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revision 1.1687 by gforget, Wed Jul 11 21:51:27 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:
547      - 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
549        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
550        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
551      - always print usual warning comment 'this file is automatically generated'
552        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:
556        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)
558        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
559    o pkg/exf, autodiff, ctrl, ecco and seaice:
560        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
561    o pkg/ctrl, ecco:
562        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
563        Depending on useAtmWind, one is inactive, and the other is active (see
564        exf_getffields.F/exf_getsurfacefluxes.F).
565    o tools/genmake2:
566      - improve error msg when failing in 2nd test of check_for_broken_Ff
567      - fix option '-makefile' short-name (-mf according to genmake2 -help)
568      - source local config file "genmake_local" just after processing the genmake2
569        command arguments (previously done before processing arg).
570    o pkg/grdchk:
571      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
572        to this routine from cost_final has been dropped in g_cost_final)
573      - improve printed information (more explicit msg, no longer using "print *,"
574         fix fcpertminus printed value).
575    o model/src:
576      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
577        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
578        this prevents getting cost-funct reset in adinitialise_varia recomputations.
579    o pkg/dic:
580      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
581        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
582    o pkg/grdchk:
583      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
584      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
585    o pkg/autodiff/ctrl/grdchk :
586      - attempt to sort out what works and what does not,
587        with regard to I/O, and to warn/stop accordingly.
588    o pkg/grdchk:
589      - attempt to fix grdchk in the case of useSingleCpuIO.
590      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
591       statements were moved from grdchk_main.F and into
592       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
593      - a global sum is applied to record numbers icvrec/layer
594       out of grdchk_loc so that they be passed to I/O routines.
595    o pkg/smooth:
596      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
597        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
598    o verification/testreport:
599      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
600      - can also use compressed (gzip) reference output file;
601      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
602        to be easier to collect by testreport.
603      - update existing TLM output (half out-of-date by more than 3 yrs).
604      - report NETCDF & LAPACK settings (from genmake2) in output dir.
605      - report run-time in each individual summary (previously only for AD test);
606        for TLM test, add also TAF version.
607      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
608    
609    checkpoint63r (2012/08/15)
610    o tools/genmake2:
611      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
612    o pkg/ecco/ecco_cost_final.F :
613      - fix fc print statements (to stdout and costfunction0000) so
614        that the printed value is always after the global sum.
615    o pkg/seaice/seaice_dynsolver.F :
616      - fix ice strength assymptote at SEAICE_area_max<1
617        (no change for the standard case of SEAICE_area_max=1)
618    o some cleaning:
619      - pkg source files: ensure that all *.F files from each pkg included the
620        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
621        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
622        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
623        includes;
624      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
625      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
626        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
627        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
628      - update option-file CPP_OPTIONS.h of all AD experiments:
629        * no longer include PACKAGES_CONFIG.h ;
630        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
631        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
632          including ECCO_CPPOPTIONS.h).
633    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
634      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
635        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
636        not necessary accurate).
637      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
638        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
639        deliberately break compilation (a remainder that it needs to be customized)
640      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
641      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
642      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
643    o tools/genamke2:
644      - check for lapack.
645    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
646      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
647        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
648        from both packages.
649      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
650      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
651      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
652        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
653    o pkg/cost : add comments to explain special and/or untested setups.
654    o pkg/exf:
655      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
656        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
657    o verification/*/code_ad:
658      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
659      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
660      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
661        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
662    o pkg/seaice :
663      - added possibility to change ice strength/PRESS0 relationship to
664        HEFF, according to the following run time parameters
665        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
666        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
667        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
668    o pkg/ggl90 :
669      - added run time flag mxlSurfFlag to include the code that ensure
670        mixing between first and second level (previously included as a comment)
671    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
672      - add test of newly added dumpAdByRec=T option where
673        we write all records to one file per variable.
674    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
675      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
676        to check that this code is ok with taf and compiles in adjoint.
677    o pkg/autodiff :
678      - added run time param dumpAdByRec : ad dump format switch.
679        If true then write all records to one file per variable.
680        Else write one file per record (remains the default).
681      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
682    o pkg/seaice:
683     - Added SEAICEuseTILT run time switch : if set to
684       false then omit the tilt term in seaice dynamics.
685     - Fix free drift calculation.
686    o pkg/shelfice:
687      When initializing SHELFICEDragQuadratic, set default to be
688      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
689      but retain option to set it independently
690      (inconsistenty spotted by Veronique Dansereau)
691    o eesupp/inc:
692      - in EEPARAMS.h, add real-type constant for some frequently used simple number
693         (0,1,2,1/2), with name explicitly referring to RS/RL type.
694    o model/src:
695      - move balancing of relaxation terms to new S/R balance_relax.F.
696    o pkg/autodiff:
697      re-write active I/O high-level (control) S/R:
698      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
699      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
700      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
701        MDS_READ/WRITE_FIELD); change loops to multi-threads.
702      - update and merge active_file_control_slice.flow into active_file_control.flow
703      - update the calls in lower level S/R (active_file.F, active_file_g.F and
704        active_file_ad.F) keeping the argument list and function unchanged.
