/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1245 by jmc, Thu Apr 1 15:32:08 2010 UTC revision 1.1410 by jmc, Thu Apr 21 15:18:17 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 new AD-test experiment: obcs_ctrl
8      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
9    o pkg/dic:
10      fix two bugs in handling water vapour pressure in carbonate chemistry
11      and air-sea fluxes. Found by Val Bennington and Galen McKinley
12      (add DIC Option = WATERVAP_BUG to recover old results)
13      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
14    o adding allowInteriorFreezing option to check for water below freezing point
15      at depth and bring the negative heat anomaly to the surface level
16    o pkgs _fields_load:
17      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
18      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
19        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
20        rbcs to get interpolation weights and time reccord number.
21      - fix multi-threading in aim_fields_load.F
22      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
23    o external_fields_load:
24      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
25       interpolation weights) to use in a periodic time-series ; do not divide by
26       time-step to convert to integer:
27       - this fixes case where externForcingPeriod is not multiple of time-step
28          (Thanks to Christopher L. Wolfe)
29       - this fixes case where externForcingPeriod is an odd multiple of time-step
30         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
31      store index of time-record which is currently loaded:
32       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
33       - needed for the adjoint but not yet used because of extensive recomputations;
34         (to be fixed soon)
35    
36    checkpoint62v (2011/04/02)
37    o verification/1D_ocean_ice_column added to test Ian Fenty's
38      pkg/seaice_growth.F modifications for improving sea ice code differentiability
39    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
40      (new velocity statistics after changing maskInW & maskInS definition)
41    o pkg/generic_advdiff with OBCS:
42      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
43      equivalent to assumption of no tracer gradient outside the OB region.
44      This will affect the results if using obcs+biharmonic diffusion.
45      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
46    o pkg/obcs:
47      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
48      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
49      in Interior region. No impact on solution but affects Velocity monitor stats.
50    o pkg/ptracers (adjoint)
51      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
52      tape file for each tracer
53    o model/inc/src and pkg/autodiff: add parameters that allow to turn
54      of parts of the adjoint code at run time. For now, there are only
55      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
56      parameters are set in data.pkg.
57      This is the lazy coward's version of doing this, but still useful for
58      debugging. In order to do it right, everything needs to be moved to
59      pkg/autodiff.
60    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
61      the end; this fixes the adjoint balancing code for open boundaries.
62    o pkg/ctrl:
63      - change behavior of xx_${varname}period to be analogous to exf-conventions:
64        xx_${varname}period =   0.,  means time-independent control part
65        xx_${varname}period = -12., means one-year-periodic monthly control part
66      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
67        clean up ctrl_init a little, remove unused variables
68      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
69      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
70    
71    checkpoint62u (2011/03/15)
72    o model/src:
73      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
74        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
75      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
76        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
77    o pkg/ctrl/obcs/ecco:
78      - remove obsolete, unused, and partially broken code:
79        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
80        ALLOW_CTRL_OBCS_BALANCE
81      - put a stop statement into ecco/cost_obcsvol.F, but also add
82        cost_obcsvol to ecco_ad_diff.list
83    o pkg/ecco: fix counting cost function contributions for obcs (code
84      by Matt M.) and diffkr for diagnostics
85    o pkg/ecco, pkg/ctrl, pkg/grdchk:
86      add cost penalty terms for initial uvel, vvel, eta controls
87      and I/O for prior error files
88    o pkg/mdsio:
89       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
90       (new argument) to check for tiled file in mdsioLocalDir : this fix the
91       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
92    o pkg/ctrl:
93     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
94       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
95       unused and superfluous variables
96     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
97    o pkg/ecco
98     - enable adjoint of Stevens OB
99    o pkg/ctrl/ecco/grdchk:
100      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
101        Fortunately, we do not have any tests for the numerous cpp-flagged
102        option of "obcs as control parameters" so we will never know
103        if this is an improvement (but at least now things compile).
104      - remove an obsolete initialization from ecco_cost_init_barfiles.F
105      - fix some problems within never used ifdefs to make the code compile
106    o pkg/obcs:
107     - Refine Interior mask definition to work with more complex OB (e.g.
108       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
109       read in Interior mask from file. Check if Interior mask is consistent
110       with OB list of indices.
