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revision 1.1729 by jmc, Tue Sep 4 01:04:23 2012 UTC revision 1.1832 by mlosch, Mon Feb 25 10:45:15 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: fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
8    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
9      - new subroutines seaice_lsr_tridiagu/v
10      - introduce loop bounds i/jmin/max to be able to use a restricted
11        additive Schwarz method, but not used for now.
12      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
13      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
14    o OpenAD support
15      Reorganize S/R call for overall time-stepping loop to facilitate
16      OpenAD revolve loop replacement
17      (new S/R main_do_loop.F)
18    o model/src:
19      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
20      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
21        ADAMS_BASHFORTH2.
22    o pkg/cheapaml:
23      - add new parameter (default=F, same as before) to disable full domain
24        (including land) periodicity in X & Y dir.
25      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
26        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
27        into single S/R CHEAPAML_TIMESTEP.
28    
29    checkpoint64d (2013/02/17)
30    o pkg/monitor (angular momentum):
31      - do not add Eta contribution to the total AM if using rigid-lid;
32      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
33      - horizontal discretisation: compute Zonal wind contribution separately for
34        each component (instead of from cell centered averaged) and use the 4
35        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
36      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
37        FreeSurf) if using vectorInvariant momentum.
38    o model/src (horizontal grid):
39      - move initialisation of all horizontal grid arrays to null value
40        from specific horizontal grid S/R to main S/R INI_GRID;
41      - add 2 new arrays to project model C-grid velocity on to zonal direction
42        (similar to AngleCosC & -AngleSinC but at U and V point location) and
43        compute them in S/R CALC_GRID_ANGLES.
44    o pkg/seaice: replace a hard coded parameter by a runtime parameter
45        SEAICE_JFNK_tolIter
46    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
47        preconditioner for JFNK (run LSR into the overlaps as far as possible,
48        i.e OLx/y-2, but overwrite the solution in the overlaps)
49      - extend loop range in seaice_calc_viscosity
50      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
51      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
52      - slightly modify loops in tridiagonal solver lsr-preconditioner
53      - by default remove the extra exchange in seaice_preconditioner with a
54        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
55      - modify offline_exf_seaice so that old results without RAS are reproduced
56        for output.dyn_jfnk.txt
57      in seaice_fgmres.F (unrelated to RAS)
58      - add a cpp-flag option for a re-ordered mapping (potentially more
59        efficient), but because this changes the results, turn it off by
60        default
61      - replace the save statement by local common blocks
62    o utils/matlab:
63      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
64      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
65        instead of local script "load_cs.m".
66    o pkg/seaice:
67      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
68        to the scalarProductMetric and the unrolling. By chance this does not
69        change the verification experiment, because of the particular domain
70        decomposition
71    o pkg/diagnostics:
72      - change default missing_value from UNSET_RL to -999.
73    o pkg/layers: improve vectorization of layers_fluxcalc.F
74      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
75        time spent in this routine by more than a factor of 3 on an NEC-SX8
76      - step 2: replace search algorithm by a bisection algorithm found in
77        Press et al. Numerical Recipes in Fortran. This algorithm can be
78        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
79        For now, use this algorithm only for TARGET_NEC_SX defined.
80      - moved the search algorithm into a separate subroutine, that is kept
81        within the same file for automatic inlining.
82      - modified catching potential errors
83    o pkg/ecco:
84      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
85    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
86      - modifications for ALLOW_GENTIM2D_CONTROL
87      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
88      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
89      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
90      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
91    o model/src:
92      - account for moist thermodynamics in (dry) potential temperature equation;
93        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
94        and cpl_aim+ocn.
95      - also switch to standard compiler (gfortran, was using ifort previously)
96        for fizhi-cs experiments reference output.
97    o pkg/ctrl:
98      - 1st step toward generic time-varying control variable (2D) via CPP option
99        ALLOW_GENTIM2D_CONTROL
100      - note new namelist ctrl_nml_genarr in data.ctrl
101    o verification/global_ocean.cs32x15:
102      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
103        thsice calling sequence and update "output.icedyn.txt" output file.
104    o pkg/ptracers:
105      - from Ryan A.: code to allow to restart a tracer at regular time interval
106        specifying a reset frequency and a reset-phase (for each tracers).
