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revision 1.1245 by jmc, Thu Apr 1 15:32:08 2010 UTC revision 1.1407 by jmc, Thu Apr 14 22:23:58 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 external_fields_load:
8      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
9       interpolation weights) to use in a periodic time-series ; do not divide by
10       time-step to convert to integer:
11       - this fixes case where externForcingPeriod is not multiple of time-step
12          (Thanks to Christopher L. Wolfe)
13       - this fixes case where externForcingPeriod is an odd multiple of time-step
14         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
15      store index of time-record which is currently loaded:
16       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
17       - needed for the adjoint but not yet used because of extensive recomputations;
18         (to be fixed soon)
19    
20    checkpoint62v (2011/04/02)
21    o verification/1D_ocean_ice_column added to test Ian Fenty's
22      pkg/seaice_growth.F modifications for improving sea ice code differentiability
23    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
24      (new velocity statistics after changing maskInW & maskInS definition)
25    o pkg/generic_advdiff with OBCS:
26      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
27      equivalent to assumption of no tracer gradient outside the OB region.
28      This will affect the results if using obcs+biharmonic diffusion.
29      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
30    o pkg/obcs:
31      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
32      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
33      in Interior region. No impact on solution but affects Velocity monitor stats.
34    o pkg/ptracers (adjoint)
35      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
36      tape file for each tracer
37    o model/inc/src and pkg/autodiff: add parameters that allow to turn
38      of parts of the adjoint code at run time. For now, there are only
39      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
40      parameters are set in data.pkg.
41      This is the lazy coward's version of doing this, but still useful for
42      debugging. In order to do it right, everything needs to be moved to
43      pkg/autodiff.
44    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
45      the end; this fixes the adjoint balancing code for open boundaries.
46    o pkg/ctrl:
47      - change behavior of xx_${varname}period to be analogous to exf-conventions:
48        xx_${varname}period =   0.,  means time-independent control part
49        xx_${varname}period = -12., means one-year-periodic monthly control part
50      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
51        clean up ctrl_init a little, remove unused variables
52      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
53      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
54    
55    checkpoint62u (2011/03/15)
56    o model/src:
57      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
58        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
59      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
60        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
61    o pkg/ctrl/obcs/ecco:
62      - remove obsolete, unused, and partially broken code:
63        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
64        ALLOW_CTRL_OBCS_BALANCE
65      - put a stop statement into ecco/cost_obcsvol.F, but also add
66        cost_obcsvol to ecco_ad_diff.list
67    o pkg/ecco: fix counting cost function contributions for obcs (code
68      by Matt M.) and diffkr for diagnostics
69    o pkg/ecco, pkg/ctrl, pkg/grdchk:
70      add cost penalty terms for initial uvel, vvel, eta controls
71      and I/O for prior error files
72    o pkg/mdsio:
73       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
74       (new argument) to check for tiled file in mdsioLocalDir : this fix the
75       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
76    o pkg/ctrl:
77     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
78       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
79       unused and superfluous variables
80     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
81    o pkg/ecco
82     - enable adjoint of Stevens OB
83    o pkg/ctrl/ecco/grdchk:
84      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
85        Fortunately, we do not have any tests for the numerous cpp-flagged
86        option of "obcs as control parameters" so we will never know
87        if this is an improvement (but at least now things compile).
88      - remove an obsolete initialization from ecco_cost_init_barfiles.F
89      - fix some problems within never used ifdefs to make the code compile
90    o pkg/obcs:
91     - Refine Interior mask definition to work with more complex OB (e.g.
92       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
93       read in Interior mask from file. Check if Interior mask is consistent
94       with OB list of indices.
95    o pkg/seaice
96     - beginning code for a seaice tracer package,
97       but currently only used for seaice age: SEAICE_AGE
98       SEAICE_num = 4
99       iTracer = 1: area-weighted ice age
100               = 2: volume-weighted ice age
101               = 3, 4: template for one-year vs. multi-year ice
102       data.seaice has new namelist SEAICE_PARM03 for arrays related to
103       SEAICE_num
104    
105    checkpoint62t (2011/03/05)
106    o pkg/obcs:
107     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
108       then normal component. This ensures that the normal component is set
109       correctly even when it conficts with tangential setting from an other OB.
