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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1819 by mlosch, Wed Feb 6 10:19:34 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/layers: improve vectorization of layers_fluxcalc.F, step 1
8      - split loops, make TatU/V 2D arrays. This along reduces the cpu time spent
9        in this routine by more than a factor of 3 on an NEC-SX8
10    o pkg/ecco :
11      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
12    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
13      - modifications for ALLOW_GENTIM2D_CONTROL
14      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
15      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
16      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
17      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
18    o model/src:
19      - account for moist thermodynamics in (dry) potential temperature equation;
20        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
21        and cpl_aim+ocn.
22      - also switch to standard compiler (gfortran, was using ifort previously)
23        for fizhi-cs experiments reference output.
24    o pkg/ctrl:
25      - 1st step toward generic time-varying control variable (2D) via CPP option
26        ALLOW_GENTIM2D_CONTROL
27      - note new namelist ctrl_nml_genarr in data.ctrl
28    o verification/global_ocean.cs32x15:
29      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
30        thsice calling sequence and update "output.icedyn.txt" output file.
31    o pkg/ptracers:
32      - from Ryan A.: code to allow to restart a tracer at regular time interval
33        specifying a reset frequency and a reset-phase (for each tracers).
34    o pkg/thsice:
35      - implement new sequence of calls for thsice+seaice:
36          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
37          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
38      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
39        in CPP_OPTIONS.h) to recover old sequence;
40      - update diagnostics for Intermediate State thsice diagnostics: now filled
41        just before advection (instead of just after advection in old sequence);
42      - update output of experiment offline_exf_seaice (standard test);
43      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
44        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
45    o pkg/aim_v23:
46      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
47      - use standard pkg/mdsio routines to read & write CO2 pickup file;
48      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
49      - Implement new sequence of calls for seaice advection (with thsice and
50        seaice diffusion): do ice advection after ice-Thermodynamic (previously
51        was done before); change aim_do_physics.F (split the bi,bj loops block);
52      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
53    o pkg/thsice:
54      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
55        where just seaice diffusion is used without seaice-dynamics.
56    
57    checkpoint64c (2013/01/18)
58    o pkg/seaice:
59      - add a parameter JFNKres_tFac that can replace JFNKres_t
60        (= JFNKres_tFac*JFNKresidual before JFNK solver)
61      - add a line search option to the JFNK solver
62      - move update of u/vIce and computation of initial residual into a separate
63        routine (same file); makes the code a little easier to read (?)
64      - the line search requires computation of the residual and for some reason
65        I cannot do the update of u/vIce at the beginning of the Newton loop
66        without changing the results, so we move computation of the new residual
67        also to the end of the Newton loop, even without the line search
68    o pkg/mdsio:
69      - write missing value (corresponding to undefined array value) to meta files;
70        skip this if missing value is one (UNSET_RL would be a better value for the
71        case of undefined missing value but it's current the default missing-value);
72        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
73    o pkg/exf & thsice:
74      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
75        diagnostics) even when SHORTWAVE_HEATING is #undef;
76    o verification/cfc_example:
77      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
78        illustrate how to use it).
79    o verification/offline_exf_seaice:
80      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
81        files to only one time-record.
82      in input.thermo: narrow the 2 bands of low initial ice-concentration near
83        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
84        snapshot output; same mcPheePiston value as in thsice with
85        surf-current=0.2m/s.
86      in input.thsice: similar set-up as in input.thermo (channel with same seaice
87        initial conditions).
88    o verification/cfc_example:
89      - update file "data" with more standard choice (default rotationPeriod,
90        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
91        set deltaTFreeSurf to deltaTtracer) and update the output.
92    o pkg/layers:
93      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
94      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
95    o verification/offline_exf_seaice:
96      - set all {field}period to zero for constant-in-time forcing (not tested
97        anywhere else).
98    o verification/offline_exf_seaice:
99      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
100      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
101    o model/src:
102      - implement Finite-Volume method for (hydrostatic) presure gradient
103        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
104    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
105      - In order to be compatible with the default EVP code, this requires changing
106        the EVP code around a little; and because any small change immediately
107        breaks the lab_sea.hb87 verification experiment, the reference output is
108        updated two times (each time the remaining aggrement was only 2 digits):
109        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
110        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
111        The adjoint test lab_sea.evp also needed to be updated.
112      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
113        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
114        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
115        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
116        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
117        kept obscure, because I need to test it a little more.
118    o pkg/cheapaml:
119      - fix few incorrect type (_RL/_RS) in subroutine calls.
120    o pkg/seaice:
121      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
122        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
123    o model/src:
124      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
125        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
126        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
127    o pkg/cheapaml:
128      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
129        update output of experiment cheapAML_box.
