/[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 1.1241 by jmc, Wed Mar 24 20:54:49 2010 UTC revision 1.1398 by mlosch, Tue Mar 15 16:12:52 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62u (2011/03/15)
8    o model/src:
9      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
10        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
11      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
12        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
13    o pkg/ctrl/obcs/ecco:
14      - remove obsolete, unused, and partially broken code:
15        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
16        ALLOW_CTRL_OBCS_BALANCE
17      - put a stop statement into ecco/cost_obcsvol.F, but also add
18        cost_obcsvol to ecco_ad_diff.list
19    o pkg/ecco: fix counting cost function contributions for obcs (code
20      by Matt M.) and diffkr for diagnostics
21    o pkg/ecco, pkg/ctrl, pkg/grdchk:
22      add cost penalty terms for initial uvel, vvel, eta controls
23      and I/O for prior error files
24    o pkg/mdsio:
25       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
26       (new argument) to check for tiled file in mdsioLocalDir : this fix the
27       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
28    o pkg/ctrl:
29     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
30       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
31       unused and superfluous variables
32     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
33    o pkg/ecco
34     - enable adjoint of Stevens OB
35    o pkg/ctrl/ecco/grdchk:
36      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
37        Fortunately, we do not have any tests for the numerous cpp-flagged
38        option of "obcs as control parameters" so we will never know
39        if this is an improvement (but at least now things compile).
40      - remove an obsolete initialization from ecco_cost_init_barfiles.F
41      - fix some problems within never used ifdefs to make the code compile
42    o pkg/obcs:
43     - Refine Interior mask definition to work with more complex OB (e.g.
44       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
45       read in Interior mask from file. Check if Interior mask is consistent
46       with OB list of indices.
47    o pkg/seaice
48     - beginning code for a seaice tracer package,
49       but currently only used for seaice age: SEAICE_AGE
50       SEAICE_num = 4
51       iTracer = 1: area-weighted ice age
52               = 2: volume-weighted ice age
53               = 3, 4: template for one-year vs. multi-year ice
54       data.seaice has new namelist SEAICE_PARM03 for arrays related to
55       SEAICE_num
56    
57    checkpoint62t (2011/03/05)
58    o pkg/obcs:
59     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
60       then normal component. This ensures that the normal component is set
61       correctly even when it conficts with tangential setting from an other OB.
62       Affects results of test-experiment seaice_obcs: update the output.txt
63    o pkg/obcs:
64     - add code to monitor statistics of dynamical fields at OB.
65     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
66       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
67       - change default: balance the Net inflow through all OB (instead of balancing
68         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
69     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
70       to match Nortern OB inflow (OBCS_balanceFacN=0).
71    o pkg/seaice:
72     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
73    o pkg/seaice (seaice_growth v 1.113):
74     - reverting seaice_growth to v 1.111 in order to have code with exact bit
75       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
76       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
77       runtime flag SEAICEareaFormula is kept but is inactive
78    o model/src:
79     - add new param to scale curvilinear grid distance and area when using
80       a different sphere radius from the grid-files.
81     - test/check multi-threads EXCH applied to local variable (cg2d_x)
82    o adjoint:
83     - enable adjoint of Stevens OB
84     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
85       (a bit delicate because of potentially modified adj. common block structure;
86       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
87    
88    checkpoint62s (2011/02/15)
89    o pkg/seaice (seaice_growth v 1.112):
90     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
91       computing the ice cover tendency from effective thickness tendencies. Include
92       Ian Fenty's formula.
93     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
94       SEAICEareaFormula.
95     - simplify notations for the various d_HEFF/d_AREA terms.
96    o pkg/gmredi:
97     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
98       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
99       add a verification test-run (front_relax.bvp) to test GM_useBVP.
100    o pkg/seaice (seaice_growth v 1.111):
101     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
102     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
103       also melt ice.
104    o pkg/seaice:
105     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
106     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
107    o pkg/cheapaml:
108     - from Nico Wienders: New version of this package.
