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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1814 by jmc, Wed Jan 23 17:12:35 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 verification/global_ocean.cs32x15:
8      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
9        thsice calling sequence and update "output.icedyn.txt" output file.
10    o pkg/ptracers:
11      - from Ryan A.: code to allow to restart a tracer at regular time interval
12        specifying a reset frequency and a reset-phase (for each tracers).
13    o pkg/thsice:
14      - implement new sequence of calls for thsice+seaice:
15          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
16          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
17      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
18        in CPP_OPTIONS.h) to recover old sequence;
19      - update diagnostics for Intermediate State thsice diagnostics: now filled
20        just before advection (instead of just after advection in old sequence);
21      - update output of experiment offline_exf_seaice (standard test);
22      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
23        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
24    o pkg/aim_v23:
25      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
26      - use standard pkg/mdsio routines to read & write CO2 pickup file;
27      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
28      - Implement new sequence of calls for seaice advection (with thsice and
29        seaice diffusion): do ice advection after ice-Thermodynamic (previously
30        was done before); change aim_do_physics.F (split the bi,bj loops block);
31      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
32    o pkg/thsice:
33      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
34        where just seaice diffusion is used without seaice-dynamics.
35    
36    checkpoint64c (2013/01/18)
37    o pkg/seaice:
38      - add a parameter JFNKres_tFac that can replace JFNKres_t
39        (= JFNKres_tFac*JFNKresidual before JFNK solver)
40      - add a line search option to the JFNK solver
41      - move update of u/vIce and computation of initial residual into a separate
42        routine (same file); makes the code a little easier to read (?)
43      - the line search requires computation of the residual and for some reason
44        I cannot do the update of u/vIce at the beginning of the Newton loop
45        without changing the results, so we move computation of the new residual
46        also to the end of the Newton loop, even without the line search
47    o pkg/mdsio:
48      - write missing value (corresponding to undefined array value) to meta files;
49        skip this if missing value is one (UNSET_RL would be a better value for the
50        case of undefined missing value but it's current the default missing-value);
51        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
52    o pkg/exf & thsice:
53      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
54        diagnostics) even when SHORTWAVE_HEATING is #undef;
55    o verification/cfc_example:
56      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
57        illustrate how to use it).
58    o verification/offline_exf_seaice:
59      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
60        files to only one time-record.
61      in input.thermo: narrow the 2 bands of low initial ice-concentration near
62        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
63        snapshot output; same mcPheePiston value as in thsice with
64        surf-current=0.2m/s.
65      in input.thsice: similar set-up as in input.thermo (channel with same seaice
66        initial conditions).
67    o verification/cfc_example:
68      - update file "data" with more standard choice (default rotationPeriod,
69        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
70        set deltaTFreeSurf to deltaTtracer) and update the output.
71    o pkg/layers:
72      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
73      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
74    o verification/offline_exf_seaice:
75      - set all {field}period to zero for constant-in-time forcing (not tested
76        anywhere else).
77    o verification/offline_exf_seaice:
78      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
79      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
80    o model/src:
81      - implement Finite-Volume method for (hydrostatic) presure gradient
82        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
83    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
84      - In order to be compatible with the default EVP code, this requires changing
85        the EVP code around a little; and because any small change immediately
86        breaks the lab_sea.hb87 verification experiment, the reference output is
87        updated two times (each time the remaining aggrement was only 2 digits):
88        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
89        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
90        The adjoint test lab_sea.evp also needed to be updated.
91      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
92        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
93        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
94        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
95        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
96        kept obscure, because I need to test it a little more.
97    o pkg/cheapaml:
98      - fix few incorrect type (_RL/_RS) in subroutine calls.
99    o pkg/seaice:
100      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
101        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
102    o model/src:
103      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
104        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
105        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
106    o pkg/cheapaml:
107      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
108        update output of experiment cheapAML_box.
109      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
110        and set them only in one place (cheapaml_readparms.F).
111      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
112      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
113        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
114    o model/src/the_main_loop.F:
115      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
116    o pkg/seaice:
117      - remove legacy branch code.
118      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
119    o verification/*/code*/SEAICE_OPTIONS.h:
120      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
121        SEAICE_CAP_HEFF).
122    o pkg/cheapaml:
123      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
124        to load new forcing fields.
125      - add missing "_d 0" where it's needed; + some editing (improve indentation).
126      - remove switch to "-r8" compiler option (no longer needed) in verification
127        cheapAML_box, keep same output (small trucation error differences).
