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revision 1.1716 by jmc, Wed Aug 15 14:44:48 2012 UTC revision 1.1829 by jmc, Tue Feb 19 14:12:42 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 model/src:
8      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
9      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
10        ADAMS_BASHFORTH2.
11    o pkg/cheapaml:
12      - add new parameter (default=F, same as before) to disable full domain
13        (including land) periodicity in X & Y dir.
14      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
15        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
16        into single S/R CHEAPAML_TIMESTEP.
17    
18    checkpoint64d (2013/02/17)
19    o pkg/monitor (angular momentum):
20      - do not add Eta contribution to the total AM if using rigid-lid;
21      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
22      - horizontal discretisation: compute Zonal wind contribution separately for
23        each component (instead of from cell centered averaged) and use the 4
24        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
25      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
26        FreeSurf) if using vectorInvariant momentum.
27    o model/src (horizontal grid):
28      - move initialisation of all horizontal grid arrays to null value
29        from specific horizontal grid S/R to main S/R INI_GRID;
30      - add 2 new arrays to project model C-grid velocity on to zonal direction
31        (similar to AngleCosC & -AngleSinC but at U and V point location) and
32        compute them in S/R CALC_GRID_ANGLES.
33    o pkg/seaice: replace a hard coded parameter by a runtime parameter
34        SEAICE_JFNK_tolIter
35    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
36        preconditioner for JFNK (run LSR into the overlaps as far as possible,
37        i.e OLx/y-2, but overwrite the solution in the overlaps)
38      - extend loop range in seaice_calc_viscosity
39      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
40      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
41      - slightly modify loops in tridiagonal solver lsr-preconditioner
42      - by default remove the extra exchange in seaice_preconditioner with a
43        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
44      - modify offline_exf_seaice so that old results without RAS are reproduced
45        for output.dyn_jfnk.txt
46      in seaice_fgmres.F (unrelated to RAS)
47      - add a cpp-flag option for a re-ordered mapping (potentially more
48        efficient), but because this changes the results, turn it off by
49        default
50      - replace the save statement by local common blocks
51    o utils/matlab:
52      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
53      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
54        instead of local script "load_cs.m".
55    o pkg/seaice:
56      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
57        to the scalarProductMetric and the unrolling. By chance this does not
58        change the verification experiment, because of the particular domain
59        decomposition
60    o pkg/diagnostics:
61      - change default missing_value from UNSET_RL to -999.
62    o pkg/layers: improve vectorization of layers_fluxcalc.F
63      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
64        time spent in this routine by more than a factor of 3 on an NEC-SX8
65      - step 2: replace search algorithm by a bisection algorithm found in
66        Press et al. Numerical Recipes in Fortran. This algorithm can be
67        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
68        For now, use this algorithm only for TARGET_NEC_SX defined.
69      - moved the search algorithm into a separate subroutine, that is kept
70        within the same file for automatic inlining.
71      - modified catching potential errors
72    o pkg/ecco:
73      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
74    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
75      - modifications for ALLOW_GENTIM2D_CONTROL
76      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
77      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
78      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
79      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
80    o model/src:
81      - account for moist thermodynamics in (dry) potential temperature equation;
82        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
83        and cpl_aim+ocn.
84      - also switch to standard compiler (gfortran, was using ifort previously)
85        for fizhi-cs experiments reference output.
86    o pkg/ctrl:
87      - 1st step toward generic time-varying control variable (2D) via CPP option
88        ALLOW_GENTIM2D_CONTROL
89      - note new namelist ctrl_nml_genarr in data.ctrl
90    o verification/global_ocean.cs32x15:
91      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
92        thsice calling sequence and update "output.icedyn.txt" output file.
93    o pkg/ptracers:
94      - from Ryan A.: code to allow to restart a tracer at regular time interval
95        specifying a reset frequency and a reset-phase (for each tracers).
