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revision 1.1277 by mlosch, Fri May 21 10:16:59 2010 UTC revision 1.1420 by jmc, Mon May 2 13:06:45 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 model/src:
8      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
9      - initialise startTime & nIter0 with unlikely values: allows to set one
10        from the other without ambiguity.
11    o seaice_obcs test-exp.:
12      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
13    o pkg/obcs:
14      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
15        no longer needed with maskInC,W,S in pkg/generic_advdiff.
16    o pkg/seaice:
17      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
18        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
19      - fixed bug in the initialization of sea ice salinity variable HSALT
20        in seaice_init_varia.F  (removed dependence on ICE2WATR)
21    o fizhi-cs test exp.:
22       switch reference output convention for these 2 non-standard test-exp,
23        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
24          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
25       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
26    o model/inc:
27      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
28        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
29    o pkg/seaice:
30      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
31    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
32      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
33        and initial HSALT
34    
35    checkpoint62w (2011/04/26)
36    o pkg/mom_fluxform:
37      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
38      - use parameter "sideDragFactor" in no-slip BC side-drag part.
39      - update output of exp. global_ocean.90x40x15
40    o pkg/mom_vecinv:
41      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
42    o update seaice exp.:
43      use more consistent parameter values (remove "backward compatability only":
44       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
45      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
46       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
47    o update test-exp global_ocean.90x40x15:
48      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
49      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
50      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
51      o turn on zStar & viscA4 in standard set-up (dir input/)
52        and update output files: output.txt & output.dwnslp.txt
53    o new AD-test experiment: obcs_ctrl
54      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
55    o pkg/dic:
56      fix two bugs in handling water vapour pressure in carbonate chemistry
57      and air-sea fluxes. Found by Val Bennington and Galen McKinley
58      (add DIC Option = WATERVAP_BUG to recover old results)
59      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
60    o adding allowInteriorFreezing option to check for water below freezing point
61      at depth and bring the negative heat anomaly to the surface level
62    o pkgs _fields_load:
63      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
64      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
65        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
66        rbcs to get interpolation weights and time reccord number.
67      - fix multi-threading in aim_fields_load.F
68      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
69    o external_fields_load:
70      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
71       interpolation weights) to use in a periodic time-series ; do not divide by
72       time-step to convert to integer:
73       - this fixes case where externForcingPeriod is not multiple of time-step
74          (Thanks to Christopher L. Wolfe)
75       - this fixes case where externForcingPeriod is an odd multiple of time-step
76         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
77      store index of time-record which is currently loaded:
78       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
79       - needed for the adjoint but not yet used because of extensive recomputations;
80         (to be fixed soon)
81    
82    checkpoint62v (2011/04/02)
83    o verification/1D_ocean_ice_column added to test Ian Fenty's
84      pkg/seaice_growth.F modifications for improving sea ice code differentiability
85    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
86      (new velocity statistics after changing maskInW & maskInS definition)
87    o pkg/generic_advdiff with OBCS:
88      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
89      equivalent to assumption of no tracer gradient outside the OB region.
90      This will affect the results if using obcs+biharmonic diffusion.
91      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
92    o pkg/obcs:
93      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
94      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
95      in Interior region. No impact on solution but affects Velocity monitor stats.
96    o pkg/ptracers (adjoint)
97      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
98      tape file for each tracer
99    o model/inc/src and pkg/autodiff: add parameters that allow to turn
100      of parts of the adjoint code at run time. For now, there are only
101      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
102      parameters are set in data.pkg.
103      This is the lazy coward's version of doing this, but still useful for
104      debugging. In order to do it right, everything needs to be moved to
105      pkg/autodiff.
106    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
107      the end; this fixes the adjoint balancing code for open boundaries.