111    o pkg/seaice
112     - beginning code for a seaice tracer package,
113       but currently only used for seaice age: SEAICE_AGE
114       SEAICE_num = 4
115       iTracer = 1: area-weighted ice age
116               = 2: volume-weighted ice age
117               = 3, 4: template for one-year vs. multi-year ice
118       data.seaice has new namelist SEAICE_PARM03 for arrays related to
119       SEAICE_num
120    
121    checkpoint62t (2011/03/05)
122    o pkg/obcs:
123     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
124       then normal component. This ensures that the normal component is set
125       correctly even when it conficts with tangential setting from an other OB.
126       Affects results of test-experiment seaice_obcs: update the output.txt
127    o pkg/obcs:
128     - add code to monitor statistics of dynamical fields at OB.
129     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
130       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
131       - change default: balance the Net inflow through all OB (instead of balancing
132         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
133     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
134       to match Nortern OB inflow (OBCS_balanceFacN=0).
135    o pkg/seaice:
136     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
137    o pkg/seaice (seaice_growth v 1.113):
138     - reverting seaice_growth to v 1.111 in order to have code with exact bit
139       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
140       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
141       runtime flag SEAICEareaFormula is kept but is inactive
142    o model/src:
143     - add new param to scale curvilinear grid distance and area when using
144       a different sphere radius from the grid-files.
145     - test/check multi-threads EXCH applied to local variable (cg2d_x)
146    o adjoint:
147     - enable adjoint of Stevens OB
148     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
149       (a bit delicate because of potentially modified adj. common block structure;
150       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
151    
152    checkpoint62s (2011/02/15)
153    o pkg/seaice (seaice_growth v 1.112):
154     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
155       computing the ice cover tendency from effective thickness tendencies. Include
156       Ian Fenty's formula.
157     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
158       SEAICEareaFormula.
159     - simplify notations for the various d_HEFF/d_AREA terms.
160    o pkg/gmredi:
161     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
162       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
163       add a verification test-run (front_relax.bvp) to test GM_useBVP.
164    o pkg/seaice (seaice_growth v 1.111):
165     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
166     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
167       also melt ice.
168    o pkg/seaice:
169     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
170     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
171    o pkg/cheapaml:
172     - from Nico Wienders: New version of this package.
173    o pkg/flt:
174     - add CPP options to prevent floats to re-enter the opposite side of
175       a periodic domain (default: keep periodicity)
176    o pkg/gmredi:
177     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
178       (needed for multi-dim advection).
179     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
180    o model/src:
181     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
182    o tutorial_tracer_adjsens
183     - extend to NLFS and replace maskC by hFacC
184       (change reference output accordingly)
185    
186    checkpoint62r (2011/01/24)
187    o testreport:
188     - add option -deloutp (-do) to remove output file after successful run
189     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
190       extract exact list of procs from this file ; adjust COMMAND by
191       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
192    o pkg/ecco: replace old ineffective way of penalizing deviations from
193      first guess (of obcs) with code by Matt Mazloff
194    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
195      exf/cal
196      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
197        and handle case of obcs?period == 0
198        Not affected by these changes: There is still an inconsistency in
199        the computation of start/endrec for the obcs variables for ALLOW_CAL
200        defined (see comment by Menemenlis, 7-Mar-2003)
201      - make S/R ctrl_get_gen_rec return something meaningful even if
202        ALLOW_CAL is not defined
203      - ctrl_getobcs?: simplify code so that it does not need to use
204                       S/R exf_swapfields
205    o testreport:
206       allow to test MPI with different number of processors for each experiment:
207       create file "SIZE.h.mpi" in each build dir.
208       Note: update of "-command" argument not yet implemented.
209    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
210      alleviate the need for additional 3D tapes when using
211      the non-inear free surface in the adjoint. This is done
212      by adding an 'update' of hfacc etc. to their current
213      value at the beginning of forward_step.F.
214    o pkg/seaice
215      seaice_lsr: move stress-divergence computations out of outer pseudo-
216      timestepping loop
217    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
218      up, so that the calls of the ctrl_* subroutines are really at the end
219      of the routine.
220    o pkg/gmredi:
221      allow to specify a 2-D horizontal map and a 1-D vertical profil
222      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
223    o pkg/seaice:
224      move lsr iterations from seaice_dynsolver to seaice_lsr.
