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revision 1.1641 by dimitri, Mon Apr 2 04:34:07 2012 UTC revision 1.1807 by mlosch, Wed Jan 16 21:20:56 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: add a line search option to the JFNK solver
8    o pkg/mdsio:
9      - write missing value (corresponding to undefined array value) to meta files;
10        skip this if missing value is one (UNSET_RL would be a better value for the
11        case of undefined missing value but it's current the default missing-value);
12        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
13    o pkg/exf & thsice:
14      - for diagnostics purpose, fill-up and update Qsw array (+ fill the diagnostics)
15        even when SHORTWAVE_HEATING is #undef;
16    o verification/cfc_example:
17      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to illustrate
18        how to use it).
19    o verification/offline_exf_seaice:
20      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
21        files to only one time-record.
22      in input.thermo: narrow the 2 bands of low initial ice-concentration near
23        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
24        snapshot output; same mcPheePiston value as in thsice with surf-current=0.2m/s.
25      in input.thsice: similar set-up as in input.thermo (channel with same seaice
26        initial conditions).
27    o verification/cfc_example:
28      - update file "data" with more standard choice (default rotationPeriod,
29        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
30        set deltaTFreeSurf to deltaTtracer) and update the output.
31    o pkg/layers:
32      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
33      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
34    o verification/offline_exf_seaice:
35      - set all {field}period to zero for constant-in-time forcing (not tested
36        anywhere else).
37    o verification/offline_exf_seaice:
38      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
39      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
40    o model/src:
41      - implement Finite-Volume method for (hydrostatic) presure gradient
42        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
43    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
44      - In order to be compatible with the default EVP code, this requires changing
45        the EVP code around a little; and because any small change immediately
46        breaks the lab_sea.hb87 verification experiment, the reference output is
47        updated two times (each time the remaining aggrement was only 2 digits):
48        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
49        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
50        The adjoint test lab_sea.evp also needed to be updated.
51      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
52        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
53        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
54        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
55        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
56        kept obscure, because I need to test it a little more.
57    o pkg/cheapaml:
58      - fix few incorrect type (_RL/_RS) in subroutine calls.
59    o pkg/seaice:
60      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
61        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
62    o model/src:
63      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
64        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
65        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
66    o pkg/cheapaml:
67      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
68        update output of experiment cheapAML_box.
69      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
70        and set them only in one place (cheapaml_readparms.F).
71      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
72      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
73        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
74    o model/src/the_main_loop.F:
75      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
76    o pkg/seaice:
77      - remove legacy branch code.
78      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
79    o verification/*/code*/SEAICE_OPTIONS.h:
80      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
81        SEAICE_CAP_HEFF).
82    o pkg/cheapaml:
83      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
84        to load new forcing fields.
85      - add missing "_d 0" where it's needed; + some editing (improve indentation).
86      - remove switch to "-r8" compiler option (no longer needed) in verification
87        cheapAML_box, keep same output (small trucation error differences).
88    o verification/offline_exf_seaice:
89      - add thermodynamics only test.
90    o verification/cheapAML_box:
91      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
92        keep same output (same 14 digits for cg2d).
93      - switch on "-r8" compiler option (some numerical values are missing
94        the "_d 0") and update output (only 6 digits for cg2d were preserved).
95    
96    checkpoint64b (2012/12/24)
97    o pkg/cheapaml:
98      - remove un-used variables (Qnet,EmPmR) from pickup files.
99      - store tendency of advected variables into cheapaml pickup file
100        and fix the AB-2 restart.
101    o verification/offline_exf_seaice and lab_sea adjoint:
102      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
103      - switch to 4 time steps in offline, consistent with lab_sea.
104      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
105      - update results after change of experiment seaice.
106    o pkg/seaice:
107      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
108        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
109        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
110        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
111    o model/src:
112      - add run-time parameter to select CG2D solver minimum-residual solution
113        (in case of a poor convergence).
114    o pkg/seaice/seaice_lsr.F
115      - move calculation of matrix coefficients into new
116        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
117        file; the main purpose of this change is to be able to reuse the code
118        in S/R SEAICE_PRECONDITIONER
119      - modify the computation of the residual so that the mass of sea-ice
120        is not used twice; this simplifies the calculations, but since
121        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
122        not tested in testreport---this does not affect the testreport results.