110       Affects results of test-experiment seaice_obcs: update the output.txt
111    o pkg/obcs:
112     - add code to monitor statistics of dynamical fields at OB.
113     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
114       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
115       - change default: balance the Net inflow through all OB (instead of balancing
116         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
117     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
118       to match Nortern OB inflow (OBCS_balanceFacN=0).
119    o pkg/seaice:
120     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
121    o pkg/seaice (seaice_growth v 1.113):
122     - reverting seaice_growth to v 1.111 in order to have code with exact bit
123       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
124       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
125       runtime flag SEAICEareaFormula is kept but is inactive
126    o model/src:
127     - add new param to scale curvilinear grid distance and area when using
128       a different sphere radius from the grid-files.
129     - test/check multi-threads EXCH applied to local variable (cg2d_x)
130    o adjoint:
131     - enable adjoint of Stevens OB
132     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
133       (a bit delicate because of potentially modified adj. common block structure;
134       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
135    
136    checkpoint62s (2011/02/15)
137    o pkg/seaice (seaice_growth v 1.112):
138     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
139       computing the ice cover tendency from effective thickness tendencies. Include
140       Ian Fenty's formula.
141     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
142       SEAICEareaFormula.
143     - simplify notations for the various d_HEFF/d_AREA terms.
144    o pkg/gmredi:
145     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
146       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
147       add a verification test-run (front_relax.bvp) to test GM_useBVP.
148    o pkg/seaice (seaice_growth v 1.111):
149     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
150     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
151       also melt ice.
152    o pkg/seaice:
153     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
154     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
155    o pkg/cheapaml:
156     - from Nico Wienders: New version of this package.
157    o pkg/flt:
158     - add CPP options to prevent floats to re-enter the opposite side of
159       a periodic domain (default: keep periodicity)
160    o pkg/gmredi:
161     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
162       (needed for multi-dim advection).
163     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
164    o model/src:
165     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
166    o tutorial_tracer_adjsens
167     - extend to NLFS and replace maskC by hFacC
168       (change reference output accordingly)
169    
170    checkpoint62r (2011/01/24)
171    o testreport:
172     - add option -deloutp (-do) to remove output file after successful run
173     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
174       extract exact list of procs from this file ; adjust COMMAND by
175       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
176    o pkg/ecco: replace old ineffective way of penalizing deviations from
177      first guess (of obcs) with code by Matt Mazloff
178    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
179      exf/cal
180      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
181        and handle case of obcs?period == 0
182        Not affected by these changes: There is still an inconsistency in
183        the computation of start/endrec for the obcs variables for ALLOW_CAL
184        defined (see comment by Menemenlis, 7-Mar-2003)
185      - make S/R ctrl_get_gen_rec return something meaningful even if
186        ALLOW_CAL is not defined
187      - ctrl_getobcs?: simplify code so that it does not need to use
188                       S/R exf_swapfields
189    o testreport:
190       allow to test MPI with different number of processors for each experiment:
191       create file "SIZE.h.mpi" in each build dir.
192       Note: update of "-command" argument not yet implemented.
193    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
194      alleviate the need for additional 3D tapes when using
195      the non-inear free surface in the adjoint. This is done
196      by adding an 'update' of hfacc etc. to their current
197      value at the beginning of forward_step.F.
198    o pkg/seaice
199      seaice_lsr: move stress-divergence computations out of outer pseudo-
200      timestepping loop
201    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
202      up, so that the calls of the ctrl_* subroutines are really at the end
203      of the routine.
204    o pkg/gmredi:
205      allow to specify a 2-D horizontal map and a 1-D vertical profil
206      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
207    o pkg/seaice:
208      move lsr iterations from seaice_dynsolver to seaice_lsr.
209    o pkg/seaice:
210      reduce memory footprint of seaice mutldim advection tapes,
211      by using a 2D tape independent of the generic_advdiff ones,
212      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
213    
214    checkpoint62q (2010/12/29)
215    o model/src:
216      - check horizontal grid-spacing for unset or zero/negative values.
217      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
218    o pkg/flt:
219      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
220      - precision of input and output files set according to readBinaryPrec
221        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
222      - initial float position from tiled file was not converted to index space
223        (looks like a bug): fixed to make it similar to initial pos. global file.
