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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1825 by mlosch, Fri Feb 15 15:20:03 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: replace a hard coded parameter by a runtime parameter
8       SEAICE_JFNK_tolIter
9    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
10        preconditioner for JFNK (run LSR into the overlaps as far as possible,
11        i.e OLx/y-2, but overwrite the solution in the overlaps)
12      - extend loop range in seaice_calc_viscosity
13      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
14      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
15      - slightly modify loops in tridiagonal solver lsr-preconditioner
16      - by default remove the extra exchange in seaice_preconditioner with a
17        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
18      - modify offline_exf_seaice so that old results without RAS are reproduced
19        for output.dyn_jfnk.txt
20      in seaice_fgmres.F (unrelated to RAS)
21      - add a cpp-flag option for a re-ordered mapping (potentially more
22        efficient), but because this changes the results, turn it off by
23        default
24      - replace the save statement by local common blocks
25    o utils/matlab:
26      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
27      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
28        instead of local script "load_cs.m".
29    o pkg/seaice:
30      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
31        to the scalarProductMetric and the unrolling. By chance this does not
32        change the verification experiment, because of the particular domain
33        decomposition
34    o pkg/diagnostics:
35      - change default missing_value from UNSET_RL to -999.
36    o pkg/layers: improve vectorization of layers_fluxcalc.F
37      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
38        time spent in this routine by more than a factor of 3 on an NEC-SX8
39      - step 2: replace search algorithm by a bisection algorithm found in
40        Press et al. Numerical Recipes in Fortran. This algorithm can be
41        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
42        For now, use this algorithm only for TARGET_NEC_SX defined.
43      - moved the search algorithm into a separate subroutine, that is kept
44        within the same file for automatic inlining.
45      - modified catching potential errors
46    o pkg/ecco:
47      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
48    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
49      - modifications for ALLOW_GENTIM2D_CONTROL
50      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
51      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
52      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
53      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
54    o model/src:
55      - account for moist thermodynamics in (dry) potential temperature equation;
56        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
57        and cpl_aim+ocn.
58      - also switch to standard compiler (gfortran, was using ifort previously)
59        for fizhi-cs experiments reference output.
60    o pkg/ctrl:
61      - 1st step toward generic time-varying control variable (2D) via CPP option
62        ALLOW_GENTIM2D_CONTROL
63      - note new namelist ctrl_nml_genarr in data.ctrl
64    o verification/global_ocean.cs32x15:
65      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
66        thsice calling sequence and update "output.icedyn.txt" output file.
67    o pkg/ptracers:
68      - from Ryan A.: code to allow to restart a tracer at regular time interval
69        specifying a reset frequency and a reset-phase (for each tracers).
70    o pkg/thsice:
71      - implement new sequence of calls for thsice+seaice:
72          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
73          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
74      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
75        in CPP_OPTIONS.h) to recover old sequence;
76      - update diagnostics for Intermediate State thsice diagnostics: now filled
77        just before advection (instead of just after advection in old sequence);
78      - update output of experiment offline_exf_seaice (standard test);
79      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
80        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
81    o pkg/aim_v23:
82      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
83      - use standard pkg/mdsio routines to read & write CO2 pickup file;
84      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
85      - Implement new sequence of calls for seaice advection (with thsice and
86        seaice diffusion): do ice advection after ice-Thermodynamic (previously
87        was done before); change aim_do_physics.F (split the bi,bj loops block);
88      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
89    o pkg/thsice:
90      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
91        where just seaice diffusion is used without seaice-dynamics.
92    
93    checkpoint64c (2013/01/18)
94    o pkg/seaice:
95      - add a parameter JFNKres_tFac that can replace JFNKres_t
96        (= JFNKres_tFac*JFNKresidual before JFNK solver)
97      - add a line search option to the JFNK solver
98      - move update of u/vIce and computation of initial residual into a separate
99        routine (same file); makes the code a little easier to read (?)
