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revision 1.1597 by mlosch, Tue Feb 14 14:53:17 2012 UTC revision 1.1833 by mlosch, Thu Feb 28 17:17:29 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: remove (almost) all divisions by constants within loops  o pkg/seaice:
8    in seaice_growth.F and seaice_solve4temp.F    - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
9  o pkg/seaice :    - add runtime parameter SEAICE_JFNKepsilon for that finite difference
10    - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.      gradient in the Jacobian times vector operation (s/r seaice_jacvec)
11    1 or 2, using newly added run time parameter SEAICE_availHeatTaper.    - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
12    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
13      - new subroutines seaice_lsr_tridiagu/v
14      - introduce loop bounds i/jmin/max to be able to use a restricted
15        additive Schwarz method, but not used for now.
16      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
17      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
18    o OpenAD support
19      Reorganize S/R call for overall time-stepping loop to facilitate
20      OpenAD revolve loop replacement
21      (new S/R main_do_loop.F)
22    o model/src:
23      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
24      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
25        ADAMS_BASHFORTH2.
26    o pkg/cheapaml:
27      - add new parameter (default=F, same as before) to disable full domain
28        (including land) periodicity in X & Y dir.
29      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
30        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
31        into single S/R CHEAPAML_TIMESTEP.
32    
33    checkpoint64d (2013/02/17)
34    o pkg/monitor (angular momentum):
35      - do not add Eta contribution to the total AM if using rigid-lid;
36      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
37      - horizontal discretisation: compute Zonal wind contribution separately for
38        each component (instead of from cell centered averaged) and use the 4
39        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
40      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
41        FreeSurf) if using vectorInvariant momentum.
42    o model/src (horizontal grid):
43      - move initialisation of all horizontal grid arrays to null value
44        from specific horizontal grid S/R to main S/R INI_GRID;
45      - add 2 new arrays to project model C-grid velocity on to zonal direction
46        (similar to AngleCosC & -AngleSinC but at U and V point location) and
47        compute them in S/R CALC_GRID_ANGLES.
48    o pkg/seaice: replace a hard coded parameter by a runtime parameter
49        SEAICE_JFNK_tolIter
50    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
51        preconditioner for JFNK (run LSR into the overlaps as far as possible,
52        i.e OLx/y-2, but overwrite the solution in the overlaps)
53      - extend loop range in seaice_calc_viscosity
54      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
55      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
56      - slightly modify loops in tridiagonal solver lsr-preconditioner
57      - by default remove the extra exchange in seaice_preconditioner with a
58        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
59      - modify offline_exf_seaice so that old results without RAS are reproduced
60        for output.dyn_jfnk.txt
61      in seaice_fgmres.F (unrelated to RAS)
62      - add a cpp-flag option for a re-ordered mapping (potentially more
63        efficient), but because this changes the results, turn it off by
64        default
65      - replace the save statement by local common blocks
66    o utils/matlab:
67      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
68      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
69        instead of local script "load_cs.m".
70    o pkg/seaice:
71      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
72        to the scalarProductMetric and the unrolling. By chance this does not
73        change the verification experiment, because of the particular domain
74        decomposition
75    o pkg/diagnostics:
76      - change default missing_value from UNSET_RL to -999.
77    o pkg/layers: improve vectorization of layers_fluxcalc.F
78      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
79        time spent in this routine by more than a factor of 3 on an NEC-SX8
80      - step 2: replace search algorithm by a bisection algorithm found in
81        Press et al. Numerical Recipes in Fortran. This algorithm can be
82        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
83        For now, use this algorithm only for TARGET_NEC_SX defined.
84      - moved the search algorithm into a separate subroutine, that is kept
85        within the same file for automatic inlining.
86      - modified catching potential errors
87    o pkg/ecco:
88      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
89    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
90      - modifications for ALLOW_GENTIM2D_CONTROL
91      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
92      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
93      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
94      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
95    o model/src:
96      - account for moist thermodynamics in (dry) potential temperature equation;
97        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
98        and cpl_aim+ocn.
99      - also switch to standard compiler (gfortran, was using ifort previously)
100        for fizhi-cs experiments reference output.
101    o pkg/ctrl:
102      - 1st step toward generic time-varying control variable (2D) via CPP option
103        ALLOW_GENTIM2D_CONTROL
104      - note new namelist ctrl_nml_genarr in data.ctrl
105    o verification/global_ocean.cs32x15:
106      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
107        thsice calling sequence and update "output.icedyn.txt" output file.
108    o pkg/ptracers:
109      - from Ryan A.: code to allow to restart a tracer at regular time interval
110        specifying a reset frequency and a reset-phase (for each tracers).
111    o pkg/thsice:
112      - implement new sequence of calls for thsice+seaice:
113          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
114          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
115      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
116        in CPP_OPTIONS.h) to recover old sequence;
117      - update diagnostics for Intermediate State thsice diagnostics: now filled
118        just before advection (instead of just after advection in old sequence);
119      - update output of experiment offline_exf_seaice (standard test);
120      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
121        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
122    o pkg/aim_v23:
123      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
124      - use standard pkg/mdsio routines to read & write CO2 pickup file;
125      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
126      - Implement new sequence of calls for seaice advection (with thsice and
127        seaice diffusion): do ice advection after ice-Thermodynamic (previously
128        was done before); change aim_do_physics.F (split the bi,bj loops block);
129      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
130    o pkg/thsice:
131      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
132        where just seaice diffusion is used without seaice-dynamics.
133    
134    checkpoint64c (2013/01/18)
135    o pkg/seaice:
136      - add a parameter JFNKres_tFac that can replace JFNKres_t
137        (= JFNKres_tFac*JFNKresidual before JFNK solver)
138      - add a line search option to the JFNK solver
139      - move update of u/vIce and computation of initial residual into a separate
140        routine (same file); makes the code a little easier to read (?)