96    o pkg/thsice:
97      - implement new sequence of calls for thsice+seaice:
98          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
99          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
100      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
101        in CPP_OPTIONS.h) to recover old sequence;
102      - update diagnostics for Intermediate State thsice diagnostics: now filled
103        just before advection (instead of just after advection in old sequence);
104      - update output of experiment offline_exf_seaice (standard test);
105      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
106        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
107    o pkg/aim_v23:
108      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
109      - use standard pkg/mdsio routines to read & write CO2 pickup file;
110      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
111      - Implement new sequence of calls for seaice advection (with thsice and
112        seaice diffusion): do ice advection after ice-Thermodynamic (previously
113        was done before); change aim_do_physics.F (split the bi,bj loops block);
114      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
115    o pkg/thsice:
116      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
117        where just seaice diffusion is used without seaice-dynamics.
118    
119    checkpoint64c (2013/01/18)
120    o pkg/seaice:
121      - add a parameter JFNKres_tFac that can replace JFNKres_t
122        (= JFNKres_tFac*JFNKresidual before JFNK solver)
123      - add a line search option to the JFNK solver
124      - move update of u/vIce and computation of initial residual into a separate
125        routine (same file); makes the code a little easier to read (?)
126      - the line search requires computation of the residual and for some reason
127        I cannot do the update of u/vIce at the beginning of the Newton loop
128        without changing the results, so we move computation of the new residual
129        also to the end of the Newton loop, even without the line search
130    o pkg/mdsio:
131      - write missing value (corresponding to undefined array value) to meta files;
132        skip this if missing value is one (UNSET_RL would be a better value for the
133        case of undefined missing value but it's current the default missing-value);
134        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
135    o pkg/exf & thsice:
136      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
137        diagnostics) even when SHORTWAVE_HEATING is #undef;
138    o verification/cfc_example:
139      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
140        illustrate how to use it).
141    o verification/offline_exf_seaice:
142      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
143        files to only one time-record.
144      in input.thermo: narrow the 2 bands of low initial ice-concentration near
145        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
146        snapshot output; same mcPheePiston value as in thsice with
147        surf-current=0.2m/s.
148      in input.thsice: similar set-up as in input.thermo (channel with same seaice
149        initial conditions).
150    o verification/cfc_example:
151      - update file "data" with more standard choice (default rotationPeriod,
152        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
153        set deltaTFreeSurf to deltaTtracer) and update the output.
154    o pkg/layers:
155      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
156      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
157    o verification/offline_exf_seaice:
158      - set all {field}period to zero for constant-in-time forcing (not tested
159        anywhere else).
160    o verification/offline_exf_seaice:
161      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
162      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
163    o model/src:
164      - implement Finite-Volume method for (hydrostatic) presure gradient
165        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
166    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
167      - In order to be compatible with the default EVP code, this requires changing
168        the EVP code around a little; and because any small change immediately
169        breaks the lab_sea.hb87 verification experiment, the reference output is
170        updated two times (each time the remaining aggrement was only 2 digits):
171        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
172        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
173        The adjoint test lab_sea.evp also needed to be updated.
174      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
175        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
176        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
177        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
178        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
179        kept obscure, because I need to test it a little more.
180    o pkg/cheapaml:
181      - fix few incorrect type (_RL/_RS) in subroutine calls.
182    o pkg/seaice:
183      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
184        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
185    o model/src:
186      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
187        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
188        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
189    o pkg/cheapaml:
190      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
191        update output of experiment cheapAML_box.
192      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
193        and set them only in one place (cheapaml_readparms.F).
194      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
195      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
196        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
197    o model/src/the_main_loop.F:
198      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
199    o pkg/seaice:
200      - remove legacy branch code.
201      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
202    o verification/*/code*/SEAICE_OPTIONS.h:
203      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
204        SEAICE_CAP_HEFF).
205    o pkg/cheapaml:
206      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
207        to load new forcing fields.
208      - add missing "_d 0" where it's needed; + some editing (improve indentation).