100      - the line search requires computation of the residual and for some reason
101        I cannot do the update of u/vIce at the beginning of the Newton loop
102        without changing the results, so we move computation of the new residual
103        also to the end of the Newton loop, even without the line search
104    o pkg/mdsio:
105      - write missing value (corresponding to undefined array value) to meta files;
106        skip this if missing value is one (UNSET_RL would be a better value for the
107        case of undefined missing value but it's current the default missing-value);
108        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
109    o pkg/exf & thsice:
110      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
111        diagnostics) even when SHORTWAVE_HEATING is #undef;
112    o verification/cfc_example:
113      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
114        illustrate how to use it).
115    o verification/offline_exf_seaice:
116      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
117        files to only one time-record.
118      in input.thermo: narrow the 2 bands of low initial ice-concentration near
119        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
120        snapshot output; same mcPheePiston value as in thsice with
121        surf-current=0.2m/s.
122      in input.thsice: similar set-up as in input.thermo (channel with same seaice
123        initial conditions).
124    o verification/cfc_example:
125      - update file "data" with more standard choice (default rotationPeriod,
126        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
127        set deltaTFreeSurf to deltaTtracer) and update the output.
128    o pkg/layers:
129      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
130      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
131    o verification/offline_exf_seaice:
132      - set all {field}period to zero for constant-in-time forcing (not tested
133        anywhere else).
134    o verification/offline_exf_seaice:
135      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
136      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
137    o model/src:
138      - implement Finite-Volume method for (hydrostatic) presure gradient
139        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
140    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
141      - In order to be compatible with the default EVP code, this requires changing
142        the EVP code around a little; and because any small change immediately
143        breaks the lab_sea.hb87 verification experiment, the reference output is
144        updated two times (each time the remaining aggrement was only 2 digits):
145        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
146        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
147        The adjoint test lab_sea.evp also needed to be updated.
148      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
149        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
150        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
151        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
152        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
153        kept obscure, because I need to test it a little more.
154    o pkg/cheapaml:
155      - fix few incorrect type (_RL/_RS) in subroutine calls.
156    o pkg/seaice:
157      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
158        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
159    o model/src:
160      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
161        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
162        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
163    o pkg/cheapaml:
164      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
165        update output of experiment cheapAML_box.
166      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
167        and set them only in one place (cheapaml_readparms.F).
168      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
169      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
170        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
171    o model/src/the_main_loop.F:
172      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
173    o pkg/seaice:
174      - remove legacy branch code.
175      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
176    o verification/*/code*/SEAICE_OPTIONS.h:
177      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
178        SEAICE_CAP_HEFF).
179    o pkg/cheapaml:
180      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
181        to load new forcing fields.
182      - add missing "_d 0" where it's needed; + some editing (improve indentation).
183      - remove switch to "-r8" compiler option (no longer needed) in verification
184        cheapAML_box, keep same output (small trucation error differences).
185    o verification/offline_exf_seaice:
186      - add thermodynamics only test.
187    o verification/cheapAML_box:
188      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
189        keep same output (same 14 digits for cg2d).
190      - switch on "-r8" compiler option (some numerical values are missing
191        the "_d 0") and update output (only 6 digits for cg2d were preserved).
192    
193    checkpoint64b (2012/12/24)
194    o pkg/cheapaml:
195      - remove un-used variables (Qnet,EmPmR) from pickup files.
196      - store tendency of advected variables into cheapaml pickup file
197        and fix the AB-2 restart.
198    o verification/offline_exf_seaice and lab_sea adjoint:
199      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
200      - switch to 4 time steps in offline, consistent with lab_sea.
201      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
202      - update results after change of experiment seaice.
203    o pkg/seaice:
204      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
205        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
206        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
207        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
208    o model/src:
209      - add run-time parameter to select CG2D solver minimum-residual solution
210        (in case of a poor convergence).
211    o pkg/seaice/seaice_lsr.F
212      - move calculation of matrix coefficients into new
213        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
214        file; the main purpose of this change is to be able to reuse the code
215        in S/R SEAICE_PRECONDITIONER
216      - modify the computation of the residual so that the mass of sea-ice
217        is not used twice; this simplifies the calculations, but since
218        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
219        not tested in testreport---this does not affect the testreport results.