224    o global_ocean.cs32x15:
225       change SIZE.h of AD set-up to get same tiling as with MPI.
226       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
227    o model/src:
228       add flag to control printing of domain fields (bathymetry, hFac ...) in
229       ini_mask_etc (call to plot_fieds_xy*).
230    o pkg/thsice:
231       if useEXF, some forcing fields are not valid in overlap: fixed by computing
232       over the interior only + apply EXCH at the end (like with SEAICE advection).
233    o pkg/mdsio:
234      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
235        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
236      - change barrier call for safe multi-threads access to 3-D shared buffer.
237      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
238      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
239        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
240    o pkg/flt:
241      - add fourth-order Runge-Kutta integration
242      - add basic exch2 support (only 1 facet supported so far!)
243    o pkg/mdsio+rw:
244      new S/R to read local (or tile independent) vector (read counterpart of
245       mds_writevec_loc, and front-end write_glvec_rl/rs).
246    o global_ocean.cs32x15: additional input_ad.seaice experiment
247        that uses pkg/seaice rather than pkg/thsice.
248        (using multidim advection for seaice)
249    o towards more F95 syntax for array specification in namelist:
250      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
251        of all verification experiments.
252           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
253          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
254      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
255    o global_ocean.cs32x15: additional input.seaice experiment
256        that uses pkg/seaice rather than pkg/thsice.
257    
258    checkpoint62p (2010/12/17)
259    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
260        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
261    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
262        allow for use of multim. advection in seaice adjoint.
263    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
264      - first attempt to close budgets by taking into account the freshwater
265        flux implied by the sublimation of snow and ice. So far only the
266        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
267        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
268    o eesupp/src:
269      new S/R with new option (NML_EXTENDED_F77) to change array specification
270      from F95 standard to commonly accepted extended F77 form.
271      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
272      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
273      for less tolerant f77 compiler (e.g., pgf77, g77).
274    o globalFiles:
275      commented out in parameter file "data" since it's not safe with MPI
276      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
277      in this case); no longer commented out in restart test (tst_2+2).
278    o add adTapeDir to specify a special directory where adjoint tapes are
279      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
280      and cannot be used together with mdsioLocalDir.
281    o nesting pkgs:
282      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
283      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
284      - add parameter files + utils dir + output from short run on beagle.
285    o pkg/seaice:
286        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
287    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
288      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
289    
290    checkpoint62o (2010/11/25)
291    o pkg/exf:
292      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
293    o pkg/seaice:
294      - seaice_ocean_stress: split a loop for better vectorization of the
295        adjoint code
296      - seaice_growth.F: fix bug in conservation of freshwater connected to
297        capping of heff, put contribution into d_HEFFbyNEG
298      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
299        by something more sensible (parameters that are what their name implies)
300      - change some defaults, so that by default exf-parameters are used for
301        things like rhoAir, cpAir,latent/sensible heat parameters, in order
302        to reproduce the old results, many data.seaice now contain funny values
303        for cpAir and latent heat of sublimation
304    o packages_readparms.F: move exf_readparms up in line so that
305        exf-parameters are visible for other packages (e.g. seaice)
306    o debugMode & debugLevel=2:
307      - differentiate between debugMode & debugLevel=2:
308        debugMode: controls printing of debug messages (sequence of S/R calls).
309        debugLevel: controls printing of algorithm intermediate results and stats.
310      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
311        => allows to print debug-stats without all sequence of call messages.
312      - switch control of debug print from debugLevel to debugMode in many S/R.
313    o pkg/obcs (obcs-sponge):
314        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
315        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
316    o pkg/generic_advdiff:
317      - record overlap minimum size for each advection scheme;
318      - refine criteria on overlap minimum size;
319      - check and stop (in gad_check) if overlap size is too small.
320    o pkg/obcs:
321      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
322        once, in ptracers_implicit.F)
323      - with seaice: remove test on empty file name in obcs_apply_seaice (always
324        apply OB values when tile has OB)
325    o model/src, coriolis setting:
326      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
327        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
328        files (selectCoriMap=3) with any grid.