225    o pkg/seaice:
226      reduce memory footprint of seaice mutldim advection tapes,
227      by using a 2D tape independent of the generic_advdiff ones,
228      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
229    
230    checkpoint62q (2010/12/29)
231    o model/src:
232      - check horizontal grid-spacing for unset or zero/negative values.
233      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
234    o pkg/flt:
235      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
236      - precision of input and output files set according to readBinaryPrec
237        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
238      - initial float position from tiled file was not converted to index space
239        (looks like a bug): fixed to make it similar to initial pos. global file.
240    o global_ocean.cs32x15:
241       change SIZE.h of AD set-up to get same tiling as with MPI.
242       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
243    o model/src:
244       add flag to control printing of domain fields (bathymetry, hFac ...) in
245       ini_mask_etc (call to plot_fieds_xy*).
246    o pkg/thsice:
247       if useEXF, some forcing fields are not valid in overlap: fixed by computing
248       over the interior only + apply EXCH at the end (like with SEAICE advection).
249    o pkg/mdsio:
250      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
251        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
252      - change barrier call for safe multi-threads access to 3-D shared buffer.
253      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
254      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
255        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
256    o pkg/flt:
257      - add fourth-order Runge-Kutta integration
258      - add basic exch2 support (only 1 facet supported so far!)
259    o pkg/mdsio+rw:
260      new S/R to read local (or tile independent) vector (read counterpart of
261       mds_writevec_loc, and front-end write_glvec_rl/rs).
262    o global_ocean.cs32x15: additional input_ad.seaice experiment
263        that uses pkg/seaice rather than pkg/thsice.
264        (using multidim advection for seaice)
265    o towards more F95 syntax for array specification in namelist:
266      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
267        of all verification experiments.
268           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
269          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
270      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
271    o global_ocean.cs32x15: additional input.seaice experiment
272        that uses pkg/seaice rather than pkg/thsice.
273    
274    checkpoint62p (2010/12/17)
275    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
276        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
277    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
278        allow for use of multim. advection in seaice adjoint.
279    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
280      - first attempt to close budgets by taking into account the freshwater
281        flux implied by the sublimation of snow and ice. So far only the
282        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
283        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
284    o eesupp/src:
285      new S/R with new option (NML_EXTENDED_F77) to change array specification
286      from F95 standard to commonly accepted extended F77 form.
287      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
288      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
289      for less tolerant f77 compiler (e.g., pgf77, g77).
290    o globalFiles:
291      commented out in parameter file "data" since it's not safe with MPI
292      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
293      in this case); no longer commented out in restart test (tst_2+2).
294    o add adTapeDir to specify a special directory where adjoint tapes are
295      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
296      and cannot be used together with mdsioLocalDir.
297    o nesting pkgs:
298      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
299      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
300      - add parameter files + utils dir + output from short run on beagle.
301    o pkg/seaice:
302        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
303    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
304      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
305    
306    checkpoint62o (2010/11/25)
307    o pkg/exf:
308      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
309    o pkg/seaice:
310      - seaice_ocean_stress: split a loop for better vectorization of the
311        adjoint code
312      - seaice_growth.F: fix bug in conservation of freshwater connected to
313        capping of heff, put contribution into d_HEFFbyNEG
314      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
315        by something more sensible (parameters that are what their name implies)
316      - change some defaults, so that by default exf-parameters are used for
317        things like rhoAir, cpAir,latent/sensible heat parameters, in order
318        to reproduce the old results, many data.seaice now contain funny values
319        for cpAir and latent heat of sublimation
320    o packages_readparms.F: move exf_readparms up in line so that
321        exf-parameters are visible for other packages (e.g. seaice)
322    o debugMode & debugLevel=2:
323      - differentiate between debugMode & debugLevel=2:
324        debugMode: controls printing of debug messages (sequence of S/R calls).
325        debugLevel: controls printing of algorithm intermediate results and stats.
326      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
327        => allows to print debug-stats without all sequence of call messages.
328      - switch control of debug print from debugLevel to debugMode in many S/R.
329    o pkg/obcs (obcs-sponge):
330        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
331        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
332    o pkg/generic_advdiff:
333      - record overlap minimum size for each advection scheme;
334      - refine criteria on overlap minimum size;
335      - check and stop (in gad_check) if overlap size is too small.