108    o pkg/ctrl:
109      - change behavior of xx_${varname}period to be analogous to exf-conventions:
110        xx_${varname}period =   0.,  means time-independent control part
111        xx_${varname}period = -12., means one-year-periodic monthly control part
112      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
113        clean up ctrl_init a little, remove unused variables
114      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
115      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
116    
117    checkpoint62u (2011/03/15)
118    o model/src:
119      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
120        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
121      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
122        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
123    o pkg/ctrl/obcs/ecco:
124      - remove obsolete, unused, and partially broken code:
125        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
126        ALLOW_CTRL_OBCS_BALANCE
127      - put a stop statement into ecco/cost_obcsvol.F, but also add
128        cost_obcsvol to ecco_ad_diff.list
129    o pkg/ecco: fix counting cost function contributions for obcs (code
130      by Matt M.) and diffkr for diagnostics
131    o pkg/ecco, pkg/ctrl, pkg/grdchk:
132      add cost penalty terms for initial uvel, vvel, eta controls
133      and I/O for prior error files
134    o pkg/mdsio:
135       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
136       (new argument) to check for tiled file in mdsioLocalDir : this fix the
137       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
138    o pkg/ctrl:
139     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
140       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
141       unused and superfluous variables
142     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
143    o pkg/ecco
144     - enable adjoint of Stevens OB
145    o pkg/ctrl/ecco/grdchk:
146      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
147        Fortunately, we do not have any tests for the numerous cpp-flagged
148        option of "obcs as control parameters" so we will never know
149        if this is an improvement (but at least now things compile).
150      - remove an obsolete initialization from ecco_cost_init_barfiles.F
151      - fix some problems within never used ifdefs to make the code compile
152    o pkg/obcs:
153     - Refine Interior mask definition to work with more complex OB (e.g.
154       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
155       read in Interior mask from file. Check if Interior mask is consistent
156       with OB list of indices.
157    o pkg/seaice
158     - beginning code for a seaice tracer package,
159       but currently only used for seaice age: SEAICE_AGE
160       SEAICE_num = 4
161       iTracer = 1: area-weighted ice age
162               = 2: volume-weighted ice age
163               = 3, 4: template for one-year vs. multi-year ice
164       data.seaice has new namelist SEAICE_PARM03 for arrays related to
165       SEAICE_num
166    
167    checkpoint62t (2011/03/05)
168    o pkg/obcs:
169     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
170       then normal component. This ensures that the normal component is set
171       correctly even when it conficts with tangential setting from an other OB.
172       Affects results of test-experiment seaice_obcs: update the output.txt
173    o pkg/obcs:
174     - add code to monitor statistics of dynamical fields at OB.
175     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
176       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
177       - change default: balance the Net inflow through all OB (instead of balancing
178         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
179     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
180       to match Nortern OB inflow (OBCS_balanceFacN=0).
181    o pkg/seaice:
182     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
183    o pkg/seaice (seaice_growth v 1.113):
184     - reverting seaice_growth to v 1.111 in order to have code with exact bit
185       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
186       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
187       runtime flag SEAICEareaFormula is kept but is inactive
188    o model/src:
189     - add new param to scale curvilinear grid distance and area when using
190       a different sphere radius from the grid-files.
191     - test/check multi-threads EXCH applied to local variable (cg2d_x)
192    o adjoint:
193     - enable adjoint of Stevens OB
194     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
195       (a bit delicate because of potentially modified adj. common block structure;
196       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
197    
198    checkpoint62s (2011/02/15)
199    o pkg/seaice (seaice_growth v 1.112):
200     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
201       computing the ice cover tendency from effective thickness tendencies. Include
202       Ian Fenty's formula.
203     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
204       SEAICEareaFormula.
205     - simplify notations for the various d_HEFF/d_AREA terms.
206    o pkg/gmredi:
207     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
208       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
209       add a verification test-run (front_relax.bvp) to test GM_useBVP.
210    o pkg/seaice (seaice_growth v 1.111):
211     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
212     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
213       also melt ice.
214    o pkg/seaice:
215     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
216     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
217    o pkg/cheapaml:
218     - from Nico Wienders: New version of this package.
219    o pkg/flt:
220     - add CPP options to prevent floats to re-enter the opposite side of
221       a periodic domain (default: keep periodicity)
222    o pkg/gmredi:
223     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
224       (needed for multi-dim advection).