109    o pkg/flt:
110     - add CPP options to prevent floats to re-enter the opposite side of
111       a periodic domain (default: keep periodicity)
112    o pkg/gmredi:
113     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
114       (needed for multi-dim advection).
115     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
116    o model/src:
117     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
118    o tutorial_tracer_adjsens
119     - extend to NLFS and replace maskC by hFacC
120       (change reference output accordingly)
121    
122    checkpoint62r (2011/01/24)
123    o testreport:
124     - add option -deloutp (-do) to remove output file after successful run
125     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
126       extract exact list of procs from this file ; adjust COMMAND by
127       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
128    o pkg/ecco: replace old ineffective way of penalizing deviations from
129      first guess (of obcs) with code by Matt Mazloff
130    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
131      exf/cal
132      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
133        and handle case of obcs?period == 0
134        Not affected by these changes: There is still an inconsistency in
135        the computation of start/endrec for the obcs variables for ALLOW_CAL
136        defined (see comment by Menemenlis, 7-Mar-2003)
137      - make S/R ctrl_get_gen_rec return something meaningful even if
138        ALLOW_CAL is not defined
139      - ctrl_getobcs?: simplify code so that it does not need to use
140                       S/R exf_swapfields
141    o testreport:
142       allow to test MPI with different number of processors for each experiment:
143       create file "SIZE.h.mpi" in each build dir.
144       Note: update of "-command" argument not yet implemented.
145    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
146      alleviate the need for additional 3D tapes when using
147      the non-inear free surface in the adjoint. This is done
148      by adding an 'update' of hfacc etc. to their current
149      value at the beginning of forward_step.F.
150    o pkg/seaice
151      seaice_lsr: move stress-divergence computations out of outer pseudo-
152      timestepping loop
153    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
154      up, so that the calls of the ctrl_* subroutines are really at the end
155      of the routine.
156    o pkg/gmredi:
157      allow to specify a 2-D horizontal map and a 1-D vertical profil
158      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
159    o pkg/seaice:
160      move lsr iterations from seaice_dynsolver to seaice_lsr.
161    o pkg/seaice:
162      reduce memory footprint of seaice mutldim advection tapes,
163      by using a 2D tape independent of the generic_advdiff ones,
164      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
165    
166    checkpoint62q (2010/12/29)
167    o model/src:
168      - check horizontal grid-spacing for unset or zero/negative values.
169      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
170    o pkg/flt:
171      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
172      - precision of input and output files set according to readBinaryPrec
173        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
174      - initial float position from tiled file was not converted to index space
175        (looks like a bug): fixed to make it similar to initial pos. global file.
176    o global_ocean.cs32x15:
177       change SIZE.h of AD set-up to get same tiling as with MPI.
178       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
179    o model/src:
180       add flag to control printing of domain fields (bathymetry, hFac ...) in
181       ini_mask_etc (call to plot_fieds_xy*).
182    o pkg/thsice:
183       if useEXF, some forcing fields are not valid in overlap: fixed by computing
184       over the interior only + apply EXCH at the end (like with SEAICE advection).
185    o pkg/mdsio:
186      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
187        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
188      - change barrier call for safe multi-threads access to 3-D shared buffer.
189      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
190      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
191        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
192    o pkg/flt:
193      - add fourth-order Runge-Kutta integration
194      - add basic exch2 support (only 1 facet supported so far!)
195    o pkg/mdsio+rw:
196      new S/R to read local (or tile independent) vector (read counterpart of
197       mds_writevec_loc, and front-end write_glvec_rl/rs).
198    o global_ocean.cs32x15: additional input_ad.seaice experiment
199        that uses pkg/seaice rather than pkg/thsice.
200        (using multidim advection for seaice)
201    o towards more F95 syntax for array specification in namelist:
202      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
203        of all verification experiments.
204           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
205          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
206      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
207    o global_ocean.cs32x15: additional input.seaice experiment
208        that uses pkg/seaice rather than pkg/thsice.
209    
210    checkpoint62p (2010/12/17)
211    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
212        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
213    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
214        allow for use of multim. advection in seaice adjoint.