123    o verification/seaice_obcs:
124      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
125        verification/lab_sea/input.salt_plume; changes results/output.txt*
126    o model/src:
127      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
128    o pkg/seaice:
129      - improve description of parameters in seaice_fgmres.F and start
130        cleaning up the code
131      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
132        second argument
133      - add a metric based on grid cell area to SEAICE_SCALPROD; update
134        results of offline_exf_seaice.dyn_jfnk
135      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
136    o pkg/aim_v23:
137      - fix an other bug in dissipation heating (grid-cell area was missing).
138    o model/src + pkg/seaice:
139      - add global (multi-tile) linear solver for pair of tri-diagonal system
140        along X and Y lines, respectively for U and V component.
141        Note: 1) MPI and cube-exchange not yet coded.
142            2) probably not accurate for poorly conditioned / large size problem.
143      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
144        default: not compiled and not used.
145    o pkg/seaice:
146      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
147        introduce bi/bj loops and use global_sum_tile_rl instead of
148        mpi_allreduce in seaice_fgmres.F
149      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
150      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
151      - add a verification experiment for JFNK in offline_exf_seaice
152    o verification:
153      - change (for now, only fwd test) offline_exf_seaice experiment:
154        use a re-entrant channel with idealized coastline (trapezoidal shape)
155        at southern boundary to explore seaice dynamics and thermodynamics
156        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
157        secondary test (input.thsice) use thermodynamics only with SST relaxation.
158      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
159    o pkg/exf:
160      - disable "sstExtrapol" when Nr=1
161    o verification:
162      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
163        to test pkg/cheapaml.
164    o pkg/aim_v23 & pkg/shap_filt:
165      - fix dissipation heating (erroneous gravity multiplication factor).
166    o pkg/seaice:
167      - remove unused field pressPre from jfnk solver
168      - rename two subroutines in seaice_preconditioner.F
169    o eesupp/src:
170       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
171    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
172       - remove wrong parts of the rhs and the lhs (were in there
173         because I did not understand the concept of this preconditioner)
174       - add an exchange between u- and v-sweep. This increases communication
175         by a factor of two but improves the convergence of jfnk. Ideally,
176         one would like the u- and v-sweep to be independent. So far within
177         undocumented ifdefs
178       - reorganize the extra computations for printing the residuals
179    o tools/genmake2:
180      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
181        since it's not necessary (and was preventing to use MNC in some cases).
182    
183    checkpoint64a (2012/11/16)
184    o pkg/autodiff:
185      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
186        autodiff_readparms.F no longer depends on calling order (within
187        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
188        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
189        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
190    o pkg/obcs:
191      - adding tidal velocity forcing capability to obcs
192        for usage example, see verification/seaice_obcs/input.tides
193    o pkg/seaice:
194      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
195        SEAICE_LSRrelaxU/V
196      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
197    o pkg/aim_v23:
198      - implement heating from friction (bottom friction and stratospheric drag).
199    o pkg/shap_filt:
200      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
201        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
202    o model/src:
203      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
204        time-constant addMass field from file (addMassFile);
205      - support for heating due to friction (and Kinetic Energy dissipation):
206        add option, run-time switch and 3-D field array + support code ; each pkg
207        or S/R can add heating contribution (if there is a sink of KE); the sum is
208        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
209    o pkg/seaice:
210      - complete merge of ITD code into seaice_growth.F
211        from MITgcm_contrib/torge/itd/code/
212        no verification so far, but Torge Martin tested
213        "1-D test case and Beaufort set up;
214        deliver okay results after 1 model year."