336    o pkg/obcs:
337      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
338        once, in ptracers_implicit.F)
339      - with seaice: remove test on empty file name in obcs_apply_seaice (always
340        apply OB values when tile has OB)
341    o model/src, coriolis setting:
342      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
343        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
344        files (selectCoriMap=3) with any grid.
345      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
346    o pkg/seaice/seaice_growth.F:
347        a few cosmetic changes that reduce the number of lines of code
348    o pkg/obcs: add boundary conditions following Stevens (1990)
349      - the code follows old MOM/NAOSIM code
350      - so far it is only implemented for the eastern and western boundaries
351        and NOT for pTracers
352    o pkg/rbcs:
353      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
354        beginning of the first rbcs forcing period.
355      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
356        offline package, i.e., one file per time, labeled by iteration number;
357        deltaTrbcs sets the timestep with which the data was generated;
358        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
359      - rbcsForcingCycle=0 makes forcing non-cyclic.
360      - make arithmetic safe for negative times and odd forcing periods.
361    
362    checkpoint62n (2010/11/09)
363    o pkg/seaice:
364        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
365    o pkg/obcs:
366       New S/R to copy tracer value from the OB location to narrow band region
367        (width = same as overlap) beyond the OB: preserve OB value (needed for
368        high-order scheme) which were overwritten by EXCH call if in overlap
369        region. Applied to theta, salt, ptracer and advected seaice variables.
370       With seaice: use maskInC in similar way as in gad_advection.F,
371        in seaice_advection.F and advect.F.
372       Update output of experiment seaice_obcs and change exp4 to test OBCS with
373        4th order Adv.Scheme. for pasive salt and ptracer.
374    o tools/genmake2:
375      - when looking for an optfile (not specified), only search for Fortran compiler
376        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
377      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
378        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
379      - set default for CPP to "cpp -traditional -P" (was the case without specifying
380        an optfile, but otherwise default was just "cpp".
381      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
382      - when "CC" is not set in the optfile, look for possible C compiler
383        (instead of just setting CC=cc)
384      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
385        => add a ".F" to ".o" rule for source files with no "#include" (such as
386           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
387      - move gfortran before g77 in list of possible Fortran compiler (consistent
388        with reference compiler switch from g77 to gfortran)
389    o pkg/seaice:
390      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
391        seaice_check that stops the model, when the CPP flag is used.
392      o seaice_growth.F: make capping of ice volume conserving by returning the
393        capped ice as freshwater to EmPmR. This does not change the verification
394        experiments but will change runs where the capping is acutally active
395    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
396      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
397         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
398         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
399    o tools/genmake2:
400      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
401      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
402      - clean previous genmake log files before anything else.
403      - change Makefile to remove testreport log files (*.tr_log) and genmake log
404        files only with "CLEAN" target (instead of "Clean");
405    o pkg/generic_advdiff:
406      Change OBCS in multiDim advection (gad_advection.F):
407       Use maskInC to prevent intermediate update of tracer-field in OB regions,
408       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
409       which were applying future time-step OB values.
410      This way, all explicit calculations use current-time-step OB values
411       (simpler and more consistent).
412      Affects results when set-up uses time-varying OBC and multi-dim advection;
413       update output of experiment seaice_obcs.
414    o pkg/seaice:
415      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
416       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
417         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
418      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
419       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
420       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
421    o pkg aim (2010/10/26):
422      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
423        formulation with obliquity, eccentricity, ... as run-time parameters,
424      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
425        upward shortwave radition at the surface (all-sky and clear-sky).
426    o pkg/obcs:
427      - writing sections with globalFiles=T does not work: switch to tiled-files
428        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
429      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
430      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
431    
432    checkpoint62m (2010/10/21)
433    o pkg/seaice: vectorize seaice_solve4temp.F
434      - move iterations loops outside of i/j-loops
435      - requires 2D arrays for TB and effConduct
436      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
437        modified in this routine
438      - a little bit of clean up, adjusting indentation, etc.