128    o verification/offline_exf_seaice:
129      - add thermodynamics only test.
130    o verification/cheapAML_box:
131      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
132        keep same output (same 14 digits for cg2d).
133      - switch on "-r8" compiler option (some numerical values are missing
134        the "_d 0") and update output (only 6 digits for cg2d were preserved).
135    
136    checkpoint64b (2012/12/24)
137    o pkg/cheapaml:
138      - remove un-used variables (Qnet,EmPmR) from pickup files.
139      - store tendency of advected variables into cheapaml pickup file
140        and fix the AB-2 restart.
141    o verification/offline_exf_seaice and lab_sea adjoint:
142      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
143      - switch to 4 time steps in offline, consistent with lab_sea.
144      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
145      - update results after change of experiment seaice.
146    o pkg/seaice:
147      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
148        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
149        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
150        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
151    o model/src:
152      - add run-time parameter to select CG2D solver minimum-residual solution
153        (in case of a poor convergence).
154    o pkg/seaice/seaice_lsr.F
155      - move calculation of matrix coefficients into new
156        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
157        file; the main purpose of this change is to be able to reuse the code
158        in S/R SEAICE_PRECONDITIONER
159      - modify the computation of the residual so that the mass of sea-ice
160        is not used twice; this simplifies the calculations, but since
161        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
162        not tested in testreport---this does not affect the testreport results.
163    o verification/seaice_obcs:
164      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
165        verification/lab_sea/input.salt_plume; changes results/output.txt*
166    o model/src:
167      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
168    o pkg/seaice:
169      - improve description of parameters in seaice_fgmres.F and start
170        cleaning up the code
171      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
172        second argument
173      - add a metric based on grid cell area to SEAICE_SCALPROD; update
174        results of offline_exf_seaice.dyn_jfnk
175      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
176    o pkg/aim_v23:
177      - fix an other bug in dissipation heating (grid-cell area was missing).
178    o model/src + pkg/seaice:
179      - add global (multi-tile) linear solver for pair of tri-diagonal system
180        along X and Y lines, respectively for U and V component.
181        Note: 1) MPI and cube-exchange not yet coded.
182            2) probably not accurate for poorly conditioned / large size problem.
183      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
184        default: not compiled and not used.
185    o pkg/seaice:
186      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
187        introduce bi/bj loops and use global_sum_tile_rl instead of
188        mpi_allreduce in seaice_fgmres.F
189      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
190      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
191      - add a verification experiment for JFNK in offline_exf_seaice
192    o verification:
193      - change (for now, only fwd test) offline_exf_seaice experiment:
194        use a re-entrant channel with idealized coastline (trapezoidal shape)
195        at southern boundary to explore seaice dynamics and thermodynamics
196        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
197        secondary test (input.thsice) use thermodynamics only with SST relaxation.
198      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
199    o pkg/exf:
200      - disable "sstExtrapol" when Nr=1
201    o verification:
202      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
203        to test pkg/cheapaml.
204    o pkg/aim_v23 & pkg/shap_filt:
205      - fix dissipation heating (erroneous gravity multiplication factor).
206    o pkg/seaice:
207      - remove unused field pressPre from jfnk solver
208      - rename two subroutines in seaice_preconditioner.F
209    o eesupp/src:
210       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
211    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
212       - remove wrong parts of the rhs and the lhs (were in there
213         because I did not understand the concept of this preconditioner)
214       - add an exchange between u- and v-sweep. This increases communication
215         by a factor of two but improves the convergence of jfnk. Ideally,
216         one would like the u- and v-sweep to be independent. So far within
217         undocumented ifdefs
218       - reorganize the extra computations for printing the residuals
219    o tools/genmake2:
220      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
221        since it's not necessary (and was preventing to use MNC in some cases).
222    
223    checkpoint64a (2012/11/16)
224    o pkg/autodiff:
225      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
226        autodiff_readparms.F no longer depends on calling order (within
227        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
228        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
229        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
230    o pkg/obcs:
231      - adding tidal velocity forcing capability to obcs
232        for usage example, see verification/seaice_obcs/input.tides
233    o pkg/seaice:
234      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
235        SEAICE_LSRrelaxU/V
236      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
237    o pkg/aim_v23:
238      - implement heating from friction (bottom friction and stratospheric drag).