141      - the line search requires computation of the residual and for some reason
142        I cannot do the update of u/vIce at the beginning of the Newton loop
143        without changing the results, so we move computation of the new residual
144        also to the end of the Newton loop, even without the line search
145    o pkg/mdsio:
146      - write missing value (corresponding to undefined array value) to meta files;
147        skip this if missing value is one (UNSET_RL would be a better value for the
148        case of undefined missing value but it's current the default missing-value);
149        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
150    o pkg/exf & thsice:
151      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
152        diagnostics) even when SHORTWAVE_HEATING is #undef;
153    o verification/cfc_example:
154      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
155        illustrate how to use it).
156    o verification/offline_exf_seaice:
157      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
158        files to only one time-record.
159      in input.thermo: narrow the 2 bands of low initial ice-concentration near
160        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
161        snapshot output; same mcPheePiston value as in thsice with
162        surf-current=0.2m/s.
163      in input.thsice: similar set-up as in input.thermo (channel with same seaice
164        initial conditions).
165    o verification/cfc_example:
166      - update file "data" with more standard choice (default rotationPeriod,
167        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
168        set deltaTFreeSurf to deltaTtracer) and update the output.
169    o pkg/layers:
170      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
171      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
172    o verification/offline_exf_seaice:
173      - set all {field}period to zero for constant-in-time forcing (not tested
174        anywhere else).
175    o verification/offline_exf_seaice:
176      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
177      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
178    o model/src:
179      - implement Finite-Volume method for (hydrostatic) presure gradient
180        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
181    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
182      - In order to be compatible with the default EVP code, this requires changing
183        the EVP code around a little; and because any small change immediately
184        breaks the lab_sea.hb87 verification experiment, the reference output is
185        updated two times (each time the remaining aggrement was only 2 digits):
186        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
187        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
188        The adjoint test lab_sea.evp also needed to be updated.
189      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
190        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
191        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
192        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
193        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
194        kept obscure, because I need to test it a little more.
195    o pkg/cheapaml:
196      - fix few incorrect type (_RL/_RS) in subroutine calls.
197    o pkg/seaice:
198      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
199        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
200    o model/src:
201      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
202        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
203        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
204    o pkg/cheapaml:
205      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
206        update output of experiment cheapAML_box.
207      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
208        and set them only in one place (cheapaml_readparms.F).
209      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
210      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
211        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
212    o model/src/the_main_loop.F:
213      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
214    o pkg/seaice:
215      - remove legacy branch code.
216      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
217    o verification/*/code*/SEAICE_OPTIONS.h:
218      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
219        SEAICE_CAP_HEFF).
220    o pkg/cheapaml:
221      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
222        to load new forcing fields.
223      - add missing "_d 0" where it's needed; + some editing (improve indentation).
224      - remove switch to "-r8" compiler option (no longer needed) in verification
225        cheapAML_box, keep same output (small trucation error differences).
226    o verification/offline_exf_seaice:
227      - add thermodynamics only test.
228    o verification/cheapAML_box:
229      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
230        keep same output (same 14 digits for cg2d).
231      - switch on "-r8" compiler option (some numerical values are missing
232        the "_d 0") and update output (only 6 digits for cg2d were preserved).
233    
234    checkpoint64b (2012/12/24)
235    o pkg/cheapaml:
236      - remove un-used variables (Qnet,EmPmR) from pickup files.
237      - store tendency of advected variables into cheapaml pickup file
238        and fix the AB-2 restart.
239    o verification/offline_exf_seaice and lab_sea adjoint:
240      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
241      - switch to 4 time steps in offline, consistent with lab_sea.
242      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
243      - update results after change of experiment seaice.
244    o pkg/seaice:
245      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
246        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
247        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
248        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
249    o model/src:
250      - add run-time parameter to select CG2D solver minimum-residual solution
251        (in case of a poor convergence).
252    o pkg/seaice/seaice_lsr.F
253      - move calculation of matrix coefficients into new
254        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
255        file; the main purpose of this change is to be able to reuse the code
256        in S/R SEAICE_PRECONDITIONER
257      - modify the computation of the residual so that the mass of sea-ice
258        is not used twice; this simplifies the calculations, but since
259        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
260        not tested in testreport---this does not affect the testreport results.
261    o verification/seaice_obcs:
262      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
263        verification/lab_sea/input.salt_plume; changes results/output.txt*
264    o model/src:
265      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
266    o pkg/seaice:
267      - improve description of parameters in seaice_fgmres.F and start
268        cleaning up the code
269      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
270        second argument
271      - add a metric based on grid cell area to SEAICE_SCALPROD; update
272        results of offline_exf_seaice.dyn_jfnk
273      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
274    o pkg/aim_v23:
275      - fix an other bug in dissipation heating (grid-cell area was missing).
276    o model/src + pkg/seaice:
277      - add global (multi-tile) linear solver for pair of tri-diagonal system
278        along X and Y lines, respectively for U and V component.
279        Note: 1) MPI and cube-exchange not yet coded.
280            2) probably not accurate for poorly conditioned / large size problem.
281      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
282        default: not compiled and not used.
283    o pkg/seaice:
284      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
285        introduce bi/bj loops and use global_sum_tile_rl instead of
286        mpi_allreduce in seaice_fgmres.F
287      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
288      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
289      - add a verification experiment for JFNK in offline_exf_seaice
290    o verification:
291      - change (for now, only fwd test) offline_exf_seaice experiment:
292        use a re-entrant channel with idealized coastline (trapezoidal shape)
293        at southern boundary to explore seaice dynamics and thermodynamics
294        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
295        secondary test (input.thsice) use thermodynamics only with SST relaxation.