130      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
131        and set them only in one place (cheapaml_readparms.F).
132      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
133      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
134        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
135    o model/src/the_main_loop.F:
136      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
137    o pkg/seaice:
138      - remove legacy branch code.
139      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
140    o verification/*/code*/SEAICE_OPTIONS.h:
141      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
142        SEAICE_CAP_HEFF).
143    o pkg/cheapaml:
144      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
145        to load new forcing fields.
146      - add missing "_d 0" where it's needed; + some editing (improve indentation).
147      - remove switch to "-r8" compiler option (no longer needed) in verification
148        cheapAML_box, keep same output (small trucation error differences).
149    o verification/offline_exf_seaice:
150      - add thermodynamics only test.
151    o verification/cheapAML_box:
152      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
153        keep same output (same 14 digits for cg2d).
154      - switch on "-r8" compiler option (some numerical values are missing
155        the "_d 0") and update output (only 6 digits for cg2d were preserved).
156    
157    checkpoint64b (2012/12/24)
158    o pkg/cheapaml:
159      - remove un-used variables (Qnet,EmPmR) from pickup files.
160      - store tendency of advected variables into cheapaml pickup file
161        and fix the AB-2 restart.
162    o verification/offline_exf_seaice and lab_sea adjoint:
163      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
164      - switch to 4 time steps in offline, consistent with lab_sea.
165      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
166      - update results after change of experiment seaice.
167    o pkg/seaice:
168      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
169        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
170        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
171        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
172    o model/src:
173      - add run-time parameter to select CG2D solver minimum-residual solution
174        (in case of a poor convergence).
175    o pkg/seaice/seaice_lsr.F
176      - move calculation of matrix coefficients into new
177        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
178        file; the main purpose of this change is to be able to reuse the code
179        in S/R SEAICE_PRECONDITIONER
180      - modify the computation of the residual so that the mass of sea-ice
181        is not used twice; this simplifies the calculations, but since
182        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
183        not tested in testreport---this does not affect the testreport results.
184    o verification/seaice_obcs:
185      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
186        verification/lab_sea/input.salt_plume; changes results/output.txt*
187    o model/src:
188      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
189    o pkg/seaice:
190      - improve description of parameters in seaice_fgmres.F and start
191        cleaning up the code
192      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
193        second argument
194      - add a metric based on grid cell area to SEAICE_SCALPROD; update
195        results of offline_exf_seaice.dyn_jfnk
196      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
197    o pkg/aim_v23:
198      - fix an other bug in dissipation heating (grid-cell area was missing).
199    o model/src + pkg/seaice:
200      - add global (multi-tile) linear solver for pair of tri-diagonal system
201        along X and Y lines, respectively for U and V component.
202        Note: 1) MPI and cube-exchange not yet coded.
203            2) probably not accurate for poorly conditioned / large size problem.
204      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
205        default: not compiled and not used.
206    o pkg/seaice:
207      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
208        introduce bi/bj loops and use global_sum_tile_rl instead of
209        mpi_allreduce in seaice_fgmres.F
210      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
211      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
212      - add a verification experiment for JFNK in offline_exf_seaice
213    o verification:
214      - change (for now, only fwd test) offline_exf_seaice experiment:
215        use a re-entrant channel with idealized coastline (trapezoidal shape)
216        at southern boundary to explore seaice dynamics and thermodynamics
217        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
218        secondary test (input.thsice) use thermodynamics only with SST relaxation.
219      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
220    o pkg/exf:
221      - disable "sstExtrapol" when Nr=1
222    o verification:
223      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
224        to test pkg/cheapaml.
225    o pkg/aim_v23 & pkg/shap_filt:
226      - fix dissipation heating (erroneous gravity multiplication factor).
227    o pkg/seaice:
228      - remove unused field pressPre from jfnk solver
229      - rename two subroutines in seaice_preconditioner.F
230    o eesupp/src:
231       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
232    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
233       - remove wrong parts of the rhs and the lhs (were in there
234         because I did not understand the concept of this preconditioner)
235       - add an exchange between u- and v-sweep. This increases communication
236         by a factor of two but improves the convergence of jfnk. Ideally,
237         one would like the u- and v-sweep to be independent. So far within
238         undocumented ifdefs
239       - reorganize the extra computations for printing the residuals
240    o tools/genmake2:
241      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
242        since it's not necessary (and was preventing to use MNC in some cases).
243    
244    checkpoint64a (2012/11/16)
245    o pkg/autodiff:
246      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
247        autodiff_readparms.F no longer depends on calling order (within
248        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
249        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
250        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
251    o pkg/obcs:
252      - adding tidal velocity forcing capability to obcs
253        for usage example, see verification/seaice_obcs/input.tides
254    o pkg/seaice:
255      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
256        SEAICE_LSRrelaxU/V
257      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
258    o pkg/aim_v23:
259      - implement heating from friction (bottom friction and stratospheric drag).