220    o verification/seaice_obcs:
221      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
222        verification/lab_sea/input.salt_plume; changes results/output.txt*
223    o model/src:
224      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
225    o pkg/seaice:
226      - improve description of parameters in seaice_fgmres.F and start
227        cleaning up the code
228      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
229        second argument
230      - add a metric based on grid cell area to SEAICE_SCALPROD; update
231        results of offline_exf_seaice.dyn_jfnk
232      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
233    o pkg/aim_v23:
234      - fix an other bug in dissipation heating (grid-cell area was missing).
235    o model/src + pkg/seaice:
236      - add global (multi-tile) linear solver for pair of tri-diagonal system
237        along X and Y lines, respectively for U and V component.
238        Note: 1) MPI and cube-exchange not yet coded.
239            2) probably not accurate for poorly conditioned / large size problem.
240      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
241        default: not compiled and not used.
242    o pkg/seaice:
243      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
244        introduce bi/bj loops and use global_sum_tile_rl instead of
245        mpi_allreduce in seaice_fgmres.F
246      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
247      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
248      - add a verification experiment for JFNK in offline_exf_seaice
249    o verification:
250      - change (for now, only fwd test) offline_exf_seaice experiment:
251        use a re-entrant channel with idealized coastline (trapezoidal shape)
252        at southern boundary to explore seaice dynamics and thermodynamics
253        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
254        secondary test (input.thsice) use thermodynamics only with SST relaxation.
255      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
256    o pkg/exf:
257      - disable "sstExtrapol" when Nr=1
258    o verification:
259      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
260        to test pkg/cheapaml.
261    o pkg/aim_v23 & pkg/shap_filt:
262      - fix dissipation heating (erroneous gravity multiplication factor).
263    o pkg/seaice:
264      - remove unused field pressPre from jfnk solver
265      - rename two subroutines in seaice_preconditioner.F
266    o eesupp/src:
267       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
268    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
269       - remove wrong parts of the rhs and the lhs (were in there
270         because I did not understand the concept of this preconditioner)
271       - add an exchange between u- and v-sweep. This increases communication
272         by a factor of two but improves the convergence of jfnk. Ideally,
273         one would like the u- and v-sweep to be independent. So far within
274         undocumented ifdefs
275       - reorganize the extra computations for printing the residuals
276    o tools/genmake2:
277      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
278        since it's not necessary (and was preventing to use MNC in some cases).
279    
280    checkpoint64a (2012/11/16)
281    o pkg/autodiff:
282      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
283        autodiff_readparms.F no longer depends on calling order (within
284        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
285        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
286        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
287    o pkg/obcs:
288      - adding tidal velocity forcing capability to obcs
289        for usage example, see verification/seaice_obcs/input.tides
290    o pkg/seaice:
291      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
292        SEAICE_LSRrelaxU/V
293      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
294    o pkg/aim_v23:
295      - implement heating from friction (bottom friction and stratospheric drag).
296    o pkg/shap_filt:
297      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
298        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
299    o model/src:
300      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
301        time-constant addMass field from file (addMassFile);
302      - support for heating due to friction (and Kinetic Energy dissipation):
303        add option, run-time switch and 3-D field array + support code ; each pkg
304        or S/R can add heating contribution (if there is a sink of KE); the sum is
305        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
306    o pkg/seaice:
307      - complete merge of ITD code into seaice_growth.F
308        from MITgcm_contrib/torge/itd/code/
309        no verification so far, but Torge Martin tested
310        "1-D test case and Beaufort set up;
311        deliver okay results after 1 model year."