209      - remove switch to "-r8" compiler option (no longer needed) in verification
210        cheapAML_box, keep same output (small trucation error differences).
211    o verification/offline_exf_seaice:
212      - add thermodynamics only test.
213    o verification/cheapAML_box:
214      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
215        keep same output (same 14 digits for cg2d).
216      - switch on "-r8" compiler option (some numerical values are missing
217        the "_d 0") and update output (only 6 digits for cg2d were preserved).
218    
219    checkpoint64b (2012/12/24)
220    o pkg/cheapaml:
221      - remove un-used variables (Qnet,EmPmR) from pickup files.
222      - store tendency of advected variables into cheapaml pickup file
223        and fix the AB-2 restart.
224    o verification/offline_exf_seaice and lab_sea adjoint:
225      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
226      - switch to 4 time steps in offline, consistent with lab_sea.
227      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
228      - update results after change of experiment seaice.
229    o pkg/seaice:
230      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
231        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
232        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
233        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
234    o model/src:
235      - add run-time parameter to select CG2D solver minimum-residual solution
236        (in case of a poor convergence).
237    o pkg/seaice/seaice_lsr.F
238      - move calculation of matrix coefficients into new
239        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
240        file; the main purpose of this change is to be able to reuse the code
241        in S/R SEAICE_PRECONDITIONER
242      - modify the computation of the residual so that the mass of sea-ice
243        is not used twice; this simplifies the calculations, but since
244        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
245        not tested in testreport---this does not affect the testreport results.
246    o verification/seaice_obcs:
247      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
248        verification/lab_sea/input.salt_plume; changes results/output.txt*
249    o model/src:
250      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
251    o pkg/seaice:
252      - improve description of parameters in seaice_fgmres.F and start
253        cleaning up the code
254      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
255        second argument
256      - add a metric based on grid cell area to SEAICE_SCALPROD; update
257        results of offline_exf_seaice.dyn_jfnk
258      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
259    o pkg/aim_v23:
260      - fix an other bug in dissipation heating (grid-cell area was missing).
261    o model/src + pkg/seaice:
262      - add global (multi-tile) linear solver for pair of tri-diagonal system
263        along X and Y lines, respectively for U and V component.
264        Note: 1) MPI and cube-exchange not yet coded.
265            2) probably not accurate for poorly conditioned / large size problem.
266      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
267        default: not compiled and not used.
268    o pkg/seaice:
269      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
270        introduce bi/bj loops and use global_sum_tile_rl instead of
271        mpi_allreduce in seaice_fgmres.F
272      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
273      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
274      - add a verification experiment for JFNK in offline_exf_seaice
275    o verification:
276      - change (for now, only fwd test) offline_exf_seaice experiment:
277        use a re-entrant channel with idealized coastline (trapezoidal shape)
278        at southern boundary to explore seaice dynamics and thermodynamics
279        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
280        secondary test (input.thsice) use thermodynamics only with SST relaxation.
281      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
282    o pkg/exf:
283      - disable "sstExtrapol" when Nr=1
284    o verification:
285      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
286        to test pkg/cheapaml.
287    o pkg/aim_v23 & pkg/shap_filt:
288      - fix dissipation heating (erroneous gravity multiplication factor).
289    o pkg/seaice:
290      - remove unused field pressPre from jfnk solver
291      - rename two subroutines in seaice_preconditioner.F
292    o eesupp/src:
293       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
294    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
295       - remove wrong parts of the rhs and the lhs (were in there
296         because I did not understand the concept of this preconditioner)
297       - add an exchange between u- and v-sweep. This increases communication
298         by a factor of two but improves the convergence of jfnk. Ideally,
299         one would like the u- and v-sweep to be independent. So far within
300         undocumented ifdefs
301       - reorganize the extra computations for printing the residuals
302    o tools/genmake2:
303      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
304        since it's not necessary (and was preventing to use MNC in some cases).