225     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
226    o model/src:
227     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
228    o tutorial_tracer_adjsens
229     - extend to NLFS and replace maskC by hFacC
230       (change reference output accordingly)
231    
232    checkpoint62r (2011/01/24)
233    o testreport:
234     - add option -deloutp (-do) to remove output file after successful run
235     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
236       extract exact list of procs from this file ; adjust COMMAND by
237       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
238    o pkg/ecco: replace old ineffective way of penalizing deviations from
239      first guess (of obcs) with code by Matt Mazloff
240    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
241      exf/cal
242      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
243        and handle case of obcs?period == 0
244        Not affected by these changes: There is still an inconsistency in
245        the computation of start/endrec for the obcs variables for ALLOW_CAL
246        defined (see comment by Menemenlis, 7-Mar-2003)
247      - make S/R ctrl_get_gen_rec return something meaningful even if
248        ALLOW_CAL is not defined
249      - ctrl_getobcs?: simplify code so that it does not need to use
250                       S/R exf_swapfields
251    o testreport:
252       allow to test MPI with different number of processors for each experiment:
253       create file "SIZE.h.mpi" in each build dir.
254       Note: update of "-command" argument not yet implemented.
255    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
256      alleviate the need for additional 3D tapes when using
257      the non-inear free surface in the adjoint. This is done
258      by adding an 'update' of hfacc etc. to their current
259      value at the beginning of forward_step.F.
260    o pkg/seaice
261      seaice_lsr: move stress-divergence computations out of outer pseudo-
262      timestepping loop
263    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
264      up, so that the calls of the ctrl_* subroutines are really at the end
265      of the routine.
266    o pkg/gmredi:
267      allow to specify a 2-D horizontal map and a 1-D vertical profil
268      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
269    o pkg/seaice:
270      move lsr iterations from seaice_dynsolver to seaice_lsr.
271    o pkg/seaice:
272      reduce memory footprint of seaice mutldim advection tapes,
273      by using a 2D tape independent of the generic_advdiff ones,
274      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
275    
276    checkpoint62q (2010/12/29)
277    o model/src:
278      - check horizontal grid-spacing for unset or zero/negative values.
279      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
280    o pkg/flt:
281      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
282      - precision of input and output files set according to readBinaryPrec
283        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
284      - initial float position from tiled file was not converted to index space
285        (looks like a bug): fixed to make it similar to initial pos. global file.
286    o global_ocean.cs32x15:
287       change SIZE.h of AD set-up to get same tiling as with MPI.
288       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
289    o model/src:
290       add flag to control printing of domain fields (bathymetry, hFac ...) in
291       ini_mask_etc (call to plot_fieds_xy*).
292    o pkg/thsice:
293       if useEXF, some forcing fields are not valid in overlap: fixed by computing
294       over the interior only + apply EXCH at the end (like with SEAICE advection).
295    o pkg/mdsio:
296      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
297        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
298      - change barrier call for safe multi-threads access to 3-D shared buffer.
299      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
300      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
301        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
302    o pkg/flt:
303      - add fourth-order Runge-Kutta integration
304      - add basic exch2 support (only 1 facet supported so far!)
305    o pkg/mdsio+rw:
306      new S/R to read local (or tile independent) vector (read counterpart of
307       mds_writevec_loc, and front-end write_glvec_rl/rs).
308    o global_ocean.cs32x15: additional input_ad.seaice experiment
309        that uses pkg/seaice rather than pkg/thsice.
310        (using multidim advection for seaice)
311    o towards more F95 syntax for array specification in namelist:
312      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
313        of all verification experiments.
314           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
315          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
316      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
317    o global_ocean.cs32x15: additional input.seaice experiment
318        that uses pkg/seaice rather than pkg/thsice.
319    
320    checkpoint62p (2010/12/17)
321    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
322        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
323    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
324        allow for use of multim. advection in seaice adjoint.