107    o pkg/thsice:
108      - implement new sequence of calls for thsice+seaice:
109          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
110          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
111      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
112        in CPP_OPTIONS.h) to recover old sequence;
113      - update diagnostics for Intermediate State thsice diagnostics: now filled
114        just before advection (instead of just after advection in old sequence);
115      - update output of experiment offline_exf_seaice (standard test);
116      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
117        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
118    o pkg/aim_v23:
119      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
120      - use standard pkg/mdsio routines to read & write CO2 pickup file;
121      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
122      - Implement new sequence of calls for seaice advection (with thsice and
123        seaice diffusion): do ice advection after ice-Thermodynamic (previously
124        was done before); change aim_do_physics.F (split the bi,bj loops block);
125      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
126    o pkg/thsice:
127      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
128        where just seaice diffusion is used without seaice-dynamics.
129    
130    checkpoint64c (2013/01/18)
131    o pkg/seaice:
132      - add a parameter JFNKres_tFac that can replace JFNKres_t
133        (= JFNKres_tFac*JFNKresidual before JFNK solver)
134      - add a line search option to the JFNK solver
135      - move update of u/vIce and computation of initial residual into a separate
136        routine (same file); makes the code a little easier to read (?)
137      - the line search requires computation of the residual and for some reason
138        I cannot do the update of u/vIce at the beginning of the Newton loop
139        without changing the results, so we move computation of the new residual
140        also to the end of the Newton loop, even without the line search
141    o pkg/mdsio:
142      - write missing value (corresponding to undefined array value) to meta files;
143        skip this if missing value is one (UNSET_RL would be a better value for the
144        case of undefined missing value but it's current the default missing-value);
145        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
146    o pkg/exf & thsice:
147      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
148        diagnostics) even when SHORTWAVE_HEATING is #undef;
149    o verification/cfc_example:
150      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
151        illustrate how to use it).
152    o verification/offline_exf_seaice:
153      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
154        files to only one time-record.
155      in input.thermo: narrow the 2 bands of low initial ice-concentration near
156        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
157        snapshot output; same mcPheePiston value as in thsice with
158        surf-current=0.2m/s.
159      in input.thsice: similar set-up as in input.thermo (channel with same seaice
160        initial conditions).
161    o verification/cfc_example:
162      - update file "data" with more standard choice (default rotationPeriod,
163        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
164        set deltaTFreeSurf to deltaTtracer) and update the output.
165    o pkg/layers:
166      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
167      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
168    o verification/offline_exf_seaice:
169      - set all {field}period to zero for constant-in-time forcing (not tested
170        anywhere else).
171    o verification/offline_exf_seaice:
172      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
173      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
174    o model/src:
175      - implement Finite-Volume method for (hydrostatic) presure gradient
176        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
177    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
178      - In order to be compatible with the default EVP code, this requires changing
179        the EVP code around a little; and because any small change immediately
180        breaks the lab_sea.hb87 verification experiment, the reference output is
181        updated two times (each time the remaining aggrement was only 2 digits):
182        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
183        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
184        The adjoint test lab_sea.evp also needed to be updated.
185      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
186        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
187        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
188        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
189        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
190        kept obscure, because I need to test it a little more.
191    o pkg/cheapaml:
192      - fix few incorrect type (_RL/_RS) in subroutine calls.
193    o pkg/seaice:
194      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
195        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
196    o model/src:
197      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
198        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
199        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
200    o pkg/cheapaml:
201      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
202        update output of experiment cheapAML_box.
203      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
204        and set them only in one place (cheapaml_readparms.F).
205      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
206      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
207        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
208    o model/src/the_main_loop.F:
209      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
210    o pkg/seaice:
211      - remove legacy branch code.
212      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
213    o verification/*/code*/SEAICE_OPTIONS.h:
214      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
215        SEAICE_CAP_HEFF).
216    o pkg/cheapaml:
217      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
218        to load new forcing fields.
219      - add missing "_d 0" where it's needed; + some editing (improve indentation).
220      - remove switch to "-r8" compiler option (no longer needed) in verification
221        cheapAML_box, keep same output (small trucation error differences).