305    
306    checkpoint64a (2012/11/16)
307    o pkg/autodiff:
308      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
309        autodiff_readparms.F no longer depends on calling order (within
310        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
311        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
312        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
313    o pkg/obcs:
314      - adding tidal velocity forcing capability to obcs
315        for usage example, see verification/seaice_obcs/input.tides
316    o pkg/seaice:
317      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
318        SEAICE_LSRrelaxU/V
319      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
320    o pkg/aim_v23:
321      - implement heating from friction (bottom friction and stratospheric drag).
322    o pkg/shap_filt:
323      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
324        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
325    o model/src:
326      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
327        time-constant addMass field from file (addMassFile);
328      - support for heating due to friction (and Kinetic Energy dissipation):
329        add option, run-time switch and 3-D field array + support code ; each pkg
330        or S/R can add heating contribution (if there is a sink of KE); the sum is
331        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
332    o pkg/seaice:
333      - complete merge of ITD code into seaice_growth.F
334        from MITgcm_contrib/torge/itd/code/
335        no verification so far, but Torge Martin tested
336        "1-D test case and Beaufort set up;
337        deliver okay results after 1 model year."
338      - complete merge of SEAICE_SIZE.h into all relevant routines
339      - move computation of eta at Z-points into calc_viscosities
340        + introduce global field etaZ
341        + add different methods for computing etaZ, for now the old
342          method (simple averages of eta to Z-points) is hardwired
343        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
344          seaice_preconditioner
345      - simplify computations for SEAICE_ZETA_SMOOTHREG
346      - seaice_preconditioner:
347        + replace one remaining press by pressLoc (mistake)
348        + adjust printing of residuals
349      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
350        + add (SEAICE.h) and rename some counters (initiliased in
351          seaice_init_fixed.F)
352        + add _BEGIN/END_MASTER (myThid)  around print statements
353        + print total number of iterations and failures over SEAICE_monFreq
354          interval to STDOUT
355      - move control over output-messages by fgmres to seaice_jfnk to save
356        some operations
357      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
358        in order to make restarts with sol .ne. zero (fgmres with restarts)
359        (seaice_jfnk.F, seaice_fgmres.F)
360      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
361        a serious convergence problem when open boundaries are involved
362    o pkg/ggl90: fix computation of control volumes for the case of
363      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
364      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
365    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
366    o pkg/autodiff
367      - Add inAdMode switch for SEAICEuseDYNAMICS:
368        SEAICEuseDYNAMICSinAdMode
369        (extend logic in ADAUTODIFF_INADMODE_SET)
370    o pkg/seaice
371      - Step 1 of merging ice-thickness distribution (ITD) code from
372        MITgcm_contrib/torge/itd/ (author: Torge Martin)
373        The code implements concept laid out in Thorndike et al. (1975);
374        code is enabled via CPP flag SEAICE_ITD
375        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
376        code is not complete yet!!
377      - SEAICE_SIZE.h now included in almost all seaice routines
378    o verification (using seaice):
379      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
380        global_ocean.cs32x15.seaice ; update results.
381      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
382      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
383        offline_exf_seaice (previously compiling B-grid).
384    o pkg/exf:
385      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
386        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
387        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
388    o pkg/layers (adjust changes from Sept 19):
389      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
390        this allows to remove "layers_maxNum" dimension from all layers arrays.
391    o pkg/layers (adjust changes from Sept 19):
392      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
393      - snap-shot extended to all type of layers (not just the 1rst type);
394      - remove layers variables when corresponding CPP option is undef.
395    o pkg/layers:
396      - rename pkg/layers variable and add new output (layer exist & un-weighted
397        velocity in layer)
398    o pkg/seaice:
399      - simplify (?) ocean-drag coefficent computations by using
400        the same routine in all three solvers (saves some code lines)
401      - remove global fields DRAGA and DRAGS from C-grid code and
402        declare them locally in lsr.F (the only place where they are
403        still used)
404      - update AD output of lab_sea.evp (very sensitive anyway).