296      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
297    o pkg/exf:
298      - disable "sstExtrapol" when Nr=1
299    o verification:
300      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
301        to test pkg/cheapaml.
302    o pkg/aim_v23 & pkg/shap_filt:
303      - fix dissipation heating (erroneous gravity multiplication factor).
304    o pkg/seaice:
305      - remove unused field pressPre from jfnk solver
306      - rename two subroutines in seaice_preconditioner.F
307    o eesupp/src:
308       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
309    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
310       - remove wrong parts of the rhs and the lhs (were in there
311         because I did not understand the concept of this preconditioner)
312       - add an exchange between u- and v-sweep. This increases communication
313         by a factor of two but improves the convergence of jfnk. Ideally,
314         one would like the u- and v-sweep to be independent. So far within
315         undocumented ifdefs
316       - reorganize the extra computations for printing the residuals
317    o tools/genmake2:
318      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
319        since it's not necessary (and was preventing to use MNC in some cases).
320    
321    checkpoint64a (2012/11/16)
322    o pkg/autodiff:
323      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
324        autodiff_readparms.F no longer depends on calling order (within
325        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
326        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
327        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
328    o pkg/obcs:
329      - adding tidal velocity forcing capability to obcs
330        for usage example, see verification/seaice_obcs/input.tides
331    o pkg/seaice:
332      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
333        SEAICE_LSRrelaxU/V
334      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
335    o pkg/aim_v23:
336      - implement heating from friction (bottom friction and stratospheric drag).
337    o pkg/shap_filt:
338      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
339        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
340    o model/src:
341      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
342        time-constant addMass field from file (addMassFile);
343      - support for heating due to friction (and Kinetic Energy dissipation):
344        add option, run-time switch and 3-D field array + support code ; each pkg
345        or S/R can add heating contribution (if there is a sink of KE); the sum is
346        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
347    o pkg/seaice:
348      - complete merge of ITD code into seaice_growth.F
349        from MITgcm_contrib/torge/itd/code/
350        no verification so far, but Torge Martin tested
351        "1-D test case and Beaufort set up;
352        deliver okay results after 1 model year."
353      - complete merge of SEAICE_SIZE.h into all relevant routines
354      - move computation of eta at Z-points into calc_viscosities
355        + introduce global field etaZ
356        + add different methods for computing etaZ, for now the old
357          method (simple averages of eta to Z-points) is hardwired
358        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
359          seaice_preconditioner
360      - simplify computations for SEAICE_ZETA_SMOOTHREG
361      - seaice_preconditioner:
362        + replace one remaining press by pressLoc (mistake)
363        + adjust printing of residuals
364      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
365        + add (SEAICE.h) and rename some counters (initiliased in
366          seaice_init_fixed.F)
367        + add _BEGIN/END_MASTER (myThid)  around print statements
368        + print total number of iterations and failures over SEAICE_monFreq
369          interval to STDOUT
370      - move control over output-messages by fgmres to seaice_jfnk to save
371        some operations
372      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
373        in order to make restarts with sol .ne. zero (fgmres with restarts)
374        (seaice_jfnk.F, seaice_fgmres.F)
375      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
376        a serious convergence problem when open boundaries are involved
377    o pkg/ggl90: fix computation of control volumes for the case of
378      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
379      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
380    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
381    o pkg/autodiff
382      - Add inAdMode switch for SEAICEuseDYNAMICS:
383        SEAICEuseDYNAMICSinAdMode
384        (extend logic in ADAUTODIFF_INADMODE_SET)
385    o pkg/seaice
386      - Step 1 of merging ice-thickness distribution (ITD) code from
387        MITgcm_contrib/torge/itd/ (author: Torge Martin)
388        The code implements concept laid out in Thorndike et al. (1975);
389        code is enabled via CPP flag SEAICE_ITD
390        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
391        code is not complete yet!!
392      - SEAICE_SIZE.h now included in almost all seaice routines
393    o verification (using seaice):
394      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
395        global_ocean.cs32x15.seaice ; update results.
396      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
397      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
398        offline_exf_seaice (previously compiling B-grid).
399    o pkg/exf:
400      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
401        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
402        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
403    o pkg/layers (adjust changes from Sept 19):
404      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
405        this allows to remove "layers_maxNum" dimension from all layers arrays.
406    o pkg/layers (adjust changes from Sept 19):
407      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
408      - snap-shot extended to all type of layers (not just the 1rst type);
409      - remove layers variables when corresponding CPP option is undef.
410    o pkg/layers:
411      - rename pkg/layers variable and add new output (layer exist & un-weighted
412        velocity in layer)
413    o pkg/seaice:
414      - simplify (?) ocean-drag coefficent computations by using
415        the same routine in all three solvers (saves some code lines)
416      - remove global fields DRAGA and DRAGS from C-grid code and
417        declare them locally in lsr.F (the only place where they are
418        still used)
419      - update AD output of lab_sea.evp (very sensitive anyway).
420    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
421      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
422      and SEAICEuseJFNK=.true. A few things to note:
423      - involves a FGMRES, that is parallel but very inefficient,
424        because of many scalar products (global sums) in the Gram-Schmidt
425        orthogonalization method. Needs to be replaced. Original code
426        from J.-F. Lemieux
427      - preconditioner for FGMRES is a stripped down version of LSOR
428      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
429        preconditioner. For the preconditioner, the default is set to 10.
430      - Jacobian times vector is computed with finite differences
431      - marginally related to JFNK-solver: add a smooth regularization for
432        zeta with tanh that will improve convergence (Lemieux and Tremblay,
433        2009) for any implicit solver (not implemented for EVP because EVP
434        does not need this regularization in the first place). Define
435        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
436    o eesupp/src:
437      - check in genmake2 that intrinsic S/R flush is available.