239    o pkg/shap_filt:
240      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
241        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
242    o model/src:
243      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
244        time-constant addMass field from file (addMassFile);
245      - support for heating due to friction (and Kinetic Energy dissipation):
246        add option, run-time switch and 3-D field array + support code ; each pkg
247        or S/R can add heating contribution (if there is a sink of KE); the sum is
248        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
249    o pkg/seaice:
250      - complete merge of ITD code into seaice_growth.F
251        from MITgcm_contrib/torge/itd/code/
252        no verification so far, but Torge Martin tested
253        "1-D test case and Beaufort set up;
254        deliver okay results after 1 model year."
255      - complete merge of SEAICE_SIZE.h into all relevant routines
256      - move computation of eta at Z-points into calc_viscosities
257        + introduce global field etaZ
258        + add different methods for computing etaZ, for now the old
259          method (simple averages of eta to Z-points) is hardwired
260        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
261          seaice_preconditioner
262      - simplify computations for SEAICE_ZETA_SMOOTHREG
263      - seaice_preconditioner:
264        + replace one remaining press by pressLoc (mistake)
265        + adjust printing of residuals
266      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
267        + add (SEAICE.h) and rename some counters (initiliased in
268          seaice_init_fixed.F)
269        + add _BEGIN/END_MASTER (myThid)  around print statements
270        + print total number of iterations and failures over SEAICE_monFreq
271          interval to STDOUT
272      - move control over output-messages by fgmres to seaice_jfnk to save
273        some operations
274      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
275        in order to make restarts with sol .ne. zero (fgmres with restarts)
276        (seaice_jfnk.F, seaice_fgmres.F)
277      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
278        a serious convergence problem when open boundaries are involved
279    o pkg/ggl90: fix computation of control volumes for the case of
280      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
281      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
282    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
283    o pkg/autodiff
284      - Add inAdMode switch for SEAICEuseDYNAMICS:
285        SEAICEuseDYNAMICSinAdMode
286        (extend logic in ADAUTODIFF_INADMODE_SET)
287    o pkg/seaice
288      - Step 1 of merging ice-thickness distribution (ITD) code from
289        MITgcm_contrib/torge/itd/ (author: Torge Martin)
290        The code implements concept laid out in Thorndike et al. (1975);
291        code is enabled via CPP flag SEAICE_ITD
292        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
293        code is not complete yet!!
294      - SEAICE_SIZE.h now included in almost all seaice routines
295    o verification (using seaice):
296      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
297        global_ocean.cs32x15.seaice ; update results.
298      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
299      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
300        offline_exf_seaice (previously compiling B-grid).
301    o pkg/exf:
302      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
303        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
304        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
305    o pkg/layers (adjust changes from Sept 19):
306      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
307        this allows to remove "layers_maxNum" dimension from all layers arrays.
308    o pkg/layers (adjust changes from Sept 19):
309      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
310      - snap-shot extended to all type of layers (not just the 1rst type);
311      - remove layers variables when corresponding CPP option is undef.
312    o pkg/layers:
313      - rename pkg/layers variable and add new output (layer exist & un-weighted
314        velocity in layer)
315    o pkg/seaice:
316      - simplify (?) ocean-drag coefficent computations by using
317        the same routine in all three solvers (saves some code lines)
318      - remove global fields DRAGA and DRAGS from C-grid code and
319        declare them locally in lsr.F (the only place where they are
320        still used)
321      - update AD output of lab_sea.evp (very sensitive anyway).
322    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
323      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
324      and SEAICEuseJFNK=.true. A few things to note:
325      - involves a FGMRES, that is parallel but very inefficient,
326        because of many scalar products (global sums) in the Gram-Schmidt
327        orthogonalization method. Needs to be replaced. Original code
328        from J.-F. Lemieux
329      - preconditioner for FGMRES is a stripped down version of LSOR
330      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
331        preconditioner. For the preconditioner, the default is set to 10.
332      - Jacobian times vector is computed with finite differences
333      - marginally related to JFNK-solver: add a smooth regularization for
334        zeta with tanh that will improve convergence (Lemieux and Tremblay,
335        2009) for any implicit solver (not implemented for EVP because EVP
336        does not need this regularization in the first place). Define
337        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
338    o eesupp/src:
339      - check in genmake2 that intrinsic S/R flush is available.
340      - add S/R to flush IO unit (if intrinsic S/R flush is available)
341      - flush standard & error msg unit before MPI termination
342      - if debugMode, flush IO unit after printing msg
343    o pkg/ctrl:
344      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
345        to ctrl_set_unpack_xyz.