705      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
706        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
707      - new low-level active I/O routines, one for each type (RL/RS), for active var
708        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
709        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
710        right type.
711    o autodiff and RS=real*4:
712      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
713        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
714      - change argument type of 3-D mask argument to _RS to match type in the call
715        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
716    o pkg/thsice:
717      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
718      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
719        fresh-water flux: uniform correction or proportional to local precip.
720    o pkg/ctrl:
721      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
722      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
723                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
724      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
725    
726    checkpoint63q (2012/07/30)
727    o pkg/autodiff:
728      note about monitor and snap-shot of ad-variables:
729      a) need to apply ADEXCH before monitor or output of ad-vars to include
730       overlap contributions (was done for adjDump but missing for monitor).
731      b) since ADEXCH implies adding overlap values to interior array, machine
732       truncation error is expected when adding an ADEXCH call in the middle of
733       the time-stepping (although mathematically identical).
734      modifs:
735      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
736        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
737      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
738        apply ADEXCH before monitor or snap-shot of ad-variables:
739           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
740      - implement new method (copy+adexch) for snap-shot and monitor of main model
741        ad-vars (initially not used by default -> output unchanged).
742      - change default (set to 2) to use new method and update few output_adm.txt
743        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
744        and both tutorial_tracer_adjsens tests).
745      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
746        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
747    o pkg/ctrl:
748      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
749      generic control variables via
750      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
751      Only required customization should be S/R ctrl_map_ini_genarr.F
752      (routine in repository contains example)
753    o pkg/exf:
754      - fix and refine checking of surface-relaxation setting when using EXF
755    o verification (adjoint exp):
756      - reduce length of simulation by half for experiment global_ocean.cs32x15
757        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
758    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
759      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
760        of KE that can occur with aggressive optimization
761      + put quadratic bottom drag calculation in separated loops (only done if
762        using bottomDragQuadratic)
763    o model/src: CG2D_NSA
764      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
765         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
766      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
767         change cg2d residual target to be expressed in Wunits (=> do not normalise
768         RHS ; this fix global_max Pb with TAF); update output.
769    o verification/tutorial_tracer_adjsens:
770       improve parameter consistency (and get rid of warnings):
771       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
772       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
773       - use staggerTimeStep (for stability) in som81; use default rotation period.
774    o pkg/exch2:
775      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
776        reset to 0 = 1 long line in X)
777    o pkg/mdsio:
778      - fix reading of dimensions from meta file for large-size domain
779    o model/src:
780      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
781      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
782        Cubed-Sphere Exch with CS-corners inside the domain;
783        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
784        globalArea and to set hasWetCSCorners.
785      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
786        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
787      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
788        useCDscheme and useCubedSphereExchange).
789    o pkg/seaice/seaice_growth.F :
790      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
791        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
792        when the previous code was not correct.
793      - in all cases diagnoze the boundary condition mismatch to SIaaflux
794      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
795        that term to QNET (essentially to set the melt/freeze water to 0degC).
796        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
797  o verification/global_ocean.cs32x15/input.seaice :  o verification/global_ocean.cs32x15/input.seaice :
798   - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.    - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
799   - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).    - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
800   - update results (output.seaice.txt) accordingly.    - update results (output.seaice.txt) accordingly.
801  o verification/lab_sea/input/data.seaice :  o verification/lab_sea/input/data.seaice :
802   - remove SEAICEheatConsFix, which is now be tested    - remove SEAICEheatConsFix, which is now be tested
803     in global_ocean.cs32x15. The presently coded fix      in global_ocean.cs32x15. The presently coded fix
804     is only consistent with real fresh water + nlfs.      is only consistent with real fresh water + nlfs.
805   - update results (output.txt) accordingly.    - update results (output.txt) accordingly.
806  o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).  o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
807  o AD_CONFIG.h file:  o AD_CONFIG.h file:
808   - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;    - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
809   - remove #include "AD_CONFIG.h" from all included OPTIONS files and    - remove #include "AD_CONFIG.h" from all included OPTIONS files and
810     add it explicitly in each fortran src file where it is needed.      add it explicitly in each fortran src file where it is needed.
811     motivation: header file AD_CONFIG.h is generated/modified after "make depend"      motivation: header file AD_CONFIG.h is generated/modified after "make depend"
812     thus introducing potentially wrong dependency; therefore, better to include      thus introducing potentially wrong dependency; therefore, better to include
813     it only where it's really needed, and after any other included OPTIONS file      it only where it's really needed, and after any other included OPTIONS file
814     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN      (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
815     or ALLOW_TANGENTLINEAR_RUN).      or ALLOW_TANGENTLINEAR_RUN).
816    
817  checkpoint63p (2012/07/06)  checkpoint63p (2012/07/06)
818  o pkg/autodiff:  o pkg/autodiff:
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