438      - add S/R to flush IO unit (if intrinsic S/R flush is available)
439      - flush standard & error msg unit before MPI termination
440      - if debugMode, flush IO unit after printing msg
441    o pkg/ctrl:
442      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
443        to ctrl_set_unpack_xyz.
444    
445    checkpoint64 (2012/10/09)
446    o pkg/shelfice
447      - in mom_fluxform.F, mom_vecinv.F:
448        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
449        Bug fix KappaRU -> KappaRV
450        does not change verification/isomip but may change other setups
451        (presumably constant KappaRU=KappaRV)
452      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
453    o pkg/obcs:
454      - fixed some indexing bugs in obcs_seaice_sponge.F
455      - added obcs relaxation subroutines for HSALT and HSNOW
456      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
457    o pkg/seaice:
458      - add "multicategory" parameterization for snow in analogy to ice,
459        default is off for now.
460    o pkg/obcs:
461      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
462        see verification/seaice_obcs/input.seaiceSponge for example application.
463      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
464        index setting by master-thread. This fix multi-threads Pb in previous modifs.
465    o pkg/layers :
466      - add diagnostics to pkg/layers
467      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
468        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
469    o pkg/generic_advdiff/gad_implicit_r.F :
470      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
471    o pkg/seaice/seaice_growth.F:
472      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
473    o pkg/obcs:
474      - change default setting of OBCS_UVICE_OLD from defined to undef;
475      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
476        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
477      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
478      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
479        with Southern & Western OB at a tile edge (at least in a simple set-up).
480    o pkg/obcs:
481      - change settings of OB index in case OB coincides with tile edge (shared by
482        2 tiles), so that common OB location is registered by both tiles (instead of
483        only 1). However, for Southern and Western OB, index value = 0 is not
484        recognized as valid OB index (=default null value) and needs to be fixed.
485      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
486      - new parameter "OB_indexNone" for null index value (for now, still zero)
487        to replace hard-coded null index value of zero.
488    o pkg/exch2:
489      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
490        always check buffer-size (but outside the loop); move checking for valid
491        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
492        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
493    o pkg/ctrl (pack & unpack):
494      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
495        (locally defined) for different variables (+ remove the variable-specific
496        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
497        (to be extended to other local file names in ctrl.h).
498    o pkg/flt:
499      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
500    o pkg/mdsio:
501      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
502    o tools/genmake2:
503      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
504        (added by Alistair in version 1.51 for building without make depend);
505      - remove Header files list (H_SRC_FILES) from the dependence of targets
506         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
507        place in version 1.23): this save going through staf when unrelated header
508        file has been modified.
509       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
510        "make depend" step, still need to do "make links" before "make adtaf".
511    o eesupp/src (+ few pkg src files) & genmake2:
512      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
513      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
514      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
515         upper/lower case ; account for space between "#" and undef/define)
516    o pkg/flt (with exch2):
517      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
518      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
519    
520    checkpoint63s (2012/09/05)
521    o pkg/ecco:
522      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
523      - add more relevant #ifdef ALLOW_SMOOTH ones.
524      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
525    o pkg/ctrl:
526      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
527        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
528      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
529        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
530        ctrlSmoothCorrel3D (new).
531        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
532      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
533      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
534        controls when useAtmWind, and vice versa.
535      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
536      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
537          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
538      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
539          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
540      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
541        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
542    o pkg/smooth:
543      - remove un-necessary includes.
544      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
545        Those CPP options were never defined, and not necessary.
546    o model/src:
547      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
548      - standard treatment of useSMOOTH.
549    o pkg/autodiff:
550      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
551        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
552    o pkg/exch2:
553      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
554        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
555      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
556        and tiles to process mapping.
557      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
558        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
559        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
560        from w2_eeboot.F to w2_readparms.F.
561    o eesupp/src:
562      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
563        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
564        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
565      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
566        is defined (remove condition on usingMPI) to match cases where MPI_INIT
567        has been called.
568      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
569      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
570        (so that on 1 proc, get same myPid independently of usingMPI)
571      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
572        useCubedSphereExchange with EXCH-1 (safer).
573      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
574    o pkg/ggl90:
575      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
576        used in ALLOW_GGL90_SMOOTH code.
577    o pkg/flt:
578      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
579        floats at the Southern end of the domain).
580    o eesupp/inc:
581      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
582        but not used (and not to be used) anywhere, just for documentation.
583    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
584      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
585        a) can damage previously written records in any other multi-record files.
586        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
587    o tools/genmake2:
588      - define variable MAKE within Makefile and use it in place of 'make';
589      - update AD_CONFIG.h (if needed) before building any of the executable
590        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
591        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
592      - always print usual warning comment 'this file is automatically generated'
593        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
594    o pkg/cheapaml:
595      - updated to correspond to the code used in accepted paper (Nico Wienders).
596    o pkg/exf:
597        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
598        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
599        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
600    o pkg/exf, autodiff, ctrl, ecco and seaice:
601        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
602    o pkg/ctrl, ecco:
603        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
604        Depending on useAtmWind, one is inactive, and the other is active (see
605        exf_getffields.F/exf_getsurfacefluxes.F).
606    o tools/genmake2:
607      - improve error msg when failing in 2nd test of check_for_broken_Ff
608      - fix option '-makefile' short-name (-mf according to genmake2 -help)
609      - source local config file "genmake_local" just after processing the genmake2
610        command arguments (previously done before processing arg).
611    o pkg/grdchk:
612      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
613        to this routine from cost_final has been dropped in g_cost_final)
614      - improve printed information (more explicit msg, no longer using "print *,"
615         fix fcpertminus printed value).
616    o model/src:
617      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
618        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
619        this prevents getting cost-funct reset in adinitialise_varia recomputations.