329      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
330    o pkg/seaice/seaice_growth.F:
331        a few cosmetic changes that reduce the number of lines of code
332    o pkg/obcs: add boundary conditions following Stevens (1990)
333      - the code follows old MOM/NAOSIM code
334      - so far it is only implemented for the eastern and western boundaries
335        and NOT for pTracers
336    o pkg/rbcs:
337      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
338        beginning of the first rbcs forcing period.
339      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
340        offline package, i.e., one file per time, labeled by iteration number;
341        deltaTrbcs sets the timestep with which the data was generated;
342        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
343      - rbcsForcingCycle=0 makes forcing non-cyclic.
344      - make arithmetic safe for negative times and odd forcing periods.
345    
346    checkpoint62n (2010/11/09)
347    o pkg/seaice:
348        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
349    o pkg/obcs:
350       New S/R to copy tracer value from the OB location to narrow band region
351        (width = same as overlap) beyond the OB: preserve OB value (needed for
352        high-order scheme) which were overwritten by EXCH call if in overlap
353        region. Applied to theta, salt, ptracer and advected seaice variables.
354       With seaice: use maskInC in similar way as in gad_advection.F,
355        in seaice_advection.F and advect.F.
356       Update output of experiment seaice_obcs and change exp4 to test OBCS with
357        4th order Adv.Scheme. for pasive salt and ptracer.
358    o tools/genmake2:
359      - when looking for an optfile (not specified), only search for Fortran compiler
360        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
361      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
362        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
363      - set default for CPP to "cpp -traditional -P" (was the case without specifying
364        an optfile, but otherwise default was just "cpp".
365      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
366      - when "CC" is not set in the optfile, look for possible C compiler
367        (instead of just setting CC=cc)
368      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
369        => add a ".F" to ".o" rule for source files with no "#include" (such as
370           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
371      - move gfortran before g77 in list of possible Fortran compiler (consistent
372        with reference compiler switch from g77 to gfortran)
373    o pkg/seaice:
374      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
375        seaice_check that stops the model, when the CPP flag is used.
376      o seaice_growth.F: make capping of ice volume conserving by returning the
377        capped ice as freshwater to EmPmR. This does not change the verification
378        experiments but will change runs where the capping is acutally active
379    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
380      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
381         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
382         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
383    o tools/genmake2:
384      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
385      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
386      - clean previous genmake log files before anything else.
387      - change Makefile to remove testreport log files (*.tr_log) and genmake log
388        files only with "CLEAN" target (instead of "Clean");
389    o pkg/generic_advdiff:
390      Change OBCS in multiDim advection (gad_advection.F):
391       Use maskInC to prevent intermediate update of tracer-field in OB regions,
392       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
393       which were applying future time-step OB values.
394      This way, all explicit calculations use current-time-step OB values
395       (simpler and more consistent).
396      Affects results when set-up uses time-varying OBC and multi-dim advection;
397       update output of experiment seaice_obcs.
398    o pkg/seaice:
399      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
400       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
401         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
402      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
403       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
404       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
405    o pkg aim (2010/10/26):
406      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
407        formulation with obliquity, eccentricity, ... as run-time parameters,
408      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
409        upward shortwave radition at the surface (all-sky and clear-sky).
410    o pkg/obcs:
411      - writing sections with globalFiles=T does not work: switch to tiled-files
412        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
413      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
414      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
415    
416    checkpoint62m (2010/10/21)
417    o pkg/seaice: vectorize seaice_solve4temp.F
418      - move iterations loops outside of i/j-loops
419      - requires 2D arrays for TB and effConduct
420      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
421        modified in this routine
422      - a little bit of clean up, adjusting indentation, etc.
423      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
424        performance and '**TWO' by '**2' (because TWO is a float),
425        replaced ONE, ZERO
426    o eesupp/src:
427       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
428    o pkg/seaice/seaice_growth.F
429      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
430      merging process. The merged routine has two branches, and one activates the 'evolution'
431      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
432      In summary, here is what the '10/10 revision' did consist of
433        part 1: seaice_growth.F revisions 1.71 to 1.75
434          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
435            The emphasis here was on improving readability (e.g. by trying to use meaningful
436            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
437        part 1.5:
438          - revising the lab_sea experiment to make it a more useful (i.e. stable
439            and representative of an actual model run). This was done by generating a
440            (winter) pickup to start from, switching back the main experiment dynamic
441            solver from evp to lsr, having one of the experiments use the free drift solution.
