging phases and in adjoint runs,
519      and to allow some flexibility in tuning (adoint) I/O depending on each
520      file system behavior. With regard to tuning, most of the potential knobs
521      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
522      to specify directories, to specify the typical size of I/O calls, etc.)
523      are not yet included, and will be added if they prove useful.
524    o pkg/seaice:
525       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
526    o pkg/seaice:
527       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
528       code (seaice_budget_ice_if.F) which enable to recover old standard
529       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
530       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
531    o model/src (rStar):
532       use simple average (not area weighted) of rStarFac at U,V point when using
533       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
534       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
535    
536    checkpoint62k (2010/09/17)
537    o adjoint
538       * changed verification/global_ocean.cs32x15 ; adjoint now tests
539         Adams-Bashforth 3 + NLFS + RSTAR
540       * some more modifs required for ECCO-GODAE v4
541    o pkg/seaice
542       add SEAICE_AGE_VOL option to use volume instead of area for
543       integrating SEAICE_AGE
544    o model/src:
545       first check-in of sigma & hybrid-sigma coordinate code ; also includes
546       non-linear free-surface parts ; but pressure-gradient not yet coded.
547    o pkg/ptracers:
548       option for ptracer to convert Salt Relax into additional EmP.
549        tested in exp. global_ocean.90x40x15.dwnslp (update output)
550    
551    checkpoint62j (2010/08/25)
552    o pkg/ggl90:
553       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
554    o pkg/dic: car_flux.F, phos_flux.F
555      - reduce number of exp-calls in order to improve performance
556      - clean up a little (replace fields by their macros, etc., fix
557        typo in CPP-flag)
558    o pkg/ggl90: minor changes
559      - GGL90diffKrS was removed --> always use GGL90diffKr
560      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
561      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
562        (commented out for now)
563      - change in max/min operations to ensure that smoothing is ok
564      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
565      - always use diffKrNrT as background profile (i.e. never use diffKr field)
566    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
567    o pkg/dic:
568      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
569        vectorization
570      - small bug fix in insol for the unlikely case of a cartesian grid
571      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
572        + now vectorize, which also removes adjoint recomputations;
573        + replace integer maksp1 by _RL maskp1
574        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
575    
576    checkpoint62i (2010/07/21)
577    o pkg/flt:
578      - with OBCS: stop floats which enter the OB region
579    o model/src:
580      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
581        for implicit vertical advection.
582    o pkg/seaice:
583     - account for melting in seaice age evolution.
584     - remove double counting of seaice ridging effect on seaice age.
585    
586    checkpoint62h (2010/06/18)
587    o pkg/exch2:
588     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
589    o tools/genmake2
590      - remove "-pdefault" option: redundant with the use of "packages.conf";
591      - remove file pkg/pkg_default : set the default as a pkg group
592        ("default_pkg_list") defined in pkg/pkg_groups;
593      - fix for case pkg/pkg_depend is missing (was hanging before);
594      - add option "-pgroups" to specify a different pkg_groups than the default.
595    o verification/adjustment.cs-32x32x1:
596       add a "minimal" set-up test (code_min & input_min) which only compiles
597       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
598    o tools/genmake2
599      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
600      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
601    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
602      files are nearly the same anyway.
603      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
604       - redefinition of tau(i,i) (by a factor of ustar)
605       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
606       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
607       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
608       - replace
609         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
610         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
611         by
612         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
613         (changes results)
614       -> exf_bulkformulae v1.22,
615          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
616          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
617                    output.txt 1.63
618           offline_exf_seaice: output.seaicetd.txt 1.7
619           seaice_obcs: output.txt 1.10)
620      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
621       -> exf_bulkformulae v1.23,
622          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
623          and global_ocean.cs32x15.icedyn (only 11 matching digits)
624      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
625    o adjoint of exch-1:
626     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
627       (note: was already like this when using EXCH-2) and remove flow dir
628       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
629     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
630     - update pkg/exch2 diff list.
631    
632    checkpoint62g (2010/05/19)
633    o eesupp/src (exch-1):
634     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
635       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
636       (renamed to exch1_*rx_cube.F).
637     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
638       to call new exch1 S/R ; update Makefile and .cvsignore.
639     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
640       exch2_xy_rx later)
641      Note: after updating your code, need to run "make clean" in eesupp/src
642    o test experiment bottom_ctrl_5x5:
643       new output_adm.txt with fewer grdchk & less monitor output.
644    o model/src:
645      remove the call to ini_cori in initialise_varia.F (just keep the usual one
646       in initialise_fixed.F). More consistent with coriolis & horizontal grid
647       beeing treated in the same way (ini_grid is not called a 2nd time).