312      - complete merge of SEAICE_SIZE.h into all relevant routines
313      - move computation of eta at Z-points into calc_viscosities
314        + introduce global field etaZ
315        + add different methods for computing etaZ, for now the old
316          method (simple averages of eta to Z-points) is hardwired
317        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
318          seaice_preconditioner
319      - simplify computations for SEAICE_ZETA_SMOOTHREG
320      - seaice_preconditioner:
321        + replace one remaining press by pressLoc (mistake)
322        + adjust printing of residuals
323      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
324        + add (SEAICE.h) and rename some counters (initiliased in
325          seaice_init_fixed.F)
326        + add _BEGIN/END_MASTER (myThid)  around print statements
327        + print total number of iterations and failures over SEAICE_monFreq
328          interval to STDOUT
329      - move control over output-messages by fgmres to seaice_jfnk to save
330        some operations
331      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
332        in order to make restarts with sol .ne. zero (fgmres with restarts)
333        (seaice_jfnk.F, seaice_fgmres.F)
334      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
335        a serious convergence problem when open boundaries are involved
336    o pkg/ggl90: fix computation of control volumes for the case of
337      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
338      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
339    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
340    o pkg/autodiff
341      - Add inAdMode switch for SEAICEuseDYNAMICS:
342        SEAICEuseDYNAMICSinAdMode
343        (extend logic in ADAUTODIFF_INADMODE_SET)
344    o pkg/seaice
345      - Step 1 of merging ice-thickness distribution (ITD) code from
346        MITgcm_contrib/torge/itd/ (author: Torge Martin)
347        The code implements concept laid out in Thorndike et al. (1975);
348        code is enabled via CPP flag SEAICE_ITD
349        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
350        code is not complete yet!!
351      - SEAICE_SIZE.h now included in almost all seaice routines
352    o verification (using seaice):
353      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
354        global_ocean.cs32x15.seaice ; update results.
355      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
356      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
357        offline_exf_seaice (previously compiling B-grid).
358    o pkg/exf:
359      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
360        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
361        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
362    o pkg/layers (adjust changes from Sept 19):
363      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
364        this allows to remove "layers_maxNum" dimension from all layers arrays.
365    o pkg/layers (adjust changes from Sept 19):
366      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
367      - snap-shot extended to all type of layers (not just the 1rst type);
368      - remove layers variables when corresponding CPP option is undef.
369    o pkg/layers:
370      - rename pkg/layers variable and add new output (layer exist & un-weighted
371        velocity in layer)
372    o pkg/seaice:
373      - simplify (?) ocean-drag coefficent computations by using
374        the same routine in all three solvers (saves some code lines)
375      - remove global fields DRAGA and DRAGS from C-grid code and
376        declare them locally in lsr.F (the only place where they are
377        still used)
378      - update AD output of lab_sea.evp (very sensitive anyway).
379    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
380      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
381      and SEAICEuseJFNK=.true. A few things to note:
382      - involves a FGMRES, that is parallel but very inefficient,
383        because of many scalar products (global sums) in the Gram-Schmidt
384        orthogonalization method. Needs to be replaced. Original code
385        from J.-F. Lemieux
386      - preconditioner for FGMRES is a stripped down version of LSOR
387      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
388        preconditioner. For the preconditioner, the default is set to 10.
389      - Jacobian times vector is computed with finite differences
390      - marginally related to JFNK-solver: add a smooth regularization for
391        zeta with tanh that will improve convergence (Lemieux and Tremblay,
392        2009) for any implicit solver (not implemented for EVP because EVP
393        does not need this regularization in the first place). Define
394        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
395    o eesupp/src:
396      - check in genmake2 that intrinsic S/R flush is available.
397      - add S/R to flush IO unit (if intrinsic S/R flush is available)
398      - flush standard & error msg unit before MPI termination
399      - if debugMode, flush IO unit after printing msg
400    o pkg/ctrl:
401      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
402        to ctrl_set_unpack_xyz.
403    
404    checkpoint64 (2012/10/09)
405    o pkg/shelfice
406      - in mom_fluxform.F, mom_vecinv.F:
407        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
408        Bug fix KappaRU -> KappaRV
409        does not change verification/isomip but may change other setups
410        (presumably constant KappaRU=KappaRV)
411      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
412    o pkg/obcs:
413      - fixed some indexing bugs in obcs_seaice_sponge.F
414      - added obcs relaxation subroutines for HSALT and HSNOW
415      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
416    o pkg/seaice:
417      - add "multicategory" parameterization for snow in analogy to ice,
418        default is off for now.