442        part 2: seaice_growth.F revisions 1.76 to 1.85
443          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
444          - Sorting out the various fields units and sign (set early on and reset at the end)
445            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
446            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
447          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
448            and simplifying logical expressions to further improve readibility.
449        part 3: seaice_growth.F revisions 1.86 to 1.89
450          - Re-organize the blocks of code more logically.
451          - Merging the '_if.F' pieces that add something new.
452    o pkg/thsice:
453      - vectorize thsice_solve4temp and thsice_get_exf.
454        Problem: thsice_solve4temp has an unvectorizable statement that
455        might also be problematic for TAF
456      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
457        does not change the verifcation experiment, but will change all
458        experiments that have this flag undefined (not tested in verification);
459        a little reorganization to save a few 2D fields and recomputations
460      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
461      - 2nd step:  fix some store dirs
462        o seems to work somewhat, i.e. using ifort but not g77
463        o likely cause are incomplete init. or recomputation
464        o start verification/global_ocean.cs32x15/input_ad.thsice
465    o pkg/obcs: add support for exch2
466      - the position of the boundary and prescribed values are specified using
467        a global domain with exch2 facets stacked
468        - in x for N,S boundaries (like W2_mapIO=-1)
469        - in y for E,W boundaries (so E,W boundaries do not overlap)
470    o pkg/mdsio: add support for writing global sections with exch2
471        file layout is as for obcs described above:
472        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
473        - for y-z sections, facets are stacked in y
474    o pkg/thsice:
475       - change a few routines for better vectorization: thsice_albedo.F,
476         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
477         not affected, but in particular the latter routine has changed
478         dramatically (not necessarily easier to read now).
479       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
480       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
481    o verification/lab_sea:
482      - overhaul of the forward model experiments. The main motivation
483        for this revision is that lab_sea has proven quite fragile (when
484        changing the sea-ice code, and switching platforms) to a point
485        when failures were very hard to attribute to specific code problems.
486      - the suspected reason for this fragility is noise amplification by evp so,
487        to start with, we decided to replace evp with lsr in the main experiment.
488      - the input.lsr experiment thus became obsolete and was removed.
489      - it was replaced with the input.fd experiment that uses an
490        analytical "free drift" solution as the ice velocity field.
491      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
492        will hopefully allow us to discriminate problems due to dynamic solvers
493        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
494        us to test additional options, along with the salt plume package.
495      - Finally a pickup was generated (at the end of a one year run) to
496        make the tests more representative of an actual model run. Previously
497        the tests starting point was a 1m thickness of ice everywhere.
498    o pkg/seaice:
499      - introducing S\R seaice_freedrift.F that compute the
500        analytical solution to an approximate ice momentum
501        equation (i.e. the simple stress/coriolis balance).
502      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
503        of the free drift velocity field, and enable its use.
504        To actually use the free drift solution as the model ice
505        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
506    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
507    
508    checkpoint62l (2010/10/04)
509    o pkg/seaice:
510      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
511      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
512       version (with USE_ORIGINAL_SBI undef);
513    o add hooks for new packages OASIS, the package will follow
514      (hooks exclude the seaice pkg for now)
515    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
516      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
517      rather than mdsio_readvector.F/mdsio_writevector.F, within
518      adread_adwrite.F to read/write adjoint-related tapes to disk.
519    o eesupp and pkg/mdsio: ALLOW_WHIO
520      Option to write/read 2D fields to files including tiles halos.
521      The main purpose is for adjoint related "tape I/O".
522      The secondary purpose is for debugging phases.
523      A word on those rather specifically intended purposes.
524      The code was meant to be stripped down to the bare minimum.
525      Typically, there is a unique and basic mapping to the global
526      buffer (tile by tile, then proc by proc, then level by level), and
527      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
528      meant to generate user friendly outputs of various shapes and forms.