222    o verification/offline_exf_seaice:
223      - add thermodynamics only test.
224    o verification/cheapAML_box:
225      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
226        keep same output (same 14 digits for cg2d).
227      - switch on "-r8" compiler option (some numerical values are missing
228        the "_d 0") and update output (only 6 digits for cg2d were preserved).
229    
230    checkpoint64b (2012/12/24)
231    o pkg/cheapaml:
232      - remove un-used variables (Qnet,EmPmR) from pickup files.
233      - store tendency of advected variables into cheapaml pickup file
234        and fix the AB-2 restart.
235    o verification/offline_exf_seaice and lab_sea adjoint:
236      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
237      - switch to 4 time steps in offline, consistent with lab_sea.
238      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
239      - update results after change of experiment seaice.
240    o pkg/seaice:
241      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
242        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
243        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
244        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
245    o model/src:
246      - add run-time parameter to select CG2D solver minimum-residual solution
247        (in case of a poor convergence).
248    o pkg/seaice/seaice_lsr.F
249      - move calculation of matrix coefficients into new
250        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
251        file; the main purpose of this change is to be able to reuse the code
252        in S/R SEAICE_PRECONDITIONER
253      - modify the computation of the residual so that the mass of sea-ice
254        is not used twice; this simplifies the calculations, but since
255        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
256        not tested in testreport---this does not affect the testreport results.
257    o verification/seaice_obcs:
258      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
259        verification/lab_sea/input.salt_plume; changes results/output.txt*
260    o model/src:
261      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
262    o pkg/seaice:
263      - improve description of parameters in seaice_fgmres.F and start
264        cleaning up the code
265      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
266        second argument
267      - add a metric based on grid cell area to SEAICE_SCALPROD; update
268        results of offline_exf_seaice.dyn_jfnk
269      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
270    o pkg/aim_v23:
271      - fix an other bug in dissipation heating (grid-cell area was missing).
272    o model/src + pkg/seaice:
273      - add global (multi-tile) linear solver for pair of tri-diagonal system
274        along X and Y lines, respectively for U and V component.
275        Note: 1) MPI and cube-exchange not yet coded.
276            2) probably not accurate for poorly conditioned / large size problem.
277      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
278        default: not compiled and not used.
279    o pkg/seaice:
280      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
281        introduce bi/bj loops and use global_sum_tile_rl instead of
282        mpi_allreduce in seaice_fgmres.F
283      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
284      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
285      - add a verification experiment for JFNK in offline_exf_seaice
286    o verification:
287      - change (for now, only fwd test) offline_exf_seaice experiment:
288        use a re-entrant channel with idealized coastline (trapezoidal shape)
289        at southern boundary to explore seaice dynamics and thermodynamics
290        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
291        secondary test (input.thsice) use thermodynamics only with SST relaxation.
292      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
293    o pkg/exf:
294      - disable "sstExtrapol" when Nr=1
295    o verification:
296      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
297        to test pkg/cheapaml.
298    o pkg/aim_v23 & pkg/shap_filt:
299      - fix dissipation heating (erroneous gravity multiplication factor).
300    o pkg/seaice:
301      - remove unused field pressPre from jfnk solver
302      - rename two subroutines in seaice_preconditioner.F
303    o eesupp/src:
304       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
305    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
306       - remove wrong parts of the rhs and the lhs (were in there
307         because I did not understand the concept of this preconditioner)
308       - add an exchange between u- and v-sweep. This increases communication
309         by a factor of two but improves the convergence of jfnk. Ideally,
310         one would like the u- and v-sweep to be independent. So far within
311         undocumented ifdefs
312       - reorganize the extra computations for printing the residuals
313    o tools/genmake2:
314      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
315        since it's not necessary (and was preventing to use MNC in some cases).
316    
317    checkpoint64a (2012/11/16)
318    o pkg/autodiff:
319      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
320        autodiff_readparms.F no longer depends on calling order (within
321        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
322        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
323        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
324    o pkg/obcs:
325      - adding tidal velocity forcing capability to obcs
326        for usage example, see verification/seaice_obcs/input.tides
327    o pkg/seaice:
328      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
329        SEAICE_LSRrelaxU/V
330      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
331    o pkg/aim_v23:
332      - implement heating from friction (bottom friction and stratospheric drag).