419    o pkg/obcs:
420      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
421        see verification/seaice_obcs/input.seaiceSponge for example application.
422      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
423        index setting by master-thread. This fix multi-threads Pb in previous modifs.
424    o pkg/layers :
425      - add diagnostics to pkg/layers
426      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
427        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
428    o pkg/generic_advdiff/gad_implicit_r.F :
429      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
430    o pkg/seaice/seaice_growth.F:
431      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
432    o pkg/obcs:
433      - change default setting of OBCS_UVICE_OLD from defined to undef;
434      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
435        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
436      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
437      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
438        with Southern & Western OB at a tile edge (at least in a simple set-up).
439    o pkg/obcs:
440      - change settings of OB index in case OB coincides with tile edge (shared by
441        2 tiles), so that common OB location is registered by both tiles (instead of
442        only 1). However, for Southern and Western OB, index value = 0 is not
443        recognized as valid OB index (=default null value) and needs to be fixed.
444      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
445      - new parameter "OB_indexNone" for null index value (for now, still zero)
446        to replace hard-coded null index value of zero.
447    o pkg/exch2:
448      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
449        always check buffer-size (but outside the loop); move checking for valid
450        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
451        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
452    o pkg/ctrl (pack & unpack):
453      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
454        (locally defined) for different variables (+ remove the variable-specific
455        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
456        (to be extended to other local file names in ctrl.h).
457    o pkg/flt:
458      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
459    o pkg/mdsio:
460      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
461    o tools/genmake2:
462      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
463        (added by Alistair in version 1.51 for building without make depend);
464      - remove Header files list (H_SRC_FILES) from the dependence of targets
465         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
466        place in version 1.23): this save going through staf when unrelated header
467        file has been modified.
468       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
469        "make depend" step, still need to do "make links" before "make adtaf".
470    o eesupp/src (+ few pkg src files) & genmake2:
471      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
472      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
473      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
474         upper/lower case ; account for space between "#" and undef/define)
475    o pkg/flt (with exch2):
476      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
477      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
478    
479    checkpoint63s (2012/09/05)
480    o pkg/ecco:
481      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
482      - add more relevant #ifdef ALLOW_SMOOTH ones.
483      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
484    o pkg/ctrl:
485      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
486        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
487      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
488        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
489        ctrlSmoothCorrel3D (new).
490        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
491      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
492      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
493        controls when useAtmWind, and vice versa.
494      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
495      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
496          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
497      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
498          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
499      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
500        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
501    o pkg/smooth:
502      - remove un-necessary includes.
503      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
504        Those CPP options were never defined, and not necessary.
505    o model/src:
506      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
507      - standard treatment of useSMOOTH.
508    o pkg/autodiff:
509      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
510        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
511    o pkg/exch2:
512      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
513        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
514      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
515        and tiles to process mapping.
516      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
517        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
518        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
519        from w2_eeboot.F to w2_readparms.F.
520    o eesupp/src:
521      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
522        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
523        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
524      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
525        is defined (remove condition on usingMPI) to match cases where MPI_INIT
526        has been called.
527      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
528      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
529        (so that on 1 proc, get same myPid independently of usingMPI)
530      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
531        useCubedSphereExchange with EXCH-1 (safer).
532      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
533    o pkg/ggl90:
534      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
535        used in ALLOW_GGL90_SMOOTH code.
536    o pkg/flt:
537      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
538        floats at the Southern end of the domain).
539    o eesupp/inc:
540      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
541        but not used (and not to be used) anywhere, just for documentation.
542    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
543      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
544        a) can damage previously written records in any other multi-record files.
545        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
546  o tools/genmake2:  o tools/genmake2:
547    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
548    - update AD_CONFIG.h (if needed) before building any of the executable    - update AD_CONFIG.h (if needed) before building any of the executable
# Line 11  o tools/genmake2: Line 550  o tools/genmake2:
550      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
551    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
552      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
553    o pkg/cheapaml:
554      - updated to correspond to the code used in accepted paper (Nico Wienders).
555  o pkg/exf:  o pkg/exf:
556      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
557      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
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