215    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
216      - first attempt to close budgets by taking into account the freshwater
217        flux implied by the sublimation of snow and ice. So far only the
218        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
219        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
220    o eesupp/src:
221      new S/R with new option (NML_EXTENDED_F77) to change array specification
222      from F95 standard to commonly accepted extended F77 form.
223      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
224      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
225      for less tolerant f77 compiler (e.g., pgf77, g77).
226    o globalFiles:
227      commented out in parameter file "data" since it's not safe with MPI
228      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
229      in this case); no longer commented out in restart test (tst_2+2).
230    o add adTapeDir to specify a special directory where adjoint tapes are
231      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
232      and cannot be used together with mdsioLocalDir.
233    o nesting pkgs:
234      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
235      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
236      - add parameter files + utils dir + output from short run on beagle.
237    o pkg/seaice:
238        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
239    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
240      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
241    
242    checkpoint62o (2010/11/25)
243    o pkg/exf:
244      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
245    o pkg/seaice:
246      - seaice_ocean_stress: split a loop for better vectorization of the
247        adjoint code
248      - seaice_growth.F: fix bug in conservation of freshwater connected to
249        capping of heff, put contribution into d_HEFFbyNEG
250      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
251        by something more sensible (parameters that are what their name implies)
252      - change some defaults, so that by default exf-parameters are used for
253        things like rhoAir, cpAir,latent/sensible heat parameters, in order
254        to reproduce the old results, many data.seaice now contain funny values
255        for cpAir and latent heat of sublimation
256    o packages_readparms.F: move exf_readparms up in line so that
257        exf-parameters are visible for other packages (e.g. seaice)
258    o debugMode & debugLevel=2:
259      - differentiate between debugMode & debugLevel=2:
260        debugMode: controls printing of debug messages (sequence of S/R calls).
261        debugLevel: controls printing of algorithm intermediate results and stats.
262      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
263        => allows to print debug-stats without all sequence of call messages.
264      - switch control of debug print from debugLevel to debugMode in many S/R.
265    o pkg/obcs (obcs-sponge):
266        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
267        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
268    o pkg/generic_advdiff:
269      - record overlap minimum size for each advection scheme;
270      - refine criteria on overlap minimum size;
271      - check and stop (in gad_check) if overlap size is too small.
272    o pkg/obcs:
273      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
274        once, in ptracers_implicit.F)
275      - with seaice: remove test on empty file name in obcs_apply_seaice (always
276        apply OB values when tile has OB)
277    o model/src, coriolis setting:
278      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
279        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
280        files (selectCoriMap=3) with any grid.
281      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
282    o pkg/seaice/seaice_growth.F:
283        a few cosmetic changes that reduce the number of lines of code
284    o pkg/obcs: add boundary conditions following Stevens (1990)
285      - the code follows old MOM/NAOSIM code
286      - so far it is only implemented for the eastern and western boundaries
287        and NOT for pTracers
288    o pkg/rbcs:
289      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
290        beginning of the first rbcs forcing period.
291      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
292        offline package, i.e., one file per time, labeled by iteration number;
293        deltaTrbcs sets the timestep with which the data was generated;
294        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
295      - rbcsForcingCycle=0 makes forcing non-cyclic.
296      - make arithmetic safe for negative times and odd forcing periods.
297    
298    checkpoint62n (2010/11/09)
299    o pkg/seaice:
300        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
301    o pkg/obcs:
302       New S/R to copy tracer value from the OB location to narrow band region
303        (width = same as overlap) beyond the OB: preserve OB value (needed for
304        high-order scheme) which were overwritten by EXCH call if in overlap
305        region. Applied to theta, salt, ptracer and advected seaice variables.
306       With seaice: use maskInC in similar way as in gad_advection.F,
307        in seaice_advection.F and advect.F.
308       Update output of experiment seaice_obcs and change exp4 to test OBCS with
309        4th order Adv.Scheme. for pasive salt and ptracer.
310    o tools/genmake2:
311      - when looking for an optfile (not specified), only search for Fortran compiler
312        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
313      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
314        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
315      - set default for CPP to "cpp -traditional -P" (was the case without specifying
316        an optfile, but otherwise default was just "cpp".