529      Rather it is intended, for the knowledgeabale developers,
530      to be largely independent of the many mdsio options, to allow
531      outputs of tiles+halos in debugging phases and in adjoint runs,
532      and to allow some flexibility in tuning (adoint) I/O depending on each
533      file system behavior. With regard to tuning, most of the potential knobs
534      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
535      to specify directories, to specify the typical size of I/O calls, etc.)
536      are not yet included, and will be added if they prove useful.
537    o pkg/seaice:
538       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
539    o pkg/seaice:
540       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
541       code (seaice_budget_ice_if.F) which enable to recover old standard
542       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
543       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
544    o model/src (rStar):
545       use simple average (not area weighted) of rStarFac at U,V point when using
546       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
547       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
548    
549    checkpoint62k (2010/09/17)
550    o adjoint
551       * changed verification/global_ocean.cs32x15 ; adjoint now tests
552         Adams-Bashforth 3 + NLFS + RSTAR
553       * some more modifs required for ECCO-GODAE v4
554    o pkg/seaice
555       add SEAICE_AGE_VOL option to use volume instead of area for
556       integrating SEAICE_AGE
557    o model/src:
558       first check-in of sigma & hybrid-sigma coordinate code ; also includes
559       non-linear free-surface parts ; but pressure-gradient not yet coded.
560    o pkg/ptracers:
561       option for ptracer to convert Salt Relax into additional EmP.
562        tested in exp. global_ocean.90x40x15.dwnslp (update output)
563    
564    checkpoint62j (2010/08/25)
565    o pkg/ggl90:
566       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
567    o pkg/dic: car_flux.F, phos_flux.F
568      - reduce number of exp-calls in order to improve performance
569      - clean up a little (replace fields by their macros, etc., fix
570        typo in CPP-flag)
571    o pkg/ggl90: minor changes
572      - GGL90diffKrS was removed --> always use GGL90diffKr
573      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
574      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
575        (commented out for now)
576      - change in max/min operations to ensure that smoothing is ok
577      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
578      - always use diffKrNrT as background profile (i.e. never use diffKr field)
579    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
580    o pkg/dic:
581      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
582        vectorization
583      - small bug fix in insol for the unlikely case of a cartesian grid
584      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
585        + now vectorize, which also removes adjoint recomputations;
586        + replace integer maksp1 by _RL maskp1
587        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
588    
589    checkpoint62i (2010/07/21)
590    o pkg/flt:
591      - with OBCS: stop floats which enter the OB region
592    o model/src:
593      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
594        for implicit vertical advection.
595    o pkg/seaice:
596     - account for melting in seaice age evolution.
597     - remove double counting of seaice ridging effect on seaice age.
598    
599    checkpoint62h (2010/06/18)
600    o pkg/exch2:
601     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
602    o tools/genmake2
603      - remove "-pdefault" option: redundant with the use of "packages.conf";
604      - remove file pkg/pkg_default : set the default as a pkg group
605        ("default_pkg_list") defined in pkg/pkg_groups;
606      - fix for case pkg/pkg_depend is missing (was hanging before);
607      - add option "-pgroups" to specify a different pkg_groups than the default.
608    o verification/adjustment.cs-32x32x1:
609       add a "minimal" set-up test (code_min & input_min) which only compiles
610       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
611    o tools/genmake2
612      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
613      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
614    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
615      files are nearly the same anyway.
616      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
617       - redefinition of tau(i,i) (by a factor of ustar)
618       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
619       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
620       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
621       - replace
622         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
623         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
624         by
625         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
626         (changes results)
627       -> exf_bulkformulae v1.22,
628          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
629          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
630                    output.txt 1.63
631           offline_exf_seaice: output.seaicetd.txt 1.7
632           seaice_obcs: output.txt 1.10)
633      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
634       -> exf_bulkformulae v1.23,
635          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
636          and global_ocean.cs32x15.icedyn (only 11 matching digits)
637      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
638    o adjoint of exch-1:
639     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
640       (note: was already like this when using EXCH-2) and remove flow dir
641       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
642     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
643     - update pkg/exch2 diff list.
644    
645    checkpoint62g (2010/05/19)
646    o eesupp/src (exch-1):
647     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
648       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
649       (renamed to exch1_*rx_cube.F).
650     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
651       to call new exch1 S/R ; update Makefile and .cvsignore.