648    o pkg/exf:
649      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
650      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
651      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
652      - cosmetic changes to exf_bulkformulae.F to make it look more like
653        exf_bulk_largeyeager04.F
654    o eesupp/src (exch-1):
655      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
656      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
657        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
658        (even without using MPI).
659      - Message mode: move RecvAck setting (indicator of buffer being ready)
660        from send_put to recv_get S/R (was useless before, but not sure if
661        it's much more useful now);
662      - Switch the order of sync: MPI-proc 1rst and then threads;
663      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
664      - fix AD code for communication mode ='get' (but not used).
665    o model/src:
666      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
667      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
668    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
669    o pkg/ctrl: require a specific set of control variables and exf-flags for
670      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
671    o model/src:
672     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
673       1rst forward sweep, to avoid over-writing output files during recomputations
674       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
675     b) 2nd version:
676      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
677      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
678         writePickupAtEnd) + seaice & ptracers output;
679      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
680    o model/src:
681      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
682    o pkg/exch2:
683      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
684      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
685    o pkg/autodiff & exch2:
686      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
687      (for now, only if ALLOW_EXCH2 is defined).
688    o pkg/autodiff:
689      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
690        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
691       + clean-up comments (_RS is not always real*4)
692      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
693      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
694        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
695    o testreport (AD-tests):
696      no longer link files from dir "../input" (1rst link files from
697      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
698    
699    checkpoint62f (2010/04/29)
700    o model/src/the_main_loop.F:
701      adjust store directives for seaice evp and multicategory according to
702      pkg/ecco/the_main_loop.F
703    o adjoint:
704      global_sum_ad was incomplete (noted many times by many people ;)
705      nice description by Jean U. as follows:
706      * allreduce(var) in global_sum.F can be interpreted as
707        reduce(sum) followed by broadcast of sum.
708      * The adjoint of that is
709        sum(adjoint) followed by broadcast(summed adjoint value)
710        or in other words, allreduce(sum, adjoint vars)
711      We were missing the sum(adjoint)!
712      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
713      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
714      The fix should produce 16-digit accuracy between
715      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
716      multi-CPU single-tile (e.g. nSx=1, nPx-2)
717      We'll probably change this yet again shortly
718    o eesupp/src:
719      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
720    o pkg/icefront
721      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
722        specification of addmass array based on a 2D field, which is added
723        at bottommost wet level at each horizontal location.
724    o model/src:
725     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
726     layout; (not always compatible with delX,delY setting; commented out for now).
727    o pkg/exch2:
728     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
729     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
730    
731    checkpoint62e (2010/04/15)
732    o pkg/obcs:
733      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
734    o pkg/dic:
735      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
736        (note: not presently tested in any forward verification exp.)
737       update tutorial_global_oce_biogeo AD output file.
738    o pkg/exf:
739      - account for the variation of albedo as a function of zenith angle
740        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
741    o build_options:
742     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
743    o pkg/dic:
744      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
745      - use binary pickup file for restart;
746      - initialise atmos-CO2 box from dic_pCO2 parameter;
747      - fix multi-threaded.
748    o pkg/rbcs:
749     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
750       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
751     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
752       and update output.txt
753    o pkg/kpp:
754     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
755     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
756       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
757       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
758     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
759       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
760    o pkg/offline:
761      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
762      (bug was added in version 1.10 on 2007-08-23).
763    o pkg/offline:
764      - no need to specify periodicExternalForcing, etc ... to use offline pack
765      - offline input files no longer just single prec --> parameter offlineLoadPrec
766    o verification/lab_sea:
767      change AD test to multi-tile setup and update all 4 AD output.
768      NOTE: while cost function values remain very similar,
769      gradients are very different, although gradient checks are self-consistent
770      Should try to get to the bottom of this (cost function summation order?)
771    o pkg/dic:
772      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
773      a weakness of TAF that drops part of double precision in log10 derivative.
774      <= changes removed since problem has been fixed in current TAF version 1.9.71
775      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
776  o pkg/ecco:  o pkg/ecco:
777    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
778    update all 4 lab_sea AD output.    update all 4 lab_sea AD output.
# Line 41  o tools/build_options: Line 810  o tools/build_options:
810      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
811  o pkg/ecco  o pkg/ecco
812    - allow user defined cost function contributions    - allow user defined cost function contributions
813          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
814          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
815    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
816        the two options are complementary.        the two options are complementary.
817  o pkg/smooth  o pkg/smooth
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