317      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
318      - when "CC" is not set in the optfile, look for possible C compiler
319        (instead of just setting CC=cc)
320      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
321        => add a ".F" to ".o" rule for source files with no "#include" (such as
322           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
323      - move gfortran before g77 in list of possible Fortran compiler (consistent
324        with reference compiler switch from g77 to gfortran)
325    o pkg/seaice:
326      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
327        seaice_check that stops the model, when the CPP flag is used.
328      o seaice_growth.F: make capping of ice volume conserving by returning the
329        capped ice as freshwater to EmPmR. This does not change the verification
330        experiments but will change runs where the capping is acutally active
331    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
332      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
333         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
334         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
335    o tools/genmake2:
336      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
337      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
338      - clean previous genmake log files before anything else.
339      - change Makefile to remove testreport log files (*.tr_log) and genmake log
340        files only with "CLEAN" target (instead of "Clean");
341    o pkg/generic_advdiff:
342      Change OBCS in multiDim advection (gad_advection.F):
343       Use maskInC to prevent intermediate update of tracer-field in OB regions,
344       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
345       which were applying future time-step OB values.
346      This way, all explicit calculations use current-time-step OB values
347       (simpler and more consistent).
348      Affects results when set-up uses time-varying OBC and multi-dim advection;
349       update output of experiment seaice_obcs.
350    o pkg/seaice:
351      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
352       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
353         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
354      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
355       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
356       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
357    o pkg aim (2010/10/26):
358      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
359        formulation with obliquity, eccentricity, ... as run-time parameters,
360      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
361        upward shortwave radition at the surface (all-sky and clear-sky).
362    o pkg/obcs:
363      - writing sections with globalFiles=T does not work: switch to tiled-files
364        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
365      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
366      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
367    
368    checkpoint62m (2010/10/21)
369    o pkg/seaice: vectorize seaice_solve4temp.F
370      - move iterations loops outside of i/j-loops
371      - requires 2D arrays for TB and effConduct
372      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
373        modified in this routine
374      - a little bit of clean up, adjusting indentation, etc.
375      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
376        performance and '**TWO' by '**2' (because TWO is a float),
377        replaced ONE, ZERO
378    o eesupp/src:
379       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
380    o pkg/seaice/seaice_growth.F
381      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
382      merging process. The merged routine has two branches, and one activates the 'evolution'
383      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
384      In summary, here is what the '10/10 revision' did consist of
385        part 1: seaice_growth.F revisions 1.71 to 1.75
386          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
387            The emphasis here was on improving readability (e.g. by trying to use meaningful
388            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
389        part 1.5:
390          - revising the lab_sea experiment to make it a more useful (i.e. stable
391            and representative of an actual model run). This was done by generating a
392            (winter) pickup to start from, switching back the main experiment dynamic
393            solver from evp to lsr, having one of the experiments use the free drift solution.
394        part 2: seaice_growth.F revisions 1.76 to 1.85
395          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
396          - Sorting out the various fields units and sign (set early on and reset at the end)
397            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
398            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
399          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
400            and simplifying logical expressions to further improve readibility.
401        part 3: seaice_growth.F revisions 1.86 to 1.89
402          - Re-organize the blocks of code more logically.
403          - Merging the '_if.F' pieces that add something new.
404    o pkg/thsice:
405      - vectorize thsice_solve4temp and thsice_get_exf.
406        Problem: thsice_solve4temp has an unvectorizable statement that
407        might also be problematic for TAF
408      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
409        does not change the verifcation experiment, but will change all
410        experiments that have this flag undefined (not tested in verification);
411        a little reorganization to save a few 2D fields and recomputations
412      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
413      - 2nd step:  fix some store dirs
414        o seems to work somewhat, i.e. using ifort but not g77
415        o likely cause are incomplete init. or recomputation
416        o start verification/global_ocean.cs32x15/input_ad.thsice
417    o pkg/obcs: add support for exch2
418      - the position of the boundary and prescribed values are specified using
419        a global domain with exch2 facets stacked
420        - in x for N,S boundaries (like W2_mapIO=-1)
421        - in y for E,W boundaries (so E,W boundaries do not overlap)
422    o pkg/mdsio: add support for writing global sections with exch2
423        file layout is as for obcs described above:
424        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
425        - for y-z sections, facets are stacked in y
426    o pkg/thsice:
427       - change a few routines for better vectorization: thsice_albedo.F,
428         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
429         not affected, but in particular the latter routine has changed
430         dramatically (not necessarily easier to read now).