405    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
406      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
407      and SEAICEuseJFNK=.true. A few things to note:
408      - involves a FGMRES, that is parallel but very inefficient,
409        because of many scalar products (global sums) in the Gram-Schmidt
410        orthogonalization method. Needs to be replaced. Original code
411        from J.-F. Lemieux
412      - preconditioner for FGMRES is a stripped down version of LSOR
413      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
414        preconditioner. For the preconditioner, the default is set to 10.
415      - Jacobian times vector is computed with finite differences
416      - marginally related to JFNK-solver: add a smooth regularization for
417        zeta with tanh that will improve convergence (Lemieux and Tremblay,
418        2009) for any implicit solver (not implemented for EVP because EVP
419        does not need this regularization in the first place). Define
420        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
421    o eesupp/src:
422      - check in genmake2 that intrinsic S/R flush is available.
423      - add S/R to flush IO unit (if intrinsic S/R flush is available)
424      - flush standard & error msg unit before MPI termination
425      - if debugMode, flush IO unit after printing msg
426    o pkg/ctrl:
427      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
428        to ctrl_set_unpack_xyz.
429    
430    checkpoint64 (2012/10/09)
431    o pkg/shelfice
432      - in mom_fluxform.F, mom_vecinv.F:
433        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
434        Bug fix KappaRU -> KappaRV
435        does not change verification/isomip but may change other setups
436        (presumably constant KappaRU=KappaRV)
437      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
438    o pkg/obcs:
439      - fixed some indexing bugs in obcs_seaice_sponge.F
440      - added obcs relaxation subroutines for HSALT and HSNOW
441      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
442    o pkg/seaice:
443      - add "multicategory" parameterization for snow in analogy to ice,
444        default is off for now.
445    o pkg/obcs:
446      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
447        see verification/seaice_obcs/input.seaiceSponge for example application.
448      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
449        index setting by master-thread. This fix multi-threads Pb in previous modifs.
450    o pkg/layers :
451      - add diagnostics to pkg/layers
452      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
453        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
454    o pkg/generic_advdiff/gad_implicit_r.F :
455      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
456    o pkg/seaice/seaice_growth.F:
457      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
458    o pkg/obcs:
459      - change default setting of OBCS_UVICE_OLD from defined to undef;
460      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
461        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
462      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
463      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
464        with Southern & Western OB at a tile edge (at least in a simple set-up).
465    o pkg/obcs:
466      - change settings of OB index in case OB coincides with tile edge (shared by
467        2 tiles), so that common OB location is registered by both tiles (instead of
468        only 1). However, for Southern and Western OB, index value = 0 is not
469        recognized as valid OB index (=default null value) and needs to be fixed.
470      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
471      - new parameter "OB_indexNone" for null index value (for now, still zero)
472        to replace hard-coded null index value of zero.
473    o pkg/exch2:
474      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
475        always check buffer-size (but outside the loop); move checking for valid
476        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
477        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
478    o pkg/ctrl (pack & unpack):
479      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
480        (locally defined) for different variables (+ remove the variable-specific
481        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
482        (to be extended to other local file names in ctrl.h).
483    o pkg/flt:
484      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
485    o pkg/mdsio:
486      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
487    o tools/genmake2:
488      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
489        (added by Alistair in version 1.51 for building without make depend);
490      - remove Header files list (H_SRC_FILES) from the dependence of targets
491         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
492        place in version 1.23): this save going through staf when unrelated header
493        file has been modified.
494       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
495        "make depend" step, still need to do "make links" before "make adtaf".
496    o eesupp/src (+ few pkg src files) & genmake2:
497      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
498      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
499      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
500         upper/lower case ; account for space between "#" and undef/define)
501    o pkg/flt (with exch2):
502      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
503      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
504    
505    checkpoint63s (2012/09/05)
506    o pkg/ecco:
507      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
508      - add more relevant #ifdef ALLOW_SMOOTH ones.