215      - complete merge of SEAICE_SIZE.h into all relevant routines
216      - move computation of eta at Z-points into calc_viscosities
217        + introduce global field etaZ
218        + add different methods for computing etaZ, for now the old
219          method (simple averages of eta to Z-points) is hardwired
220        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
221          seaice_preconditioner
222      - simplify computations for SEAICE_ZETA_SMOOTHREG
223      - seaice_preconditioner:
224        + replace one remaining press by pressLoc (mistake)
225        + adjust printing of residuals
226      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
227        + add (SEAICE.h) and rename some counters (initiliased in
228          seaice_init_fixed.F)
229        + add _BEGIN/END_MASTER (myThid)  around print statements
230        + print total number of iterations and failures over SEAICE_monFreq
231          interval to STDOUT
232      - move control over output-messages by fgmres to seaice_jfnk to save
233        some operations
234      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
235        in order to make restarts with sol .ne. zero (fgmres with restarts)
236        (seaice_jfnk.F, seaice_fgmres.F)
237      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
238        a serious convergence problem when open boundaries are involved
239    o pkg/ggl90: fix computation of control volumes for the case of
240      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
241      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
242    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
243    o pkg/autodiff
244      - Add inAdMode switch for SEAICEuseDYNAMICS:
245        SEAICEuseDYNAMICSinAdMode
246        (extend logic in ADAUTODIFF_INADMODE_SET)
247    o pkg/seaice
248      - Step 1 of merging ice-thickness distribution (ITD) code from
249        MITgcm_contrib/torge/itd/ (author: Torge Martin)
250        The code implements concept laid out in Thorndike et al. (1975);
251        code is enabled via CPP flag SEAICE_ITD
252        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
253        code is not complete yet!!
254      - SEAICE_SIZE.h now included in almost all seaice routines
255    o verification (using seaice):
256      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
257        global_ocean.cs32x15.seaice ; update results.
258      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
259      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
260        offline_exf_seaice (previously compiling B-grid).
261    o pkg/exf:
262      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
263        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
264        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
265    o pkg/layers (adjust changes from Sept 19):
266      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
267        this allows to remove "layers_maxNum" dimension from all layers arrays.
268    o pkg/layers (adjust changes from Sept 19):
269      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
270      - snap-shot extended to all type of layers (not just the 1rst type);
271      - remove layers variables when corresponding CPP option is undef.
272    o pkg/layers:
273      - rename pkg/layers variable and add new output (layer exist & un-weighted
274        velocity in layer)
275    o pkg/seaice:
276      - simplify (?) ocean-drag coefficent computations by using
277        the same routine in all three solvers (saves some code lines)
278      - remove global fields DRAGA and DRAGS from C-grid code and
279        declare them locally in lsr.F (the only place where they are
280        still used)
281      - update AD output of lab_sea.evp (very sensitive anyway).
282    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
283      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
284      and SEAICEuseJFNK=.true. A few things to note:
285      - involves a FGMRES, that is parallel but very inefficient,
286        because of many scalar products (global sums) in the Gram-Schmidt
287        orthogonalization method. Needs to be replaced. Original code
288        from J.-F. Lemieux
289      - preconditioner for FGMRES is a stripped down version of LSOR
290      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
291        preconditioner. For the preconditioner, the default is set to 10.
292      - Jacobian times vector is computed with finite differences
293      - marginally related to JFNK-solver: add a smooth regularization for
294        zeta with tanh that will improve convergence (Lemieux and Tremblay,
295        2009) for any implicit solver (not implemented for EVP because EVP
296        does not need this regularization in the first place). Define
297        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
298    o eesupp/src:
299      - check in genmake2 that intrinsic S/R flush is available.
300      - add S/R to flush IO unit (if intrinsic S/R flush is available)
301      - flush standard & error msg unit before MPI termination
302      - if debugMode, flush IO unit after printing msg
303    o pkg/ctrl:
304      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
305        to ctrl_set_unpack_xyz.
306    
307    checkpoint64 (2012/10/09)
308    o pkg/shelfice
309      - in mom_fluxform.F, mom_vecinv.F:
310        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
311        Bug fix KappaRU -> KappaRV
312        does not change verification/isomip but may change other setups
313        (presumably constant KappaRU=KappaRV)
314      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
315    o pkg/obcs:
316      - fixed some indexing bugs in obcs_seaice_sponge.F
317      - added obcs relaxation subroutines for HSALT and HSNOW
318      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
319    o pkg/seaice:
320      - add "multicategory" parameterization for snow in analogy to ice,
321        default is off for now.
322    o pkg/obcs:
323      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
324        see verification/seaice_obcs/input.seaiceSponge for example application.