325    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
326      - first attempt to close budgets by taking into account the freshwater
327        flux implied by the sublimation of snow and ice. So far only the
328        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
329        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
330    o eesupp/src:
331      new S/R with new option (NML_EXTENDED_F77) to change array specification
332      from F95 standard to commonly accepted extended F77 form.
333      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
334      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
335      for less tolerant f77 compiler (e.g., pgf77, g77).
336    o globalFiles:
337      commented out in parameter file "data" since it's not safe with MPI
338      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
339      in this case); no longer commented out in restart test (tst_2+2).
340    o add adTapeDir to specify a special directory where adjoint tapes are
341      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
342      and cannot be used together with mdsioLocalDir.
343    o nesting pkgs:
344      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
345      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
346      - add parameter files + utils dir + output from short run on beagle.
347    o pkg/seaice:
348        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
349    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
350      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
351    
352    checkpoint62o (2010/11/25)
353    o pkg/exf:
354      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
355    o pkg/seaice:
356      - seaice_ocean_stress: split a loop for better vectorization of the
357        adjoint code
358      - seaice_growth.F: fix bug in conservation of freshwater connected to
359        capping of heff, put contribution into d_HEFFbyNEG
360      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
361        by something more sensible (parameters that are what their name implies)
362      - change some defaults, so that by default exf-parameters are used for
363        things like rhoAir, cpAir,latent/sensible heat parameters, in order
364        to reproduce the old results, many data.seaice now contain funny values
365        for cpAir and latent heat of sublimation
366    o packages_readparms.F: move exf_readparms up in line so that
367        exf-parameters are visible for other packages (e.g. seaice)
368    o debugMode & debugLevel=2:
369      - differentiate between debugMode & debugLevel=2:
370        debugMode: controls printing of debug messages (sequence of S/R calls).
371        debugLevel: controls printing of algorithm intermediate results and stats.
372      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
373        => allows to print debug-stats without all sequence of call messages.
374      - switch control of debug print from debugLevel to debugMode in many S/R.
375    o pkg/obcs (obcs-sponge):
376        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
377        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
378    o pkg/generic_advdiff:
379      - record overlap minimum size for each advection scheme;
380      - refine criteria on overlap minimum size;
381      - check and stop (in gad_check) if overlap size is too small.
382    o pkg/obcs:
383      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
384        once, in ptracers_implicit.F)
385      - with seaice: remove test on empty file name in obcs_apply_seaice (always
386        apply OB values when tile has OB)
387    o model/src, coriolis setting:
388      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
389        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
390        files (selectCoriMap=3) with any grid.
391      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
392    o pkg/seaice/seaice_growth.F:
393        a few cosmetic changes that reduce the number of lines of code
394    o pkg/obcs: add boundary conditions following Stevens (1990)
395      - the code follows old MOM/NAOSIM code
396      - so far it is only implemented for the eastern and western boundaries
397        and NOT for pTracers
398    o pkg/rbcs:
399      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
400        beginning of the first rbcs forcing period.
401      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
402        offline package, i.e., one file per time, labeled by iteration number;
403        deltaTrbcs sets the timestep with which the data was generated;
404        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
405      - rbcsForcingCycle=0 makes forcing non-cyclic.
406      - make arithmetic safe for negative times and odd forcing periods.
407    
408    checkpoint62n (2010/11/09)
409    o pkg/seaice:
410        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
411    o pkg/obcs:
412       New S/R to copy tracer value from the OB location to narrow band region
413        (width = same as overlap) beyond the OB: preserve OB value (needed for
414        high-order scheme) which were overwritten by EXCH call if in overlap
415        region. Applied to theta, salt, ptracer and advected seaice variables.
416       With seaice: use maskInC in similar way as in gad_advection.F,
417        in seaice_advection.F and advect.F.
418       Update output of experiment seaice_obcs and change exp4 to test OBCS with
419        4th order Adv.Scheme. for pasive salt and ptracer.
420    o tools/genmake2:
421      - when looking for an optfile (not specified), only search for Fortran compiler
422        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
423      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
424        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
425      - set default for CPP to "cpp -traditional -P" (was the case without specifying
426        an optfile, but otherwise default was just "cpp".