346    
347    checkpoint64 (2012/10/09)
348    o pkg/shelfice
349      - in mom_fluxform.F, mom_vecinv.F:
350        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
351        Bug fix KappaRU -> KappaRV
352        does not change verification/isomip but may change other setups
353        (presumably constant KappaRU=KappaRV)
354      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
355    o pkg/obcs:
356      - fixed some indexing bugs in obcs_seaice_sponge.F
357      - added obcs relaxation subroutines for HSALT and HSNOW
358      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
359    o pkg/seaice:
360      - add "multicategory" parameterization for snow in analogy to ice,
361        default is off for now.
362    o pkg/obcs:
363      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
364        see verification/seaice_obcs/input.seaiceSponge for example application.
365      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
366        index setting by master-thread. This fix multi-threads Pb in previous modifs.
367    o pkg/layers :
368      - add diagnostics to pkg/layers
369      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
370        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
371    o pkg/generic_advdiff/gad_implicit_r.F :
372      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
373    o pkg/seaice/seaice_growth.F:
374      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
375    o pkg/obcs:
376      - change default setting of OBCS_UVICE_OLD from defined to undef;
377      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
378        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
379      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
380      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
381        with Southern & Western OB at a tile edge (at least in a simple set-up).
382    o pkg/obcs:
383      - change settings of OB index in case OB coincides with tile edge (shared by
384        2 tiles), so that common OB location is registered by both tiles (instead of
385        only 1). However, for Southern and Western OB, index value = 0 is not
386        recognized as valid OB index (=default null value) and needs to be fixed.
387      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
388      - new parameter "OB_indexNone" for null index value (for now, still zero)
389        to replace hard-coded null index value of zero.
390    o pkg/exch2:
391      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
392        always check buffer-size (but outside the loop); move checking for valid
393        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
394        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
395    o pkg/ctrl (pack & unpack):
396      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
397        (locally defined) for different variables (+ remove the variable-specific
398        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
399        (to be extended to other local file names in ctrl.h).
400    o pkg/flt:
401      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
402    o pkg/mdsio:
403      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
404    o tools/genmake2:
405      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
406        (added by Alistair in version 1.51 for building without make depend);
407      - remove Header files list (H_SRC_FILES) from the dependence of targets
408         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
409        place in version 1.23): this save going through staf when unrelated header
410        file has been modified.
411       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
412        "make depend" step, still need to do "make links" before "make adtaf".
413    o eesupp/src (+ few pkg src files) & genmake2:
414      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
415      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
416      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
417         upper/lower case ; account for space between "#" and undef/define)
418    o pkg/flt (with exch2):
419      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
420      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
421    
422    checkpoint63s (2012/09/05)
423    o pkg/ecco:
424      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
425      - add more relevant #ifdef ALLOW_SMOOTH ones.
426      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
427    o pkg/ctrl:
428      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
429        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
430      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
431        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
432        ctrlSmoothCorrel3D (new).
433        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
434      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
435      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
436        controls when useAtmWind, and vice versa.
437      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
438      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
439          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
440      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
441          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
442      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
443        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
444    o pkg/smooth:
445      - remove un-necessary includes.
446      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
447        Those CPP options were never defined, and not necessary.
448    o model/src:
449      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
450      - standard treatment of useSMOOTH.
451    o pkg/autodiff:
452      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
453        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
454    o pkg/exch2:
455      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
456        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
457      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
458        and tiles to process mapping.
459      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
460        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
461        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
462        from w2_eeboot.F to w2_readparms.F.
463    o eesupp/src:
464      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
465        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
466        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
467      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
468        is defined (remove condition on usingMPI) to match cases where MPI_INIT
469        has been called.
470      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
471      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
472        (so that on 1 proc, get same myPid independently of usingMPI)
473      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
474        useCubedSphereExchange with EXCH-1 (safer).
475      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
476    o pkg/ggl90:
477      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
478        used in ALLOW_GGL90_SMOOTH code.
479    o pkg/flt:
480      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
481        floats at the Southern end of the domain).
482    o eesupp/inc:
483      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
484        but not used (and not to be used) anywhere, just for documentation.
485    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
486      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
487        a) can damage previously written records in any other multi-record files.
488        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
489  o tools/genmake2:  o tools/genmake2:
490    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
491    - 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 493  o tools/genmake2:
493      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;
494    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
495      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
496    o pkg/cheapaml:
497      - updated to correspond to the code used in accepted paper (Nico Wienders).
498  o pkg/exf:  o pkg/exf:
499      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
500      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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