325      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
326        index setting by master-thread. This fix multi-threads Pb in previous modifs.
327    o pkg/layers :
328      - add diagnostics to pkg/layers
329      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
330        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
331    o pkg/generic_advdiff/gad_implicit_r.F :
332      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
333    o pkg/seaice/seaice_growth.F:
334      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
335    o pkg/obcs:
336      - change default setting of OBCS_UVICE_OLD from defined to undef;
337      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
338        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
339      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
340      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
341        with Southern & Western OB at a tile edge (at least in a simple set-up).
342    o pkg/obcs:
343      - change settings of OB index in case OB coincides with tile edge (shared by
344        2 tiles), so that common OB location is registered by both tiles (instead of
345        only 1). However, for Southern and Western OB, index value = 0 is not
346        recognized as valid OB index (=default null value) and needs to be fixed.
347      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
348      - new parameter "OB_indexNone" for null index value (for now, still zero)
349        to replace hard-coded null index value of zero.
350    o pkg/exch2:
351      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
352        always check buffer-size (but outside the loop); move checking for valid
353        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
354        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
355    o pkg/ctrl (pack & unpack):
356      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
357        (locally defined) for different variables (+ remove the variable-specific
358        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
359        (to be extended to other local file names in ctrl.h).
360    o pkg/flt:
361      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
362    o pkg/mdsio:
363      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
364    o tools/genmake2:
365      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
366        (added by Alistair in version 1.51 for building without make depend);
367      - remove Header files list (H_SRC_FILES) from the dependence of targets
368         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
369        place in version 1.23): this save going through staf when unrelated header
370        file has been modified.
371       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
372        "make depend" step, still need to do "make links" before "make adtaf".
373    o eesupp/src (+ few pkg src files) & genmake2:
374      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
375      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
376      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
377         upper/lower case ; account for space between "#" and undef/define)
378    o pkg/flt (with exch2):
379      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
380      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
381    
382    checkpoint63s (2012/09/05)
383    o pkg/ecco:
384      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
385      - add more relevant #ifdef ALLOW_SMOOTH ones.
386      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
387    o pkg/ctrl:
388      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
389        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
390      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
391        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
392        ctrlSmoothCorrel3D (new).
393        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
394      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
395      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
396        controls when useAtmWind, and vice versa.
397      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
398      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
399          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
400      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
401          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
402      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
403        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
404    o pkg/smooth:
405      - remove un-necessary includes.
406      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
407        Those CPP options were never defined, and not necessary.
408    o model/src:
409      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
410      - standard treatment of useSMOOTH.
411    o pkg/autodiff:
412      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
413        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
414    o pkg/exch2:
415      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
416        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
417      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
418        and tiles to process mapping.
419      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
420        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
421        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
422        from w2_eeboot.F to w2_readparms.F.
423    o eesupp/src:
424      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
425        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
426        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
427      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
428        is defined (remove condition on usingMPI) to match cases where MPI_INIT
429        has been called.
430      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
431      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
432        (so that on 1 proc, get same myPid independently of usingMPI)
433      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
434        useCubedSphereExchange with EXCH-1 (safer).
435      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
436    o pkg/ggl90:
437      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
438        used in ALLOW_GGL90_SMOOTH code.
439    o pkg/flt:
440      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
441        floats at the Southern end of the domain).
442    o eesupp/inc:
443      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
444        but not used (and not to be used) anywhere, just for documentation.
445    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
446      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
447        a) can damage previously written records in any other multi-record files.
448        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
449    o tools/genmake2:
450      - define variable MAKE within Makefile and use it in place of 'make';
451      - update AD_CONFIG.h (if needed) before building any of the executable
452        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
453        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
454      - always print usual warning comment 'this file is automatically generated'
455        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
456    o pkg/cheapaml:
457      - updated to correspond to the code used in accepted paper (Nico Wienders).
458    o pkg/exf:
459        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
460        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
461        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
462    o pkg/exf, autodiff, ctrl, ecco and seaice:
463        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
464    o pkg/ctrl, ecco:
465        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
466        Depending on useAtmWind, one is inactive, and the other is active (see
467        exf_getffields.F/exf_getsurfacefluxes.F).