620    o pkg/dic:
621      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
622        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
623    o pkg/grdchk:
624      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
625      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
626    o pkg/autodiff/ctrl/grdchk :
627      - attempt to sort out what works and what does not,
628        with regard to I/O, and to warn/stop accordingly.
629    o pkg/grdchk:
630      - attempt to fix grdchk in the case of useSingleCpuIO.
631      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
632       statements were moved from grdchk_main.F and into
633       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
634      - a global sum is applied to record numbers icvrec/layer
635       out of grdchk_loc so that they be passed to I/O routines.
636    o pkg/smooth:
637      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
638        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
639    o verification/testreport:
640      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
641      - can also use compressed (gzip) reference output file;
642      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
643        to be easier to collect by testreport.
644      - update existing TLM output (half out-of-date by more than 3 yrs).
645      - report NETCDF & LAPACK settings (from genmake2) in output dir.
646      - report run-time in each individual summary (previously only for AD test);
647        for TLM test, add also TAF version.
648      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
649    
650    checkpoint63r (2012/08/15)
651    o tools/genmake2:
652      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
653    o pkg/ecco/ecco_cost_final.F :
654      - fix fc print statements (to stdout and costfunction0000) so
655        that the printed value is always after the global sum.
656    o pkg/seaice/seaice_dynsolver.F :
657      - fix ice strength assymptote at SEAICE_area_max<1
658        (no change for the standard case of SEAICE_area_max=1)
659    o some cleaning:
660      - pkg source files: ensure that all *.F files from each pkg included the
661        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
662        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
663        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
664        includes;
665      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
666      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
667        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
668        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
669      - update option-file CPP_OPTIONS.h of all AD experiments:
670        * no longer include PACKAGES_CONFIG.h ;
671        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
672        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
673          including ECCO_CPPOPTIONS.h).
674    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
675      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
676        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
677        not necessary accurate).
678      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
679        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
680        deliberately break compilation (a remainder that it needs to be customized)
681      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
682      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
683      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
684    o tools/genamke2:
685      - check for lapack.
686    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
687      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
688        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
689        from both packages.
690      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
691      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
692      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
693        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
694    o pkg/cost : add comments to explain special and/or untested setups.
695    o pkg/exf:
696      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
697        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
698    o verification/*/code_ad:
699      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
700      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
701      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
702        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
703    o pkg/seaice :
704      - added possibility to change ice strength/PRESS0 relationship to
705        HEFF, according to the following run time parameters
706        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
707        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
708        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
709    o pkg/ggl90 :
710      - added run time flag mxlSurfFlag to include the code that ensure
711        mixing between first and second level (previously included as a comment)
712    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
713      - add test of newly added dumpAdByRec=T option where
714        we write all records to one file per variable.
715    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
716      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
717        to check that this code is ok with taf and compiles in adjoint.
718    o pkg/autodiff :
719      - added run time param dumpAdByRec : ad dump format switch.
720        If true then write all records to one file per variable.
721        Else write one file per record (remains the default).
722      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
723    o pkg/seaice:
724     - Added SEAICEuseTILT run time switch : if set to
725       false then omit the tilt term in seaice dynamics.
726     - Fix free drift calculation.
727    o pkg/shelfice:
728      When initializing SHELFICEDragQuadratic, set default to be
729      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
730      but retain option to set it independently
731      (inconsistenty spotted by Veronique Dansereau)
732    o eesupp/inc:
733      - in EEPARAMS.h, add real-type constant for some frequently used simple number
734         (0,1,2,1/2), with name explicitly referring to RS/RL type.
735    o model/src:
736      - move balancing of relaxation terms to new S/R balance_relax.F.
737    o pkg/autodiff:
738      re-write active I/O high-level (control) S/R:
739      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
740      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
741      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
742        MDS_READ/WRITE_FIELD); change loops to multi-threads.
743      - update and merge active_file_control_slice.flow into active_file_control.flow
744      - update the calls in lower level S/R (active_file.F, active_file_g.F and
745        active_file_ad.F) keeping the argument list and function unchanged.
746      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
747        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
748      - new low-level active I/O routines, one for each type (RL/RS), for active var
749        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
750        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
751        right type.
752    o autodiff and RS=real*4:
753      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
754        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
755      - change argument type of 3-D mask argument to _RS to match type in the call
756        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
757    o pkg/thsice:
758      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
759      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
760        fresh-water flux: uniform correction or proportional to local precip.
761    o pkg/ctrl:
762      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
763      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
764                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
765      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
766    
767    checkpoint63q (2012/07/30)
768    o pkg/autodiff:
769      note about monitor and snap-shot of ad-variables:
770      a) need to apply ADEXCH before monitor or output of ad-vars to include
771       overlap contributions (was done for adjDump but missing for monitor).
772      b) since ADEXCH implies adding overlap values to interior array, machine
773       truncation error is expected when adding an ADEXCH call in the middle of
774       the time-stepping (although mathematically identical).
775      modifs:
776      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
777        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
778      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
779        apply ADEXCH before monitor or snap-shot of ad-variables:
780           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
781      - implement new method (copy+adexch) for snap-shot and monitor of main model
782        ad-vars (initially not used by default -> output unchanged).
783      - change default (set to 2) to use new method and update few output_adm.txt
784        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
785        and both tutorial_tracer_adjsens tests).
786      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
787        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
788    o pkg/ctrl:
789      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
790      generic control variables via
791      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
792      Only required customization should be S/R ctrl_map_ini_genarr.F
793      (routine in repository contains example)
794    o pkg/exf:
795      - fix and refine checking of surface-relaxation setting when using EXF
796    o verification (adjoint exp):
797      - reduce length of simulation by half for experiment global_ocean.cs32x15
798        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
799    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
800      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
801        of KE that can occur with aggressive optimization
802      + put quadratic bottom drag calculation in separated loops (only done if
803        using bottomDragQuadratic)
804    o model/src: CG2D_NSA
805      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
806         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
807      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
808         change cg2d residual target to be expressed in Wunits (=> do not normalise
809         RHS ; this fix global_max Pb with TAF); update output.
810    o verification/tutorial_tracer_adjsens:
811       improve parameter consistency (and get rid of warnings):
812       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
813       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
814       - use staggerTimeStep (for stability) in som81; use default rotation period.