427      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
428      - when "CC" is not set in the optfile, look for possible C compiler
429        (instead of just setting CC=cc)
430      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
431        => add a ".F" to ".o" rule for source files with no "#include" (such as
432           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
433      - move gfortran before g77 in list of possible Fortran compiler (consistent
434        with reference compiler switch from g77 to gfortran)
435    o pkg/seaice:
436      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
437        seaice_check that stops the model, when the CPP flag is used.
438      o seaice_growth.F: make capping of ice volume conserving by returning the
439        capped ice as freshwater to EmPmR. This does not change the verification
440        experiments but will change runs where the capping is acutally active
441    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
442      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
443         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
444         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
445    o tools/genmake2:
446      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
447      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
448      - clean previous genmake log files before anything else.
449      - change Makefile to remove testreport log files (*.tr_log) and genmake log
450        files only with "CLEAN" target (instead of "Clean");
451    o pkg/generic_advdiff:
452      Change OBCS in multiDim advection (gad_advection.F):
453       Use maskInC to prevent intermediate update of tracer-field in OB regions,
454       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
455       which were applying future time-step OB values.
456      This way, all explicit calculations use current-time-step OB values
457       (simpler and more consistent).
458      Affects results when set-up uses time-varying OBC and multi-dim advection;
459       update output of experiment seaice_obcs.
460    o pkg/seaice:
461      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
462       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
463         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
464      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
465       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
466       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
467    o pkg aim (2010/10/26):
468      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
469        formulation with obliquity, eccentricity, ... as run-time parameters,
470      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
471        upward shortwave radition at the surface (all-sky and clear-sky).
472    o pkg/obcs:
473      - writing sections with globalFiles=T does not work: switch to tiled-files
474        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
475      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
476      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
477    
478    checkpoint62m (2010/10/21)
479    o pkg/seaice: vectorize seaice_solve4temp.F
480      - move iterations loops outside of i/j-loops
481      - requires 2D arrays for TB and effConduct
482      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
483        modified in this routine
484      - a little bit of clean up, adjusting indentation, etc.
485      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
486        performance and '**TWO' by '**2' (because TWO is a float),
487        replaced ONE, ZERO
488    o eesupp/src:
489       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
490    o pkg/seaice/seaice_growth.F
491      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
492      merging process. The merged routine has two branches, and one activates the 'evolution'
493      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
494      In summary, here is what the '10/10 revision' did consist of
495        part 1: seaice_growth.F revisions 1.71 to 1.75
496          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
497            The emphasis here was on improving readability (e.g. by trying to use meaningful
498            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
499        part 1.5:
500          - revising the lab_sea experiment to make it a more useful (i.e. stable
501            and representative of an actual model run). This was done by generating a
502            (winter) pickup to start from, switching back the main experiment dynamic
503            solver from evp to lsr, having one of the experiments use the free drift solution.
504        part 2: seaice_growth.F revisions 1.76 to 1.85
505          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
506          - Sorting out the various fields units and sign (set early on and reset at the end)
507            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
508            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
509          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
510            and simplifying logical expressions to further improve readibility.
511        part 3: seaice_growth.F revisions 1.86 to 1.89
512          - Re-organize the blocks of code more logically.
513          - Merging the '_if.F' pieces that add something new.
514    o pkg/thsice:
515      - vectorize thsice_solve4temp and thsice_get_exf.
516        Problem: thsice_solve4temp has an unvectorizable statement that
517        might also be problematic for TAF
518      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
519        does not change the verifcation experiment, but will change all
520        experiments that have this flag undefined (not tested in verification);
521        a little reorganization to save a few 2D fields and recomputations
522      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
523      - 2nd step:  fix some store dirs
524        o seems to work somewhat, i.e. using ifort but not g77
525        o likely cause are incomplete init. or recomputation
526        o start verification/global_ocean.cs32x15/input_ad.thsice
527    o pkg/obcs: add support for exch2
528      - the position of the boundary and prescribed values are specified using
529        a global domain with exch2 facets stacked
530        - in x for N,S boundaries (like W2_mapIO=-1)
531        - in y for E,W boundaries (so E,W boundaries do not overlap)
532    o pkg/mdsio: add support for writing global sections with exch2
533        file layout is as for obcs described above:
534        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
535        - for y-z sections, facets are stacked in y
536    o pkg/thsice:
537       - change a few routines for better vectorization: thsice_albedo.F,
538         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
539         not affected, but in particular the latter routine has changed
540         dramatically (not necessarily easier to read now).