468    o tools/genmake2:
469      - improve error msg when failing in 2nd test of check_for_broken_Ff
470      - fix option '-makefile' short-name (-mf according to genmake2 -help)
471      - source local config file "genmake_local" just after processing the genmake2
472        command arguments (previously done before processing arg).
473    o pkg/grdchk:
474      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
475        to this routine from cost_final has been dropped in g_cost_final)
476      - improve printed information (more explicit msg, no longer using "print *,"
477         fix fcpertminus printed value).
478    o model/src:
479      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
480        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
481        this prevents getting cost-funct reset in adinitialise_varia recomputations.
482    o pkg/dic:
483      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
484        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
485    o pkg/grdchk:
486      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
487      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
488    o pkg/autodiff/ctrl/grdchk :
489      - attempt to sort out what works and what does not,
490        with regard to I/O, and to warn/stop accordingly.
491    o pkg/grdchk:
492      - attempt to fix grdchk in the case of useSingleCpuIO.
493      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
494       statements were moved from grdchk_main.F and into
495       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
496      - a global sum is applied to record numbers icvrec/layer
497       out of grdchk_loc so that they be passed to I/O routines.
498    o pkg/smooth:
499      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
500        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
501    o verification/testreport:
502      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
503      - can also use compressed (gzip) reference output file;
504      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
505        to be easier to collect by testreport.
506      - update existing TLM output (half out-of-date by more than 3 yrs).
507      - report NETCDF & LAPACK settings (from genmake2) in output dir.
508      - report run-time in each individual summary (previously only for AD test);
509        for TLM test, add also TAF version.
510      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
511    
512    checkpoint63r (2012/08/15)
513    o tools/genmake2:
514      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
515    o pkg/ecco/ecco_cost_final.F :
516      - fix fc print statements (to stdout and costfunction0000) so
517        that the printed value is always after the global sum.
518    o pkg/seaice/seaice_dynsolver.F :
519      - fix ice strength assymptote at SEAICE_area_max<1
520        (no change for the standard case of SEAICE_area_max=1)
521    o some cleaning:
522      - pkg source files: ensure that all *.F files from each pkg included the
523        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
524        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
525        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
526        includes;
527      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
528      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
529        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
530        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
531      - update option-file CPP_OPTIONS.h of all AD experiments:
532        * no longer include PACKAGES_CONFIG.h ;
533        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
534        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
535          including ECCO_CPPOPTIONS.h).
536    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
537      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
538        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
539        not necessary accurate).
540      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
541        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
542        deliberately break compilation (a remainder that it needs to be customized)
543      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
544      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
545      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
546    o tools/genamke2:
547      - check for lapack.
548    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
549      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
550        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
551        from both packages.
552      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
553      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
554      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
555        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
556    o pkg/cost : add comments to explain special and/or untested setups.
557    o pkg/exf:
558      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
559        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
560    o verification/*/code_ad:
561      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
562      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
563      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
564        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
565    o pkg/seaice :
566      - added possibility to change ice strength/PRESS0 relationship to
567        HEFF, according to the following run time parameters
568        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
569        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
570        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
571    o pkg/ggl90 :
572      - added run time flag mxlSurfFlag to include the code that ensure
573        mixing between first and second level (previously included as a comment)
574    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
575      - add test of newly added dumpAdByRec=T option where
576        we write all records to one file per variable.
577    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
578      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
579        to check that this code is ok with taf and compiles in adjoint.
580    o pkg/autodiff :
581      - added run time param dumpAdByRec : ad dump format switch.
582        If true then write all records to one file per variable.
583        Else write one file per record (remains the default).
584      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
585    o pkg/seaice:
586     - Added SEAICEuseTILT run time switch : if set to
587       false then omit the tilt term in seaice dynamics.
588     - Fix free drift calculation.
589    o pkg/shelfice:
590      When initializing SHELFICEDragQuadratic, set default to be
591      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
592      but retain option to set it independently
593      (inconsistenty spotted by Veronique Dansereau)
594    o eesupp/inc:
595      - in EEPARAMS.h, add real-type constant for some frequently used simple number
596         (0,1,2,1/2), with name explicitly referring to RS/RL type.