439      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
440        performance and '**TWO' by '**2' (because TWO is a float),
441        replaced ONE, ZERO
442    o eesupp/src:
443       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
444    o pkg/seaice/seaice_growth.F
445      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
446      merging process. The merged routine has two branches, and one activates the 'evolution'
447      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
448      In summary, here is what the '10/10 revision' did consist of
449        part 1: seaice_growth.F revisions 1.71 to 1.75
450          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
451            The emphasis here was on improving readability (e.g. by trying to use meaningful
452            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
453        part 1.5:
454          - revising the lab_sea experiment to make it a more useful (i.e. stable
455            and representative of an actual model run). This was done by generating a
456            (winter) pickup to start from, switching back the main experiment dynamic
457            solver from evp to lsr, having one of the experiments use the free drift solution.
458        part 2: seaice_growth.F revisions 1.76 to 1.85
459          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
460          - Sorting out the various fields units and sign (set early on and reset at the end)
461            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
462            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
463          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
464            and simplifying logical expressions to further improve readibility.
465        part 3: seaice_growth.F revisions 1.86 to 1.89
466          - Re-organize the blocks of code more logically.
467          - Merging the '_if.F' pieces that add something new.
468    o pkg/thsice:
469      - vectorize thsice_solve4temp and thsice_get_exf.
470        Problem: thsice_solve4temp has an unvectorizable statement that
471        might also be problematic for TAF
472      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
473        does not change the verifcation experiment, but will change all
474        experiments that have this flag undefined (not tested in verification);
475        a little reorganization to save a few 2D fields and recomputations
476      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
477      - 2nd step:  fix some store dirs
478        o seems to work somewhat, i.e. using ifort but not g77
479        o likely cause are incomplete init. or recomputation
480        o start verification/global_ocean.cs32x15/input_ad.thsice
481    o pkg/obcs: add support for exch2
482      - the position of the boundary and prescribed values are specified using
483        a global domain with exch2 facets stacked
484        - in x for N,S boundaries (like W2_mapIO=-1)
485        - in y for E,W boundaries (so E,W boundaries do not overlap)
486    o pkg/mdsio: add support for writing global sections with exch2
487        file layout is as for obcs described above:
488        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
489        - for y-z sections, facets are stacked in y
490    o pkg/thsice:
491       - change a few routines for better vectorization: thsice_albedo.F,
492         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
493         not affected, but in particular the latter routine has changed
494         dramatically (not necessarily easier to read now).
495       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
496       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
497    o verification/lab_sea:
498      - overhaul of the forward model experiments. The main motivation
499        for this revision is that lab_sea has proven quite fragile (when
500        changing the sea-ice code, and switching platforms) to a point
501        when failures were very hard to attribute to specific code problems.
502      - the suspected reason for this fragility is noise amplification by evp so,
503        to start with, we decided to replace evp with lsr in the main experiment.
504      - the input.lsr experiment thus became obsolete and was removed.
505      - it was replaced with the input.fd experiment that uses an
506        analytical "free drift" solution as the ice velocity field.
507      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
508        will hopefully allow us to discriminate problems due to dynamic solvers
509        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
510        us to test additional options, along with the salt plume package.
511      - Finally a pickup was generated (at the end of a one year run) to
512        make the tests more representative of an actual model run. Previously
513        the tests starting point was a 1m thickness of ice everywhere.
514    o pkg/seaice:
515      - introducing S\R seaice_freedrift.F that compute the
516        analytical solution to an approximate ice momentum
517        equation (i.e. the simple stress/coriolis balance).
518      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
519        of the free drift velocity field, and enable its use.
520        To actually use the free drift solution as the model ice
521        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
522    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
523    
524    checkpoint62l (2010/10/04)
525    o pkg/seaice:
526      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
527      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
528       version (with USE_ORIGINAL_SBI undef);
529    o add hooks for new packages OASIS, the package will follow
530      (hooks exclude the seaice pkg for now)
531    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
532      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
533      rather than mdsio_readvector.F/mdsio_writevector.F, within
534      adread_adwrite.F to read/write adjoint-related tapes to disk.
535    o eesupp and pkg/mdsio: ALLOW_WHIO
536      Option to write/read 2D fields to files including tiles halos.
537      The main purpose is for adjoint related "tape I/O".
538      The secondary purpose is for debugging phases.
539      A word on those rather specifically intended purposes.
540      The code was meant to be stripped down to the bare minimum.
541      Typically, there is a unique and basic mapping to the global
542      buffer (tile by tile, then proc by proc, then level by level), and
543      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
544      meant to generate user friendly outputs of various shapes and forms.