431       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
432       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
433    o verification/lab_sea:
434      - overhaul of the forward model experiments. The main motivation
435        for this revision is that lab_sea has proven quite fragile (when
436        changing the sea-ice code, and switching platforms) to a point
437        when failures were very hard to attribute to specific code problems.
438      - the suspected reason for this fragility is noise amplification by evp so,
439        to start with, we decided to replace evp with lsr in the main experiment.
440      - the input.lsr experiment thus became obsolete and was removed.
441      - it was replaced with the input.fd experiment that uses an
442        analytical "free drift" solution as the ice velocity field.
443      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
444        will hopefully allow us to discriminate problems due to dynamic solvers
445        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
446        us to test additional options, along with the salt plume package.
447      - Finally a pickup was generated (at the end of a one year run) to
448        make the tests more representative of an actual model run. Previously
449        the tests starting point was a 1m thickness of ice everywhere.
450    o pkg/seaice:
451      - introducing S\R seaice_freedrift.F that compute the
452        analytical solution to an approximate ice momentum
453        equation (i.e. the simple stress/coriolis balance).
454      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
455        of the free drift velocity field, and enable its use.
456        To actually use the free drift solution as the model ice
457        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
458    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
459    
460    checkpoint62l (2010/10/04)
461    o pkg/seaice:
462      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
463      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
464       version (with USE_ORIGINAL_SBI undef);
465    o add hooks for new packages OASIS, the package will follow
466      (hooks exclude the seaice pkg for now)
467    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
468      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
469      rather than mdsio_readvector.F/mdsio_writevector.F, within
470      adread_adwrite.F to read/write adjoint-related tapes to disk.
471    o eesupp and pkg/mdsio: ALLOW_WHIO
472      Option to write/read 2D fields to files including tiles halos.
473      The main purpose is for adjoint related "tape I/O".
474      The secondary purpose is for debugging phases.
475      A word on those rather specifically intended purposes.
476      The code was meant to be stripped down to the bare minimum.
477      Typically, there is a unique and basic mapping to the global
478      buffer (tile by tile, then proc by proc, then level by level), and
479      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
480      meant to generate user friendly outputs of various shapes and forms.
481      Rather it is intended, for the knowledgeabale developers,
482      to be largely independent of the many mdsio options, to allow
483      outputs of tiles+halos in debugging phases and in adjoint runs,
484      and to allow some flexibility in tuning (adoint) I/O depending on each
485      file system behavior. With regard to tuning, most of the potential knobs
486      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
487      to specify directories, to specify the typical size of I/O calls, etc.)
488      are not yet included, and will be added if they prove useful.
489    o pkg/seaice:
490       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
491    o pkg/seaice:
492       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
493       code (seaice_budget_ice_if.F) which enable to recover old standard
494       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
495       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
496    o model/src (rStar):
497       use simple average (not area weighted) of rStarFac at U,V point when using
498       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
499       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
500    
501    checkpoint62k (2010/09/17)
502    o adjoint
503       * changed verification/global_ocean.cs32x15 ; adjoint now tests
504         Adams-Bashforth 3 + NLFS + RSTAR
505       * some more modifs required for ECCO-GODAE v4
506    o pkg/seaice
507       add SEAICE_AGE_VOL option to use volume instead of area for
508       integrating SEAICE_AGE
509    o model/src:
510       first check-in of sigma & hybrid-sigma coordinate code ; also includes
511       non-linear free-surface parts ; but pressure-gradient not yet coded.