815    o pkg/exch2:
816      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
817        reset to 0 = 1 long line in X)
818    o pkg/mdsio:
819      - fix reading of dimensions from meta file for large-size domain
820    o model/src:
821      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
822      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
823        Cubed-Sphere Exch with CS-corners inside the domain;
824        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
825        globalArea and to set hasWetCSCorners.
826      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
827        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
828      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
829        useCDscheme and useCubedSphereExchange).
830    o pkg/seaice/seaice_growth.F :
831      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
832        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
833        when the previous code was not correct.
834      - in all cases diagnoze the boundary condition mismatch to SIaaflux
835      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
836        that term to QNET (essentially to set the melt/freeze water to 0degC).
837        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
838    o verification/global_ocean.cs32x15/input.seaice :
839      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
840      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
841      - update results (output.seaice.txt) accordingly.
842    o verification/lab_sea/input/data.seaice :
843      - remove SEAICEheatConsFix, which is now be tested
844        in global_ocean.cs32x15. The presently coded fix
845        is only consistent with real fresh water + nlfs.
846      - update results (output.txt) accordingly.
847    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
848    o AD_CONFIG.h file:
849      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
850      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
851        add it explicitly in each fortran src file where it is needed.
852        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
853        thus introducing potentially wrong dependency; therefore, better to include
854        it only where it's really needed, and after any other included OPTIONS file
855        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
856        or ALLOW_TANGENTLINEAR_RUN).
857    
858    checkpoint63p (2012/07/06)
859    o pkg/autodiff:
860      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
861      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
862        which are now read from new parameter file "data.autodiff" (inAdExact
863        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
864      - add file "data.autodiff" in all verification/*/input_ad/ directories.
865      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
866        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
867    o verification/tutorial_tracer_adjsens/
868      - add extra sub-verification which uses "SOM" advection scheme
869        (2nd Order-Moment Advection Scheme, Prather Limiter) with
870          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
871        and in data:
872          multiDimAdvection=.TRUE.,
873          tempAdvScheme=81,
874          saltAdvScheme=81,
875    o model/src:
876      - introduce ALLOW_BALANCE_RELAX which allow the removal
877       of the global mean of relaxation terms by setting
878       balanceThetaClimRelax and balanceSaltClimRelax
879      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
880       This case is now treated appropriately in seaice_growth.F
881    o pkg/seaice:
882      - do balanceEmPmR and balanceQnet based on the net fluxes
883        (SItflux) that enter the ocean+ice system rather than QNET
884        and EMPMR. Works best in real fresh water.
885      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
886        out of the diagnotics bloc, and stored in global arrays.
887    
888    checkpoint63o (2012/06/29)
889    o vertical mixing schemes:
890      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
891      - replace computation of density (in Function STATE1, opps_calc.F) by a call
892        to S/R FIND_RHO_SCALAR
893      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
894        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
895        affects output (vermix.ggl90) at truncation level.
896    o testreport:
897      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
898        (nSx,nSy) for the number of threads (from eedata.mth)
899    o model/src:
900      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
901        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
902    o verification/tutorial_tracer_adjsens/
903      - compile with ALLOW_CG2D_NSA
904      - run with nonlinFreeSurf=3
905      - update reference output_adm.txt
906    o tools/genmake2:
907      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
908        refine usePROFILES switching off (only when NetCDF is not available).
909    o verification (atmospheric set-up):
910      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
911    o pkg/profiles : refine profiles and files handling.
912    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
913    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
914      - changes to use model/src/the_main_loop.F rather than the ecco version
915        in ecco type adjoint runs.
916    o model/src:
917      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
918      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
919      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
920    o model/src:
921      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
922        update output of test experiment bottom_ctrl_5x5.
923    o pkg/generic_advdiff:
924      - implement vertical bi-harmonic diffusion (for now, only for T & S and
925        only explicitly).
926    o verification/bottom_ctrl_5x5/
927      update reference output (results changed quite some time ago,
928      not sure when; but new reference results look ok in terms of grdchk)
929    o verification/1D_ocean_ice_column/
930      For verification purposes, the exact adjoint rather than an approx.
931      should be used (e.g., to comare against F.D. or TLM).
932      removed autodiff_inadmode*_ad.F routines in code_ad/
933      Update results/ accordingly.
934    o pkg/cal:
935      - change cal_getdate.F so that output date is function of input time only
936        (less ambiguous, not mixed up with input iteration number).
937      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
938    o pkg/diagnostics:
939      - implement calendarDumps also for stats-diags
940      - implement calendarDumps also for snap-shot output (negative freq)
941      - for now, ignores calendarDumps if non-zero phase-lag.
942    
943    checkpoint63n (2012/06/04)
944    o model/src:
945      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
946        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
947      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
948        similar to calc_r_star.F); update results of experiment internal_wave and
949        tutorial_global_oce_in_p (affected @ truncation level).
950    o pkg/shelfice:
951      - add parameterisation of advective-diffusive flux into the ice shelf
952        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
953      - simply eps3/3a computation
954    o eesupp:
955     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
956       between tiles, just fill-in edges assuming locally periodic subdomain) and
957       add corresponding exchange subroutines (EXCH0);
958     - new CG-solver version (_EX0) for disconnected-tiles special case.