545      Rather it is intended, for the knowledgeabale developers,
546      to be largely independent of the many mdsio options, to allow
547      outputs of tiles+halos in debugging phases and in adjoint runs,
548      and to allow some flexibility in tuning (adoint) I/O depending on each
549      file system behavior. With regard to tuning, most of the potential knobs
550      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
551      to specify directories, to specify the typical size of I/O calls, etc.)
552      are not yet included, and will be added if they prove useful.
553    o pkg/seaice:
554       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
555    o pkg/seaice:
556       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
557       code (seaice_budget_ice_if.F) which enable to recover old standard
558       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
559       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
560    o model/src (rStar):
561       use simple average (not area weighted) of rStarFac at U,V point when using
562       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
563       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
564    
565    checkpoint62k (2010/09/17)
566    o adjoint
567       * changed verification/global_ocean.cs32x15 ; adjoint now tests
568         Adams-Bashforth 3 + NLFS + RSTAR
569       * some more modifs required for ECCO-GODAE v4
570    o pkg/seaice
571       add SEAICE_AGE_VOL option to use volume instead of area for
572       integrating SEAICE_AGE
573    o model/src:
574       first check-in of sigma & hybrid-sigma coordinate code ; also includes
575       non-linear free-surface parts ; but pressure-gradient not yet coded.
576    o pkg/ptracers:
577       option for ptracer to convert Salt Relax into additional EmP.
578        tested in exp. global_ocean.90x40x15.dwnslp (update output)
579    
580    checkpoint62j (2010/08/25)
581    o pkg/ggl90:
582       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
583    o pkg/dic: car_flux.F, phos_flux.F
584      - reduce number of exp-calls in order to improve performance
585      - clean up a little (replace fields by their macros, etc., fix
586        typo in CPP-flag)
587    o pkg/ggl90: minor changes
588      - GGL90diffKrS was removed --> always use GGL90diffKr
589      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
590      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
591        (commented out for now)
592      - change in max/min operations to ensure that smoothing is ok
593      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
594      - always use diffKrNrT as background profile (i.e. never use diffKr field)
595    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
596    o pkg/dic:
597      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
598        vectorization
599      - small bug fix in insol for the unlikely case of a cartesian grid
600      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
601        + now vectorize, which also removes adjoint recomputations;
602        + replace integer maksp1 by _RL maskp1
603        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
604    
605    checkpoint62i (2010/07/21)
606    o pkg/flt:
607      - with OBCS: stop floats which enter the OB region
608    o model/src:
609      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
610        for implicit vertical advection.
611    o pkg/seaice:
612     - account for melting in seaice age evolution.
613     - remove double counting of seaice ridging effect on seaice age.
614    
615    checkpoint62h (2010/06/18)
616    o pkg/exch2:
617     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
618    o tools/genmake2
619      - remove "-pdefault" option: redundant with the use of "packages.conf";
620      - remove file pkg/pkg_default : set the default as a pkg group
621        ("default_pkg_list") defined in pkg/pkg_groups;
622      - fix for case pkg/pkg_depend is missing (was hanging before);
623      - add option "-pgroups" to specify a different pkg_groups than the default.
624    o verification/adjustment.cs-32x32x1:
625       add a "minimal" set-up test (code_min & input_min) which only compiles
626       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
627    o tools/genmake2
628      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
629      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
630    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
631      files are nearly the same anyway.
632      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
633       - redefinition of tau(i,i) (by a factor of ustar)
634       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
635       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
636       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
637       - replace
638         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
639         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
640         by
641         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
642         (changes results)
643       -> exf_bulkformulae v1.22,
644          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
645          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
646                    output.txt 1.63
647           offline_exf_seaice: output.seaicetd.txt 1.7
648           seaice_obcs: output.txt 1.10)
649      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
650       -> exf_bulkformulae v1.23,
651          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
652          and global_ocean.cs32x15.icedyn (only 11 matching digits)
653      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
654    o adjoint of exch-1:
655     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
656       (note: was already like this when using EXCH-2) and remove flow dir
657       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
658     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
659     - update pkg/exch2 diff list.
660    
661    checkpoint62g (2010/05/19)
662    o eesupp/src (exch-1):
663     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
664       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
665       (renamed to exch1_*rx_cube.F).