509      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
510    o pkg/ctrl:
511      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
512        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
513      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
514        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
515        ctrlSmoothCorrel3D (new).
516        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
517      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
518      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
519        controls when useAtmWind, and vice versa.
520      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
521      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
522          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
523      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
524          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
525      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
526        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
527    o pkg/smooth:
528      - remove un-necessary includes.
529      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
530        Those CPP options were never defined, and not necessary.
531    o model/src:
532      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
533      - standard treatment of useSMOOTH.
534    o pkg/autodiff:
535      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
536        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
537    o pkg/exch2:
538      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
539        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
540      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
541        and tiles to process mapping.
542      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
543        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
544        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
545        from w2_eeboot.F to w2_readparms.F.
546    o eesupp/src:
547      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
548        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
549        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
550      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
551        is defined (remove condition on usingMPI) to match cases where MPI_INIT
552        has been called.
553      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
554      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
555        (so that on 1 proc, get same myPid independently of usingMPI)
556      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
557        useCubedSphereExchange with EXCH-1 (safer).
558      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
559    o pkg/ggl90:
560      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
561        used in ALLOW_GGL90_SMOOTH code.
562    o pkg/flt:
563      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
564        floats at the Southern end of the domain).
565    o eesupp/inc:
566      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
567        but not used (and not to be used) anywhere, just for documentation.
568    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
569      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
570        a) can damage previously written records in any other multi-record files.
571        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
572    o tools/genmake2:
573      - define variable MAKE within Makefile and use it in place of 'make';
574      - update AD_CONFIG.h (if needed) before building any of the executable
575        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
576        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
577      - always print usual warning comment 'this file is automatically generated'
578        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
579    o pkg/cheapaml:
580      - updated to correspond to the code used in accepted paper (Nico Wienders).
581    o pkg/exf:
582        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
583        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
584        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
585    o pkg/exf, autodiff, ctrl, ecco and seaice:
586        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
587    o pkg/ctrl, ecco:
588        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
589        Depending on useAtmWind, one is inactive, and the other is active (see
590        exf_getffields.F/exf_getsurfacefluxes.F).
591    o tools/genmake2:
592      - improve error msg when failing in 2nd test of check_for_broken_Ff
593      - fix option '-makefile' short-name (-mf according to genmake2 -help)
594      - source local config file "genmake_local" just after processing the genmake2
595        command arguments (previously done before processing arg).
596    o pkg/grdchk:
597      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
598        to this routine from cost_final has been dropped in g_cost_final)
599      - improve printed information (more explicit msg, no longer using "print *,"
600         fix fcpertminus printed value).
601    o model/src:
602      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
603        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
604        this prevents getting cost-funct reset in adinitialise_varia recomputations.
605    o pkg/dic:
606      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
607        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
608    o pkg/grdchk:
609      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
610      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
611    o pkg/autodiff/ctrl/grdchk :
612      - attempt to sort out what works and what does not,
613        with regard to I/O, and to warn/stop accordingly.
614    o pkg/grdchk:
615      - attempt to fix grdchk in the case of useSingleCpuIO.
616      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
617       statements were moved from grdchk_main.F and into
618       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
619      - a global sum is applied to record numbers icvrec/layer
620       out of grdchk_loc so that they be passed to I/O routines.
621    o pkg/smooth:
622      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
623        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
624    o verification/testreport:
625      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
626      - can also use compressed (gzip) reference output file;
627      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
628        to be easier to collect by testreport.
629      - update existing TLM output (half out-of-date by more than 3 yrs).
630      - report NETCDF & LAPACK settings (from genmake2) in output dir.
631      - report run-time in each individual summary (previously only for AD test);
632        for TLM test, add also TAF version.
633      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
634    
635  checkpoint63r (2012/08/15)  checkpoint63r (2012/08/15)
636  o tools/genmake2:  o tools/genmake2:
637    - fix Makefile for target ftlall (+ update files to clean after make ftlall)    - fix Makefile for target ftlall (+ update files to clean after make ftlall)
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