333    o pkg/shap_filt:
334      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
335        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
336    o model/src:
337      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
338        time-constant addMass field from file (addMassFile);
339      - support for heating due to friction (and Kinetic Energy dissipation):
340        add option, run-time switch and 3-D field array + support code ; each pkg
341        or S/R can add heating contribution (if there is a sink of KE); the sum is
342        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
343    o pkg/seaice:
344      - complete merge of ITD code into seaice_growth.F
345        from MITgcm_contrib/torge/itd/code/
346        no verification so far, but Torge Martin tested
347        "1-D test case and Beaufort set up;
348        deliver okay results after 1 model year."
349      - complete merge of SEAICE_SIZE.h into all relevant routines
350      - move computation of eta at Z-points into calc_viscosities
351        + introduce global field etaZ
352        + add different methods for computing etaZ, for now the old
353          method (simple averages of eta to Z-points) is hardwired
354        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
355          seaice_preconditioner
356      - simplify computations for SEAICE_ZETA_SMOOTHREG
357      - seaice_preconditioner:
358        + replace one remaining press by pressLoc (mistake)
359        + adjust printing of residuals
360      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
361        + add (SEAICE.h) and rename some counters (initiliased in
362          seaice_init_fixed.F)
363        + add _BEGIN/END_MASTER (myThid)  around print statements
364        + print total number of iterations and failures over SEAICE_monFreq
365          interval to STDOUT
366      - move control over output-messages by fgmres to seaice_jfnk to save
367        some operations
368      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
369        in order to make restarts with sol .ne. zero (fgmres with restarts)
370        (seaice_jfnk.F, seaice_fgmres.F)
371      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
372        a serious convergence problem when open boundaries are involved
373    o pkg/ggl90: fix computation of control volumes for the case of
374      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
375      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
376    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
377    o pkg/autodiff
378      - Add inAdMode switch for SEAICEuseDYNAMICS:
379        SEAICEuseDYNAMICSinAdMode
380        (extend logic in ADAUTODIFF_INADMODE_SET)
381    o pkg/seaice
382      - Step 1 of merging ice-thickness distribution (ITD) code from
383        MITgcm_contrib/torge/itd/ (author: Torge Martin)
384        The code implements concept laid out in Thorndike et al. (1975);
385        code is enabled via CPP flag SEAICE_ITD
386        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
387        code is not complete yet!!
388      - SEAICE_SIZE.h now included in almost all seaice routines
389    o verification (using seaice):
390      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
391        global_ocean.cs32x15.seaice ; update results.
392      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
393      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
394        offline_exf_seaice (previously compiling B-grid).
395    o pkg/exf:
396      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
397        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
398        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
399    o pkg/layers (adjust changes from Sept 19):
400      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
401        this allows to remove "layers_maxNum" dimension from all layers arrays.
402    o pkg/layers (adjust changes from Sept 19):
403      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
404      - snap-shot extended to all type of layers (not just the 1rst type);
405      - remove layers variables when corresponding CPP option is undef.
406    o pkg/layers:
407      - rename pkg/layers variable and add new output (layer exist & un-weighted
408        velocity in layer)
409    o pkg/seaice:
410      - simplify (?) ocean-drag coefficent computations by using
411        the same routine in all three solvers (saves some code lines)
412      - remove global fields DRAGA and DRAGS from C-grid code and
413        declare them locally in lsr.F (the only place where they are
414        still used)
415      - update AD output of lab_sea.evp (very sensitive anyway).
416    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
417      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
418      and SEAICEuseJFNK=.true. A few things to note:
419      - involves a FGMRES, that is parallel but very inefficient,
420        because of many scalar products (global sums) in the Gram-Schmidt
421        orthogonalization method. Needs to be replaced. Original code
422        from J.-F. Lemieux
423      - preconditioner for FGMRES is a stripped down version of LSOR
424      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
425        preconditioner. For the preconditioner, the default is set to 10.