666     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
667       to call new exch1 S/R ; update Makefile and .cvsignore.
668     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
669       exch2_xy_rx later)
670      Note: after updating your code, need to run "make clean" in eesupp/src
671    o test experiment bottom_ctrl_5x5:
672       new output_adm.txt with fewer grdchk & less monitor output.
673    o model/src:
674      remove the call to ini_cori in initialise_varia.F (just keep the usual one
675       in initialise_fixed.F). More consistent with coriolis & horizontal grid
676       beeing treated in the same way (ini_grid is not called a 2nd time).
677    o pkg/exf:
678      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
679      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
680      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
681      - cosmetic changes to exf_bulkformulae.F to make it look more like
682        exf_bulk_largeyeager04.F
683    o eesupp/src (exch-1):
684      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
685      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
686        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
687        (even without using MPI).
688      - Message mode: move RecvAck setting (indicator of buffer being ready)
689        from send_put to recv_get S/R (was useless before, but not sure if
690        it's much more useful now);
691      - Switch the order of sync: MPI-proc 1rst and then threads;
692      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
693      - fix AD code for communication mode ='get' (but not used).
694    o model/src:
695      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
696      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
697    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
698    o pkg/ctrl: require a specific set of control variables and exf-flags for
699      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
700    o model/src:
701     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
702       1rst forward sweep, to avoid over-writing output files during recomputations
703       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
704     b) 2nd version:
705      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
706      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
707         writePickupAtEnd) + seaice & ptracers output;
708      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
709    o model/src:
710      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
711    o pkg/exch2:
712      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
713      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
714    o pkg/autodiff & exch2:
715      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
716      (for now, only if ALLOW_EXCH2 is defined).
717    o pkg/autodiff:
718      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
719        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
720       + clean-up comments (_RS is not always real*4)
721      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
722      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
723        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
724    o testreport (AD-tests):
725      no longer link files from dir "../input" (1rst link files from
726      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
727    
728    checkpoint62f (2010/04/29)
729    o model/src/the_main_loop.F:
730      adjust store directives for seaice evp and multicategory according to
731      pkg/ecco/the_main_loop.F
732    o adjoint:
733      global_sum_ad was incomplete (noted many times by many people ;)
734      nice description by Jean U. as follows:
735      * allreduce(var) in global_sum.F can be interpreted as
736        reduce(sum) followed by broadcast of sum.
737      * The adjoint of that is
738        sum(adjoint) followed by broadcast(summed adjoint value)
739        or in other words, allreduce(sum, adjoint vars)
740      We were missing the sum(adjoint)!
741      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
742      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
743      The fix should produce 16-digit accuracy between
744      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
745      multi-CPU single-tile (e.g. nSx=1, nPx-2)
746      We'll probably change this yet again shortly
747    o eesupp/src:
748      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
749    o pkg/icefront
750      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
751        specification of addmass array based on a 2D field, which is added
752        at bottommost wet level at each horizontal location.
753    o model/src:
754     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
755     layout; (not always compatible with delX,delY setting; commented out for now).
756    o pkg/exch2:
757     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
758     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
759    
760    checkpoint62e (2010/04/15)
761    o pkg/obcs:
762      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
763    o pkg/dic:
764      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
765        (note: not presently tested in any forward verification exp.)
766       update tutorial_global_oce_biogeo AD output file.
767    o pkg/exf:
768      - account for the variation of albedo as a function of zenith angle
769        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
770    o build_options:
771     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
772    o pkg/dic:
773      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
774      - use binary pickup file for restart;
775      - initialise atmos-CO2 box from dic_pCO2 parameter;
776      - fix multi-threaded.
777    o pkg/rbcs:
778     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
779       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
780     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
781       and update output.txt
782    o pkg/kpp:
783     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
784     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
785       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
786       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
787     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
788       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
789  o pkg/offline:  o pkg/offline:
790    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor    fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
791    (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 839  o tools/build_options:
839      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
840  o pkg/ecco  o pkg/ecco
841    - allow user defined cost function contributions    - allow user defined cost function contributions
842          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
843          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
844    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
845        the two options are complementary.        the two options are complementary.
846  o pkg/smooth  o pkg/smooth
Legend:
Removed from v.1.1245  
changed lines
  Added in v.1.1410
  ViewVC Help
Powered by ViewVC 1.1.22