541       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
542       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
543    o verification/lab_sea:
544      - overhaul of the forward model experiments. The main motivation
545        for this revision is that lab_sea has proven quite fragile (when
546        changing the sea-ice code, and switching platforms) to a point
547        when failures were very hard to attribute to specific code problems.
548      - the suspected reason for this fragility is noise amplification by evp so,
549        to start with, we decided to replace evp with lsr in the main experiment.
550      - the input.lsr experiment thus became obsolete and was removed.
551      - it was replaced with the input.fd experiment that uses an
552        analytical "free drift" solution as the ice velocity field.
553      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
554        will hopefully allow us to discriminate problems due to dynamic solvers
555        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
556        us to test additional options, along with the salt plume package.
557      - Finally a pickup was generated (at the end of a one year run) to
558        make the tests more representative of an actual model run. Previously
559        the tests starting point was a 1m thickness of ice everywhere.
560    o pkg/seaice:
561      - introducing S\R seaice_freedrift.F that compute the
562        analytical solution to an approximate ice momentum
563        equation (i.e. the simple stress/coriolis balance).
564      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
565        of the free drift velocity field, and enable its use.
566        To actually use the free drift solution as the model ice
567        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
568    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
569    
570    checkpoint62l (2010/10/04)
571    o pkg/seaice:
572      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
573      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
574       version (with USE_ORIGINAL_SBI undef);
575    o add hooks for new packages OASIS, the package will follow
576      (hooks exclude the seaice pkg for now)
577    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
578      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
579      rather than mdsio_readvector.F/mdsio_writevector.F, within
580      adread_adwrite.F to read/write adjoint-related tapes to disk.
581    o eesupp and pkg/mdsio: ALLOW_WHIO
582      Option to write/read 2D fields to files including tiles halos.
583      The main purpose is for adjoint related "tape I/O".
584      The secondary purpose is for debugging phases.
585      A word on those rather specifically intended purposes.
586      The code was meant to be stripped down to the bare minimum.
587      Typically, there is a unique and basic mapping to the global
588      buffer (tile by tile, then proc by proc, then level by level), and
589      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
590      meant to generate user friendly outputs of various shapes and forms.
591      Rather it is intended, for the knowledgeabale developers,
592      to be largely independent of the many mdsio options, to allow
593      outputs of tiles+halos in debugging phases and in adjoint runs,
594      and to allow some flexibility in tuning (adoint) I/O depending on each
595      file system behavior. With regard to tuning, most of the potential knobs
596      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
597      to specify directories, to specify the typical size of I/O calls, etc.)
598      are not yet included, and will be added if they prove useful.
599    o pkg/seaice:
600       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
601    o pkg/seaice:
602       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
603       code (seaice_budget_ice_if.F) which enable to recover old standard
604       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
605       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
606    o model/src (rStar):
607       use simple average (not area weighted) of rStarFac at U,V point when using
608       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
609       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
610    
611    checkpoint62k (2010/09/17)
612    o adjoint
613       * changed verification/global_ocean.cs32x15 ; adjoint now tests
614         Adams-Bashforth 3 + NLFS + RSTAR
615       * some more modifs required for ECCO-GODAE v4
616    o pkg/seaice
617       add SEAICE_AGE_VOL option to use volume instead of area for
618       integrating SEAICE_AGE
619    o model/src:
620       first check-in of sigma & hybrid-sigma coordinate code ; also includes
621       non-linear free-surface parts ; but pressure-gradient not yet coded.
622    o pkg/ptracers:
623       option for ptracer to convert Salt Relax into additional EmP.