959    o model/src (CG-solvers):
960     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
961       (similar final residual output and max-Iter number as with standard version);
962     - allows to store and use lowest-residual solution (standard & _SR versions);
963     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
964     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
965    o eesup/src:
966     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
967       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
968    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
969    
970    checkpoint63m (2012/04/27)
971    o pkg/shelfice:
972     - account for partical cells in surface level below ice-shelf for hydrostatic
973       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
974    o ad test experiments:
975     - update and rename to "ad_optfile.local" local AD-optfile specific to a
976       particular adjoint verification experiment (in verification/*/code_ad/)
977    o pkg/seaice & pkg/exf:
978     - Part two of ECCO-CLIVAR code merges.
979       Completes merge of seaice area relax. code.
980       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
981       to be set in EXF_OPTIONS.h since this pkg controls its I/O
982       (and avoids second CPP option in SEAICE_OPTIONS.h)
983     - change default value of costIceStart & costIceEnd to a valid date.
984     - add snowPrecip to HSNOW in seaice_growth
985    o pkg/ptracers:
986     - move ptracers summary and setup check into separated S/R ; add a check for
987       valid PTRACERS_Iter0 value (error+stop or just warning).
988    o pkg/cal (+ pkg/ecco):
989     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
990       as input; and for AD, unless both are not differentiable (e.g., k index)).
991    o model/src:
992     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
993       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
994       temporary set to usingZCoords value (to be changed to F when using shelfice).
995     - hydrostatic pressure: implement partial cell near the surface also for
996       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
997       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
998    o pkg/ctrl/ctrl_init.F:
999     - add a formal parameter to s/r ctrl_init_rec to print
1000       xx_$(ctrl_valiable)_file for easier debugging
1001     - move call of cal_* routines into the if-block where they are really
1002       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1003       to specify a startdate
1004    o pkg/seaice:
1005     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1006       global_ocean.cs32x15/code versions).
1007     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1008       verification experiment global_ocean.cs32x15.seaice and update results.
1009    o pkg/exf:
1010     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1011       (according to useExfYearlyFields).
1012    o pkg/cal:
1013     - move calendar setting & summary (previously in cal_readparams.F) into new
1014       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1015       length of the simulation is set (after SET_PARMS call); This is an attempt
1016       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1017     - For safety: keep a record of pkg/cal parameter settings status
1018               to allow to STOP if one pkg/cal S/R is called too early.
1019     - add a stop in all basic pkg/cal subroutines if called before setting is done.
1020     - modify cal_getdate.F: stop when nothing was returned;
1021       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1022       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1023    
1024    checkpoint63l (2012/04/04)
1025    o pkg/bbl:
1026      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1027        update global_with_exf output.yearly.txt file.
1028    o pkg/cal:
1029      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1030      - remove 2 unsused and very short (1 line only) functions ;
1031      - remove unsused subroutines from AD-Diff list.
1032    o model/src:
1033      - start to implement clean wait to stop in initialization S/R (config_check.F,
1034         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1035    o folowing PRINT_MESSAGE changes:
1036      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1037    o pkg/bbl:
1038      - modification so it can work with z*
1039      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1040      - global_with_exf/input.yearly verification; changes output.yearly.txt
1041    o eesupp/src:
1042      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1043        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1044      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1045        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1046      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1047      - when using MPI, always set usingMPI=T ; set default accordingly and stop
1048        if not consistent.
1049      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1050        argument is zero (in case called within single-thread section).
1051    o pkg/fizhi:
1052        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1053        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1054    o pkg/exch2:
1055      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1056        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1057      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1058        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1059        with bad ones coming from a not-yet-updated halo.
1060        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1061    o pkg/frazil:
1062        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1063        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1064    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1065    o verification/lab_sea
1066      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1067      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1068      * nTimeSteps 3 -> 4
1069      * changed reference output accordingly
1070    o pkg/ctrl:
1071      * fix ctrl_get_gen for xx_sst, xx_sss
1072    o pkg/fizhi:
1073      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1074        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1075      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1076        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1077        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1078    o pkg/gmredi:
1079      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1080    o pkg/fizhi:
1081      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1082        (old)aces open64 tuv test.
1083    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1084    o pkg/mom_vecinv:
1085      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1086        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1087        with non-lin free-surf).
1088    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1089      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1090      some compilers (gfortran 4.6.0 on MacOS)
1091    o momentum:
1092      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1093        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1094        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1095    
1096    checkpoint63k (2012/03/17)
1097    o model/src:
1098       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1099         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1100       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1101         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1102    o model/src: solve_*diagonal.F
1103       - replace division with multiplication by inverse (similar to original version)
1104         update output of AD exp. global_ocean.90x40x15.
1105       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1106         to enable the use of the vectorized & differentiable solve_tridiagonal.F
1107       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1108         vertical advection (to get solve_tridiagonal tested in AD mode).
1109    o pkg/seaice: ECCO-CLIVAR merge:
1110      1. seaice AREA relaxation
1111         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1112         * runtime flag: SEAICE_tauAreaObsRelax
1113      2. modified global mean cost imbalance code: CPP option
1114          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1115    o another iteration on solve_*diagonal.F
1116       Make choices independent of AUTODIFF
1117       Default will be the adjoinable vectorized version.
1118       Alternative choices are:
1119       * non-adjoinable original version with low memory footprint:
1120         #define SOLVE_DIAGONAL_LOWMEMORY
1121       * still adjoinable but does not vectorize (k as inner-most loop):
1122         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1123    o testreport
1124     - add option to use a home made wrapper around "make"
1125     - remove MITGCM_IEEE env. variable (no longer active)
1126    o pkg/shelfice
1127     - improve computation of friction velocity for velocity dependent
1128       exchange coefficients: include velocities into SHELFICEBoundaryLayer
1129       block to average velocities vertically
1130     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
1131    o Modify diagonal solvers, now three versions (upon request):
1132      #ifndef SOLVE_DIAGONAL_AUTODIFF
1133        1. default version (dating back a while ago)
1134      #else /* def SOLVE_DIAGONAL_AUTODIFF */
1135      # ifdef SOLVE_DIAGONAL_KINNER
1136        2. adjoinable version with k-innermost loop (G. Forget)
1137      # else
1138        3. adjoinable vectorized version of 2.