512    o pkg/ptracers:
513       option for ptracer to convert Salt Relax into additional EmP.
514        tested in exp. global_ocean.90x40x15.dwnslp (update output)
515    
516    checkpoint62j (2010/08/25)
517    o pkg/ggl90:
518       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
519    o pkg/dic: car_flux.F, phos_flux.F
520      - reduce number of exp-calls in order to improve performance
521      - clean up a little (replace fields by their macros, etc., fix
522        typo in CPP-flag)
523    o pkg/ggl90: minor changes
524      - GGL90diffKrS was removed --> always use GGL90diffKr
525      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
526      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
527        (commented out for now)
528      - change in max/min operations to ensure that smoothing is ok
529      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
530      - always use diffKrNrT as background profile (i.e. never use diffKr field)
531    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
532    o pkg/dic:
533      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
534        vectorization
535      - small bug fix in insol for the unlikely case of a cartesian grid
536      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
537        + now vectorize, which also removes adjoint recomputations;
538        + replace integer maksp1 by _RL maskp1
539        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
540    
541    checkpoint62i (2010/07/21)
542    o pkg/flt:
543      - with OBCS: stop floats which enter the OB region
544    o model/src:
545      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
546        for implicit vertical advection.
547    o pkg/seaice:
548     - account for melting in seaice age evolution.
549     - remove double counting of seaice ridging effect on seaice age.
550    
551    checkpoint62h (2010/06/18)
552    o pkg/exch2:
553     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
554    o tools/genmake2
555      - remove "-pdefault" option: redundant with the use of "packages.conf";
556      - remove file pkg/pkg_default : set the default as a pkg group
557        ("default_pkg_list") defined in pkg/pkg_groups;
558      - fix for case pkg/pkg_depend is missing (was hanging before);
559      - add option "-pgroups" to specify a different pkg_groups than the default.
560    o verification/adjustment.cs-32x32x1:
561       add a "minimal" set-up test (code_min & input_min) which only compiles
562       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
563    o tools/genmake2
564      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
565      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
566    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
567      files are nearly the same anyway.
568      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
569       - redefinition of tau(i,i) (by a factor of ustar)
570       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
571       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
572       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
573       - replace
574         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
575         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
576         by
577         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
578         (changes results)
579       -> exf_bulkformulae v1.22,
580          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
581          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
582                    output.txt 1.63
583           offline_exf_seaice: output.seaicetd.txt 1.7
584           seaice_obcs: output.txt 1.10)
585      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
586       -> exf_bulkformulae v1.23,
587          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
588          and global_ocean.cs32x15.icedyn (only 11 matching digits)
589      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
590    o adjoint of exch-1:
591     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
592       (note: was already like this when using EXCH-2) and remove flow dir
593       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
594     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
595     - update pkg/exch2 diff list.
596    
597    checkpoint62g (2010/05/19)
598    o eesupp/src (exch-1):
599     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
600       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
601       (renamed to exch1_*rx_cube.F).
602     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
603       to call new exch1 S/R ; update Makefile and .cvsignore.
604     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
605       exch2_xy_rx later)
606      Note: after updating your code, need to run "make clean" in eesupp/src
607    o test experiment bottom_ctrl_5x5:
608       new output_adm.txt with fewer grdchk & less monitor output.
609    o model/src:
610      remove the call to ini_cori in initialise_varia.F (just keep the usual one
611       in initialise_fixed.F). More consistent with coriolis & horizontal grid
612       beeing treated in the same way (ini_grid is not called a 2nd time).
613    o pkg/exf:
614      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
615      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
616      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
617      - cosmetic changes to exf_bulkformulae.F to make it look more like
618        exf_bulk_largeyeager04.F
619    o eesupp/src (exch-1):
620      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
621      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
622        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
623        (even without using MPI).
624      - Message mode: move RecvAck setting (indicator of buffer being ready)
625        from send_put to recv_get S/R (was useless before, but not sure if
626        it's much more useful now);
627      - Switch the order of sync: MPI-proc 1rst and then threads;
628      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
629      - fix AD code for communication mode ='get' (but not used).