624        tested in exp. global_ocean.90x40x15.dwnslp (update output)
625    
626    checkpoint62j (2010/08/25)
627    o pkg/ggl90:
628       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
629    o pkg/dic: car_flux.F, phos_flux.F
630      - reduce number of exp-calls in order to improve performance
631      - clean up a little (replace fields by their macros, etc., fix
632        typo in CPP-flag)
633    o pkg/ggl90: minor changes
634      - GGL90diffKrS was removed --> always use GGL90diffKr
635      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
636      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
637        (commented out for now)
638      - change in max/min operations to ensure that smoothing is ok
639      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
640      - always use diffKrNrT as background profile (i.e. never use diffKr field)
641    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
642    o pkg/dic:
643      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
644        vectorization
645      - small bug fix in insol for the unlikely case of a cartesian grid
646      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
647        + now vectorize, which also removes adjoint recomputations;
648        + replace integer maksp1 by _RL maskp1
649        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
650    
651    checkpoint62i (2010/07/21)
652    o pkg/flt:
653      - with OBCS: stop floats which enter the OB region
654    o model/src:
655      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
656        for implicit vertical advection.
657    o pkg/seaice:
658     - account for melting in seaice age evolution.
659     - remove double counting of seaice ridging effect on seaice age.
660    
661    checkpoint62h (2010/06/18)
662    o pkg/exch2:
663     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
664    o tools/genmake2
665      - remove "-pdefault" option: redundant with the use of "packages.conf";
666      - remove file pkg/pkg_default : set the default as a pkg group
667        ("default_pkg_list") defined in pkg/pkg_groups;
668      - fix for case pkg/pkg_depend is missing (was hanging before);
669      - add option "-pgroups" to specify a different pkg_groups than the default.
670    o verification/adjustment.cs-32x32x1:
671       add a "minimal" set-up test (code_min & input_min) which only compiles
672       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
673    o tools/genmake2
674      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
675      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
676  o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these  o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
677    files are nearly the same anyway.    files are nearly the same anyway.
678    Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:    Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
# Line 12  o pkg/exf: merge exf_bulk_largeyeager04 Line 680  o pkg/exf: merge exf_bulk_largeyeager04
680     - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)     - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
681     - replace rhonil by rhoConstFresh in computation of evap (bug fix)     - replace rhonil by rhoConstFresh in computation of evap (bug fix)
682     - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)     - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
683     - replace     - replace
684       rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )       rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
685       shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)       shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
686       by       by
687       shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )       shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
688       (changes results)       (changes results)
689     -> exf_bulkformulae v1.22,     -> exf_bulkformulae v1.22,
690        update verification experiments lab_sea, offline_exf_seaice, seaice_obcs        update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
691        (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,        (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
692                  output.txt 1.63                        output.txt 1.63
693         offline_exf_seaice: output.seaicetd.txt 1.7         offline_exf_seaice: output.seaicetd.txt 1.7
694         seaice_obcs: output.txt 1.10)         seaice_obcs: output.txt 1.10)
695    Step 2: do the actual merge and remove exf_bulk_largeyeager04.F    Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
696     -> exf_bulkformulae v1.23,     -> exf_bulkformulae v1.23,
697        unfortunately requires updating lab_sea.salt_plume (6 matching digits),        unfortunately requires updating lab_sea.salt_plume (6 matching digits),
698        and global_ocean.cs32x15.icedyn (only 11 matching digits)        and global_ocean.cs32x15.icedyn (only 11 matching digits)
699      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
700  o adjoint of exch-1:  o adjoint of exch-1:
701   - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)   - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
702     (note: was already like this when using EXCH-2) and remove flow dir     (note: was already like this when using EXCH-2) and remove flow dir
# Line 216  o tools/build_options: Line 885  o tools/build_options:
885      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
886  o pkg/ecco  o pkg/ecco
887    - allow user defined cost function contributions    - allow user defined cost function contributions
888          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
889          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
890    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
891        the two options are complementary.        the two options are complementary.
892  o pkg/smooth  o pkg/smooth
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