652     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
653       exch2_xy_rx later)
654      Note: after updating your code, need to run "make clean" in eesupp/src
655    o test experiment bottom_ctrl_5x5:
656       new output_adm.txt with fewer grdchk & less monitor output.
657    o model/src:
658      remove the call to ini_cori in initialise_varia.F (just keep the usual one
659       in initialise_fixed.F). More consistent with coriolis & horizontal grid
660       beeing treated in the same way (ini_grid is not called a 2nd time).
661    o pkg/exf:
662      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
663      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
664      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
665      - cosmetic changes to exf_bulkformulae.F to make it look more like
666        exf_bulk_largeyeager04.F
667    o eesupp/src (exch-1):
668      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
669      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
670        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
671        (even without using MPI).
672      - Message mode: move RecvAck setting (indicator of buffer being ready)
673        from send_put to recv_get S/R (was useless before, but not sure if
674        it's much more useful now);
675      - Switch the order of sync: MPI-proc 1rst and then threads;
676      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
677      - fix AD code for communication mode ='get' (but not used).
678    o model/src:
679      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
680      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
681    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
682    o pkg/ctrl: require a specific set of control variables and exf-flags for
683      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
684    o model/src:
685     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
686       1rst forward sweep, to avoid over-writing output files during recomputations
687       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
688     b) 2nd version:
689      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
690      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
691         writePickupAtEnd) + seaice & ptracers output;
692      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
693    o model/src:
694      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
695    o pkg/exch2:
696      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
697      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
698    o pkg/autodiff & exch2:
699      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
700      (for now, only if ALLOW_EXCH2 is defined).
701    o pkg/autodiff:
702      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
703        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
704       + clean-up comments (_RS is not always real*4)
705      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
706      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
707        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
708    o testreport (AD-tests):
709      no longer link files from dir "../input" (1rst link files from
710      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
711    
712    checkpoint62f (2010/04/29)
713    o model/src/the_main_loop.F:
714      adjust store directives for seaice evp and multicategory according to
715      pkg/ecco/the_main_loop.F
716    o adjoint:
717      global_sum_ad was incomplete (noted many times by many people ;)
718      nice description by Jean U. as follows:
719      * allreduce(var) in global_sum.F can be interpreted as
720        reduce(sum) followed by broadcast of sum.
721      * The adjoint of that is
722        sum(adjoint) followed by broadcast(summed adjoint value)
723        or in other words, allreduce(sum, adjoint vars)
724      We were missing the sum(adjoint)!
725      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
726      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
727      The fix should produce 16-digit accuracy between
728      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
729      multi-CPU single-tile (e.g. nSx=1, nPx-2)
730      We'll probably change this yet again shortly
731    o eesupp/src:
732      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
733    o pkg/icefront
734      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
735        specification of addmass array based on a 2D field, which is added
736        at bottommost wet level at each horizontal location.
737    o model/src:
738     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
739     layout; (not always compatible with delX,delY setting; commented out for now).
740    o pkg/exch2:
741     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
742     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
743    
744    checkpoint62e (2010/04/15)
745    o pkg/obcs:
746      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
747    o pkg/dic:
748      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
749        (note: not presently tested in any forward verification exp.)
750       update tutorial_global_oce_biogeo AD output file.
751    o pkg/exf:
752      - account for the variation of albedo as a function of zenith angle
753        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
754    o build_options:
755     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
756    o pkg/dic:
757      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
758      - use binary pickup file for restart;
759      - initialise atmos-CO2 box from dic_pCO2 parameter;
760      - fix multi-threaded.
761    o pkg/rbcs:
762     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
763       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
764     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
765       and update output.txt
766    o pkg/kpp:
767     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
768     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
769       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
770       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
771     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
772       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
773  o pkg/offline:  o pkg/offline:
774    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
775    (bug was added in version 1.10 on 2007-08-23).    (bug was added in version 1.10 on 2007-08-23).
# Line 57  o tools/build_options: Line 823  o tools/build_options:
823      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
824  o pkg/ecco  o pkg/ecco
825    - allow user defined cost function contributions    - allow user defined cost function contributions
826          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
827          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
828    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
829        the two options are complementary.        the two options are complementary.
830  o pkg/smooth  o pkg/smooth
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