260    o pkg/shap_filt:
261      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
262        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
263    o model/src:
264      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
265        time-constant addMass field from file (addMassFile);
266      - support for heating due to friction (and Kinetic Energy dissipation):
267        add option, run-time switch and 3-D field array + support code ; each pkg
268        or S/R can add heating contribution (if there is a sink of KE); the sum is
269        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
270    o pkg/seaice:
271      - complete merge of ITD code into seaice_growth.F
272        from MITgcm_contrib/torge/itd/code/
273        no verification so far, but Torge Martin tested
274        "1-D test case and Beaufort set up;
275        deliver okay results after 1 model year."
276      - complete merge of SEAICE_SIZE.h into all relevant routines
277      - move computation of eta at Z-points into calc_viscosities
278        + introduce global field etaZ
279        + add different methods for computing etaZ, for now the old
280          method (simple averages of eta to Z-points) is hardwired
281        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
282          seaice_preconditioner
283      - simplify computations for SEAICE_ZETA_SMOOTHREG
284      - seaice_preconditioner:
285        + replace one remaining press by pressLoc (mistake)
286        + adjust printing of residuals
287      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
288        + add (SEAICE.h) and rename some counters (initiliased in
289          seaice_init_fixed.F)
290        + add _BEGIN/END_MASTER (myThid)  around print statements
291        + print total number of iterations and failures over SEAICE_monFreq
292          interval to STDOUT
293      - move control over output-messages by fgmres to seaice_jfnk to save
294        some operations
295      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
296        in order to make restarts with sol .ne. zero (fgmres with restarts)
297        (seaice_jfnk.F, seaice_fgmres.F)
298      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
299        a serious convergence problem when open boundaries are involved
300    o pkg/ggl90: fix computation of control volumes for the case of
301      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
302      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
303    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
304    o pkg/autodiff
305      - Add inAdMode switch for SEAICEuseDYNAMICS:
306        SEAICEuseDYNAMICSinAdMode
307        (extend logic in ADAUTODIFF_INADMODE_SET)
308    o pkg/seaice
309      - Step 1 of merging ice-thickness distribution (ITD) code from
310        MITgcm_contrib/torge/itd/ (author: Torge Martin)
311        The code implements concept laid out in Thorndike et al. (1975);
312        code is enabled via CPP flag SEAICE_ITD
313        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
314        code is not complete yet!!
315      - SEAICE_SIZE.h now included in almost all seaice routines
316    o verification (using seaice):
317      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
318        global_ocean.cs32x15.seaice ; update results.
319      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
320      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
321        offline_exf_seaice (previously compiling B-grid).
322    o pkg/exf:
323      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
324        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
325        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
326    o pkg/layers (adjust changes from Sept 19):
327      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
328        this allows to remove "layers_maxNum" dimension from all layers arrays.
329    o pkg/layers (adjust changes from Sept 19):
330      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
331      - snap-shot extended to all type of layers (not just the 1rst type);
332      - remove layers variables when corresponding CPP option is undef.
333    o pkg/layers:
334      - rename pkg/layers variable and add new output (layer exist & un-weighted
335        velocity in layer)
336    o pkg/seaice:
337      - simplify (?) ocean-drag coefficent computations by using
338        the same routine in all three solvers (saves some code lines)
339      - remove global fields DRAGA and DRAGS from C-grid code and
340        declare them locally in lsr.F (the only place where they are
341        still used)
342      - update AD output of lab_sea.evp (very sensitive anyway).
343    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
344      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
345      and SEAICEuseJFNK=.true. A few things to note:
346      - involves a FGMRES, that is parallel but very inefficient,
347        because of many scalar products (global sums) in the Gram-Schmidt
348        orthogonalization method. Needs to be replaced. Original code
349        from J.-F. Lemieux
350      - preconditioner for FGMRES is a stripped down version of LSOR
351      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
352        preconditioner. For the preconditioner, the default is set to 10.
353      - Jacobian times vector is computed with finite differences
354      - marginally related to JFNK-solver: add a smooth regularization for
355        zeta with tanh that will improve convergence (Lemieux and Tremblay,
356        2009) for any implicit solver (not implemented for EVP because EVP
357        does not need this regularization in the first place). Define
358        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
359    o eesupp/src:
360      - check in genmake2 that intrinsic S/R flush is available.
361      - add S/R to flush IO unit (if intrinsic S/R flush is available)
362      - flush standard & error msg unit before MPI termination
363      - if debugMode, flush IO unit after printing msg
364    o pkg/ctrl:
365      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
366        to ctrl_set_unpack_xyz.