1139      # endif
1140      #endif /* SOLVE_DIAGONAL_AUTODIFF */
1141      All flags are currently set within routines, but could/should be moved to CPP-options.
1142      Array bounds for 1. are as before, for 2.,3. cover the entire domain
1143      (could be changed for 1. too).
1144    o verification/lab_sea (fwd):
1145      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
1146        use 7 categories (except hb87), new solve4temp params (except salt_plume),
1147        constant salinity (=4) or variable salinity (salt_plume) done through
1148        SItracer.
1149    o pkg/seaice:
1150      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
1151      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
1152         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
1153        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
1154        SEAICE_freeze got retired) but already better than previously with
1155        SEAICE_freeze=123456.7 deg.C;
1156      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
1157        (safer multi-threaded setting); always set SEAICEuseEVP;
1158      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
1159        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
1160        stop if multiple specifications for the same coeff; make sure default
1161        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
1162    o pkg/obcs:
1163      - allow to switch to upwind 1rst order advection scheme for the advective
1164        flux computation at the open-boundary; disabled for adjoint built.
1165    o pkg/ptracers:
1166      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
1167      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
1168      - add parameter to decide when to start a tracer; use internal flag to
1169        know which tracer to step-forward; switch this internal flag at the top
1170        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
1171        for adjoint built.
1172    o pkg/seaice:
1173      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
1174      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
1175      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
1176    o pkg/ecco:
1177      - fix writing of output file DiagnosCost_ClimSalt/Theta
1178        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
1179    o pkg/seaice:
1180      - add missing initialisation of COR_ICE array in dynsolver.F
1181      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
1182        compiled either way, and is tested in all exps (multidim was only tested
1183        in lab_sea ad before).
1184      - cosmetic change to prepare for future addition of ITD. no change to results.
1185        no defaults change.
1186      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
1187      - by lack of adequate verification experiments, I further used custom versions
1188        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
1189        should be correct.
1190      - avoid recomputations in ad.
1191    o array initialisation in adjoint mode:
1192      1) pkg/mom_common/mom_calc_ke.F:
1193        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
1194        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
1195        part this initialisation is gone, resulting in Floating Point Exception
1196        (caught by open64 compiler with debug option).
1197      2) model/src/convective_weights.F
1198        set output convectCount over the full array range (instead of doing
1199        an update): this fix a similar issue when called within recomputation (adjoint)
1200        which could by-pass the initialisation (normally done in the caller S/R).
1201    o pkg/seaice:
1202      - final version of turbulent flux params, as agreed at MIT ice meet:
1203           SEAICE_mcPheePiston (default is ~ 0.000875)
1204           SEAICE_mcPheeTaper (default is 0.)
1205           SEAICE_frazilFrac (defualt is 1.)
1206           SEAICE_mcPheeStepFunc (default is false)
1207      - changes results at trunction error level
1208      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
1209    o added pkg/frazil:
1210      - see frazil_description.tex for details
1211      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
1212    o pkg/shelfice/shelfice_thermodynamics.F
1213      - fix exponents for velocity dependent exchange coefficients: change
1214        from 2/3(=0) to 0.66666666666666667
1215      - move computation of velocity dependent exchange coefficients into
1216        separate loop, so that it applies to both thermodynamics
1217      - move some divisions by constants out of loops
1218    
1219    checkpoint63j (2012/02/16)
1220    o pkg/seaice:
1221      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
1222      - SItracer:  added run time params, and allow coupling to ocn salinity.
1223    o pkg/seaice: remove (almost) all divisions by constants within loops
1224      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
1225      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
1226      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
1227      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
1228    o pkg/seaice :
1229      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
1230        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
1231    - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.    - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
1232    - add permanent SItflux diag that corresponds to TFLUX but includes    - add permanent SItflux diag that corresponds to TFLUX but includes
1233    ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
1234    - allow activation/testing of a fix for suspected missing term in    - allow activation/testing of a fix for suspected missing term in
1235    ocn-ice heat budget (to be confirmed). To test this, you want to      ocn-ice heat budget (to be confirmed). To test this, you want to
1236    undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
1237    SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
1238    - no change in results, fwd or ad.    - no change in results, fwd or ad.
1239  o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.  o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
1240    - switch to variable freezing point.    - switch to variable freezing point.
1241         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
1242    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
1243         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
1244    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
1245         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
1246  o pkg/seaice:  o pkg/seaice:
1247    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
1248   is now the default, and the old default constant freezing point is recovered with      is now the default, and the old default constant freezing point is recovered
1249   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
1250   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
1251    - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.    - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
1252    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
1253    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
1254   activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.      activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
1255    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
1256   was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).      was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
1257    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
1258   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
1259    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
1260    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
1261    to variable freezing point (see above item for detail).    - results did not change except for global_ocean.cs32x15, mostly due to the
1262        switch to variable freezing point (see above item for detail).
1263  o pkg/thsice:  o pkg/thsice:
1264    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
1265      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
1266  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
1267    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
1268    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
1269                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
1270    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
1271    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
1272    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
1273      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
1274      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
1275    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1276      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1277    - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).    - seaice_summary.F : add missing report of read turbulent flux term set up
1278    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
1279      - seaice_check.F : check range; inform and stop if retired CPPs are used
1280                         (incl. SEAICE_AGE).
1281    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1282          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
1283    - change results at the truncation level.    - change results at the truncation level.
1284  o pkg/seaice:  o pkg/seaice:
1285    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
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