597    o model/src:
598      - move balancing of relaxation terms to new S/R balance_relax.F.
599    o pkg/autodiff:
600      re-write active I/O high-level (control) S/R:
601      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
602      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
603      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
604        MDS_READ/WRITE_FIELD); change loops to multi-threads.
605      - update and merge active_file_control_slice.flow into active_file_control.flow
606      - update the calls in lower level S/R (active_file.F, active_file_g.F and
607        active_file_ad.F) keeping the argument list and function unchanged.
608      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
609        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
610      - new low-level active I/O routines, one for each type (RL/RS), for active var
611        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
612        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
613        right type.
614    o autodiff and RS=real*4:
615      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
616        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
617      - change argument type of 3-D mask argument to _RS to match type in the call
618        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
619    o pkg/thsice:
620      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
621      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
622        fresh-water flux: uniform correction or proportional to local precip.
623    o pkg/ctrl:
624      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
625      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
626                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
627      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
628    
629    checkpoint63q (2012/07/30)
630    o pkg/autodiff:
631      note about monitor and snap-shot of ad-variables:
632      a) need to apply ADEXCH before monitor or output of ad-vars to include
633       overlap contributions (was done for adjDump but missing for monitor).
634      b) since ADEXCH implies adding overlap values to interior array, machine
635       truncation error is expected when adding an ADEXCH call in the middle of
636       the time-stepping (although mathematically identical).
637      modifs:
638      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
639        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
640      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
641        apply ADEXCH before monitor or snap-shot of ad-variables:
642           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
643      - implement new method (copy+adexch) for snap-shot and monitor of main model
644        ad-vars (initially not used by default -> output unchanged).
645      - change default (set to 2) to use new method and update few output_adm.txt
646        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
647        and both tutorial_tracer_adjsens tests).
648      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
649        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
650    o pkg/ctrl:
651      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
652      generic control variables via
653      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
654      Only required customization should be S/R ctrl_map_ini_genarr.F
655      (routine in repository contains example)
656    o pkg/exf:
657      - fix and refine checking of surface-relaxation setting when using EXF
658    o verification (adjoint exp):
659      - reduce length of simulation by half for experiment global_ocean.cs32x15
660        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
661    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
662      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
663        of KE that can occur with aggressive optimization
664      + put quadratic bottom drag calculation in separated loops (only done if
665        using bottomDragQuadratic)
666    o model/src: CG2D_NSA
667      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
668         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
669      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
670         change cg2d residual target to be expressed in Wunits (=> do not normalise
671         RHS ; this fix global_max Pb with TAF); update output.
672    o verification/tutorial_tracer_adjsens:
673       improve parameter consistency (and get rid of warnings):
674       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
675       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
676       - use staggerTimeStep (for stability) in som81; use default rotation period.
677    o pkg/exch2:
678      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
679        reset to 0 = 1 long line in X)
680    o pkg/mdsio:
681      - fix reading of dimensions from meta file for large-size domain
682    o model/src:
683      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
684      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
685        Cubed-Sphere Exch with CS-corners inside the domain;
686        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
687        globalArea and to set hasWetCSCorners.
688      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
689        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
690      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
691        useCDscheme and useCubedSphereExchange).
692    o pkg/seaice/seaice_growth.F :
693      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
694        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
695        when the previous code was not correct.
696      - in all cases diagnoze the boundary condition mismatch to SIaaflux
697      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
698        that term to QNET (essentially to set the melt/freeze water to 0degC).
699        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
700    o verification/global_ocean.cs32x15/input.seaice :
701      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
702      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
703      - update results (output.seaice.txt) accordingly.
704    o verification/lab_sea/input/data.seaice :
705      - remove SEAICEheatConsFix, which is now be tested
706        in global_ocean.cs32x15. The presently coded fix
707        is only consistent with real fresh water + nlfs.
708      - update results (output.txt) accordingly.
709    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
710    o AD_CONFIG.h file:
711      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
712      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
713        add it explicitly in each fortran src file where it is needed.
714        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
715        thus introducing potentially wrong dependency; therefore, better to include
716        it only where it's really needed, and after any other included OPTIONS file
717        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
718        or ALLOW_TANGENTLINEAR_RUN).