367    
368    checkpoint64 (2012/10/09)
369    o pkg/shelfice
370      - in mom_fluxform.F, mom_vecinv.F:
371        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
372        Bug fix KappaRU -> KappaRV
373        does not change verification/isomip but may change other setups
374        (presumably constant KappaRU=KappaRV)
375      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
376    o pkg/obcs:
377      - fixed some indexing bugs in obcs_seaice_sponge.F
378      - added obcs relaxation subroutines for HSALT and HSNOW
379      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
380    o pkg/seaice:
381      - add "multicategory" parameterization for snow in analogy to ice,
382        default is off for now.
383    o pkg/obcs:
384      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
385        see verification/seaice_obcs/input.seaiceSponge for example application.
386      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
387        index setting by master-thread. This fix multi-threads Pb in previous modifs.
388    o pkg/layers :
389      - add diagnostics to pkg/layers
390      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
391        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
392    o pkg/generic_advdiff/gad_implicit_r.F :
393      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
394    o pkg/seaice/seaice_growth.F:
395      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
396    o pkg/obcs:
397      - change default setting of OBCS_UVICE_OLD from defined to undef;
398      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
399        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
400      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
401      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
402        with Southern & Western OB at a tile edge (at least in a simple set-up).
403    o pkg/obcs:
404      - change settings of OB index in case OB coincides with tile edge (shared by
405        2 tiles), so that common OB location is registered by both tiles (instead of
406        only 1). However, for Southern and Western OB, index value = 0 is not
407        recognized as valid OB index (=default null value) and needs to be fixed.
408      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
409      - new parameter "OB_indexNone" for null index value (for now, still zero)
410        to replace hard-coded null index value of zero.
411    o pkg/exch2:
412      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
413        always check buffer-size (but outside the loop); move checking for valid
414        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
415        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
416    o pkg/ctrl (pack & unpack):
417      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
418        (locally defined) for different variables (+ remove the variable-specific
419        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
420        (to be extended to other local file names in ctrl.h).
421    o pkg/flt:
422      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
423    o pkg/mdsio:
424      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
425    o tools/genmake2:
426      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
427        (added by Alistair in version 1.51 for building without make depend);
428      - remove Header files list (H_SRC_FILES) from the dependence of targets
429         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
430        place in version 1.23): this save going through staf when unrelated header
431        file has been modified.
432       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
433        "make depend" step, still need to do "make links" before "make adtaf".
434    o eesupp/src (+ few pkg src files) & genmake2:
435      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
436      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
437      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
438         upper/lower case ; account for space between "#" and undef/define)
439    o pkg/flt (with exch2):
440      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
441      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
442    
443    checkpoint63s (2012/09/05)
444    o pkg/ecco:
445      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
446      - add more relevant #ifdef ALLOW_SMOOTH ones.
447      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
448    o pkg/ctrl:
449      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
450        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
451      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
452        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
453        ctrlSmoothCorrel3D (new).
454        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
455      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
456      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
457        controls when useAtmWind, and vice versa.
458      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
459      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
460          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
461      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
462          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
463      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
464        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
465    o pkg/smooth:
466      - remove un-necessary includes.
467      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
468        Those CPP options were never defined, and not necessary.
469    o model/src:
470      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
471      - standard treatment of useSMOOTH.
472    o pkg/autodiff:
473      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
474        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
475    o pkg/exch2:
476      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
477        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
478      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
479        and tiles to process mapping.
480      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
481        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
482        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
483        from w2_eeboot.F to w2_readparms.F.
484    o eesupp/src:
485      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
486        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
487        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
488      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
489        is defined (remove condition on usingMPI) to match cases where MPI_INIT
490        has been called.
491      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
492      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
493        (so that on 1 proc, get same myPid independently of usingMPI)
494      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
495        useCubedSphereExchange with EXCH-1 (safer).
496      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
497    o pkg/ggl90:
498      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
499        used in ALLOW_GGL90_SMOOTH code.
500    o pkg/flt:
501      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
502        floats at the Southern end of the domain).
503    o eesupp/inc:
504      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
505        but not used (and not to be used) anywhere, just for documentation.
506    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
507      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
508        a) can damage previously written records in any other multi-record files.
509        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
510  o tools/genmake2:  o tools/genmake2:
511    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
512    - update AD_CONFIG.h (if needed) before building any of the executable    - update AD_CONFIG.h (if needed) before building any of the executable
# Line 11  o tools/genmake2: Line 514  o tools/genmake2:
514      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
515    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
516      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
517    o pkg/cheapaml:
518      - updated to correspond to the code used in accepted paper (Nico Wienders).
519  o pkg/exf:  o pkg/exf:
520      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
521      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
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