426      - Jacobian times vector is computed with finite differences
427      - marginally related to JFNK-solver: add a smooth regularization for
428        zeta with tanh that will improve convergence (Lemieux and Tremblay,
429        2009) for any implicit solver (not implemented for EVP because EVP
430        does not need this regularization in the first place). Define
431        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
432    o eesupp/src:
433      - check in genmake2 that intrinsic S/R flush is available.
434      - add S/R to flush IO unit (if intrinsic S/R flush is available)
435      - flush standard & error msg unit before MPI termination
436      - if debugMode, flush IO unit after printing msg
437    o pkg/ctrl:
438      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
439        to ctrl_set_unpack_xyz.
440    
441    checkpoint64 (2012/10/09)
442    o pkg/shelfice
443      - in mom_fluxform.F, mom_vecinv.F:
444        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
445        Bug fix KappaRU -> KappaRV
446        does not change verification/isomip but may change other setups
447        (presumably constant KappaRU=KappaRV)
448      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
449    o pkg/obcs:
450      - fixed some indexing bugs in obcs_seaice_sponge.F
451      - added obcs relaxation subroutines for HSALT and HSNOW
452      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
453    o pkg/seaice:
454      - add "multicategory" parameterization for snow in analogy to ice,
455        default is off for now.
456    o pkg/obcs:
457      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
458        see verification/seaice_obcs/input.seaiceSponge for example application.
459      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
460        index setting by master-thread. This fix multi-threads Pb in previous modifs.
461    o pkg/layers :
462      - add diagnostics to pkg/layers
463      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
464        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
465    o pkg/generic_advdiff/gad_implicit_r.F :
466      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
467    o pkg/seaice/seaice_growth.F:
468      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
469    o pkg/obcs:
470      - change default setting of OBCS_UVICE_OLD from defined to undef;
471      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
472        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
473      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
474      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
475        with Southern & Western OB at a tile edge (at least in a simple set-up).
476    o pkg/obcs:
477      - change settings of OB index in case OB coincides with tile edge (shared by
478        2 tiles), so that common OB location is registered by both tiles (instead of
479        only 1). However, for Southern and Western OB, index value = 0 is not
480        recognized as valid OB index (=default null value) and needs to be fixed.
481      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
482      - new parameter "OB_indexNone" for null index value (for now, still zero)
483        to replace hard-coded null index value of zero.
484    o pkg/exch2:
485      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
486        always check buffer-size (but outside the loop); move checking for valid
487        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
488        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
489    o pkg/ctrl (pack & unpack):
490      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
491        (locally defined) for different variables (+ remove the variable-specific
492        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
493        (to be extended to other local file names in ctrl.h).
494    o pkg/flt:
495      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
496    o pkg/mdsio:
497      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
498    o tools/genmake2:
499      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
500        (added by Alistair in version 1.51 for building without make depend);
501      - remove Header files list (H_SRC_FILES) from the dependence of targets
502         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
503        place in version 1.23): this save going through staf when unrelated header
504        file has been modified.
505       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
506        "make depend" step, still need to do "make links" before "make adtaf".
507    o eesupp/src (+ few pkg src files) & genmake2:
508      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
509      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
510      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
511         upper/lower case ; account for space between "#" and undef/define)
512    o pkg/flt (with exch2):
513      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
514      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
515    
516    checkpoint63s (2012/09/05)
517    o pkg/ecco:
518      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
519      - add more relevant #ifdef ALLOW_SMOOTH ones.
520      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
521    o pkg/ctrl:
522      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
523        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
524      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
525        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
526        ctrlSmoothCorrel3D (new).
527        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
528      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
529      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
530        controls when useAtmWind, and vice versa.
531      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
532      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
533          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
534      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
535          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
536      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
537        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
538    o pkg/smooth:
539      - remove un-necessary includes.
540      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
541        Those CPP options were never defined, and not necessary.
542    o model/src:
543      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
544      - standard treatment of useSMOOTH.
545    o pkg/autodiff:
546      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
547        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
548  o pkg/exch2:  o pkg/exch2:
549    - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)    - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
550      + to remove ALWAYS_USE_MPI in source code that TAF does not see.      + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
551    - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag    - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
552      and tiles to process mapping.      and tiles to process mapping.
553    - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)    - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
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