630    o model/src:
631      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
632      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
633    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
634    o pkg/ctrl: require a specific set of control variables and exf-flags for
635      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
636    o model/src:
637     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
638       1rst forward sweep, to avoid over-writing output files during recomputations
639       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
640     b) 2nd version:
641      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
642      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
643         writePickupAtEnd) + seaice & ptracers output;
644      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
645    o model/src:
646      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
647    o pkg/exch2:
648      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
649      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
650    o pkg/autodiff & exch2:
651      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
652      (for now, only if ALLOW_EXCH2 is defined).
653    o pkg/autodiff:
654      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
655        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
656       + clean-up comments (_RS is not always real*4)
657      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
658      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
659        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
660    o testreport (AD-tests):
661      no longer link files from dir "../input" (1rst link files from
662      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
663    
664    checkpoint62f (2010/04/29)
665    o model/src/the_main_loop.F:
666      adjust store directives for seaice evp and multicategory according to
667      pkg/ecco/the_main_loop.F
668    o adjoint:
669      global_sum_ad was incomplete (noted many times by many people ;)
670      nice description by Jean U. as follows:
671      * allreduce(var) in global_sum.F can be interpreted as
672        reduce(sum) followed by broadcast of sum.
673      * The adjoint of that is
674        sum(adjoint) followed by broadcast(summed adjoint value)
675        or in other words, allreduce(sum, adjoint vars)
676      We were missing the sum(adjoint)!
677      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
678      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
679      The fix should produce 16-digit accuracy between
680      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
681      multi-CPU single-tile (e.g. nSx=1, nPx-2)
682      We'll probably change this yet again shortly
683    o eesupp/src:
684      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
685    o pkg/icefront
686      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
687        specification of addmass array based on a 2D field, which is added
688        at bottommost wet level at each horizontal location.
689    o model/src:
690     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
691     layout; (not always compatible with delX,delY setting; commented out for now).
692    o pkg/exch2:
693     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
694     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
695    
696    checkpoint62e (2010/04/15)
697    o pkg/obcs:
698      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
699    o pkg/dic:
700      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
701        (note: not presently tested in any forward verification exp.)
702       update tutorial_global_oce_biogeo AD output file.
703    o pkg/exf:
704      - account for the variation of albedo as a function of zenith angle
705        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
706    o build_options:
707     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
708    o pkg/dic:
709      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
710      - use binary pickup file for restart;
711      - initialise atmos-CO2 box from dic_pCO2 parameter;
712      - fix multi-threaded.
713    o pkg/rbcs:
714     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
715       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
716     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
717       and update output.txt
718    o pkg/kpp:
719     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
720     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
721       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
722       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
723     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
724       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
725    o pkg/offline:
726      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
727      (bug was added in version 1.10 on 2007-08-23).
728    o pkg/offline:
729      - no need to specify periodicExternalForcing, etc ... to use offline pack
730      - offline input files no longer just single prec --> parameter offlineLoadPrec
731    o verification/lab_sea:
732      change AD test to multi-tile setup and update all 4 AD output.
733      NOTE: while cost function values remain very similar,
734      gradients are very different, although gradient checks are self-consistent
735      Should try to get to the bottom of this (cost function summation order?)
736  o pkg/dic:  o pkg/dic:
737    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
738    a weakness of TAF that drops part of double precision in log10 derivative.    a weakness of TAF that drops part of double precision in log10 derivative.
739      <= changes removed since problem has been fixed in current TAF version 1.9.71
740    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
741  o pkg/ecco:  o pkg/ecco:
742    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
# Line 45  o tools/build_options: Line 775  o tools/build_options:
775      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
776  o pkg/ecco  o pkg/ecco
777    - allow user defined cost function contributions    - allow user defined cost function contributions
778          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
779          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
780    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
781        the two options are complementary.        the two options are complementary.
782  o pkg/smooth  o pkg/smooth
Legend:
Removed from v.1.1241  
changed lines
  Added in v.1.1398
  ViewVC Help
Powered by ViewVC 1.1.22