719    
720    checkpoint63p (2012/07/06)
721    o pkg/autodiff:
722      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
723      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
724        which are now read from new parameter file "data.autodiff" (inAdExact
725        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
726      - add file "data.autodiff" in all verification/*/input_ad/ directories.
727      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
728        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
729    o verification/tutorial_tracer_adjsens/
730      - add extra sub-verification which uses "SOM" advection scheme
731        (2nd Order-Moment Advection Scheme, Prather Limiter) with
732          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
733        and in data:
734          multiDimAdvection=.TRUE.,
735          tempAdvScheme=81,
736          saltAdvScheme=81,
737    o model/src:
738      - introduce ALLOW_BALANCE_RELAX which allow the removal
739       of the global mean of relaxation terms by setting
740       balanceThetaClimRelax and balanceSaltClimRelax
741      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
742       This case is now treated appropriately in seaice_growth.F
743    o pkg/seaice:
744      - do balanceEmPmR and balanceQnet based on the net fluxes
745        (SItflux) that enter the ocean+ice system rather than QNET
746        and EMPMR. Works best in real fresh water.
747      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
748        out of the diagnotics bloc, and stored in global arrays.
749    
750    checkpoint63o (2012/06/29)
751    o vertical mixing schemes:
752      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
753      - replace computation of density (in Function STATE1, opps_calc.F) by a call
754        to S/R FIND_RHO_SCALAR
755      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
756        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
757        affects output (vermix.ggl90) at truncation level.
758    o testreport:
759      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
760        (nSx,nSy) for the number of threads (from eedata.mth)
761    o model/src:
762      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
763        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
764    o verification/tutorial_tracer_adjsens/
765      - compile with ALLOW_CG2D_NSA
766      - run with nonlinFreeSurf=3
767      - update reference output_adm.txt
768    o tools/genmake2:
769      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
770        refine usePROFILES switching off (only when NetCDF is not available).
771    o verification (atmospheric set-up):
772      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
773    o pkg/profiles : refine profiles and files handling.
774    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
775    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
776      - changes to use model/src/the_main_loop.F rather than the ecco version
777        in ecco type adjoint runs.
778    o model/src:
779      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
780      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
781      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
782    o model/src:
783      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
784        update output of test experiment bottom_ctrl_5x5.
785    o pkg/generic_advdiff:
786      - implement vertical bi-harmonic diffusion (for now, only for T & S and
787        only explicitly).
788    o verification/bottom_ctrl_5x5/
789      update reference output (results changed quite some time ago,
790      not sure when; but new reference results look ok in terms of grdchk)
791    o verification/1D_ocean_ice_column/
792      For verification purposes, the exact adjoint rather than an approx.
793      should be used (e.g., to comare against F.D. or TLM).
794      removed autodiff_inadmode*_ad.F routines in code_ad/
795      Update results/ accordingly.
796    o pkg/cal:
797      - change cal_getdate.F so that output date is function of input time only
798        (less ambiguous, not mixed up with input iteration number).
799      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
800    o pkg/diagnostics:
801      - implement calendarDumps also for stats-diags
802      - implement calendarDumps also for snap-shot output (negative freq)
803      - for now, ignores calendarDumps if non-zero phase-lag.
804    
805    checkpoint63n (2012/06/04)
806    o model/src:
807      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
808        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
809      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
810        similar to calc_r_star.F); update results of experiment internal_wave and
811        tutorial_global_oce_in_p (affected @ truncation level).
812    o pkg/shelfice:
813      - add parameterisation of advective-diffusive flux into the ice shelf
814        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
815      - simply eps3/3a computation
816    o eesupp:
817     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
818       between tiles, just fill-in edges assuming locally periodic subdomain) and
819       add corresponding exchange subroutines (EXCH0);
820     - new CG-solver version (_EX0) for disconnected-tiles special case.
821    o model/src (CG-solvers):
822     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
823       (similar final residual output and max-Iter number as with standard version);
824     - allows to store and use lowest-residual solution (standard & _SR versions);
825     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
826     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
827    o eesup/src:
828     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
829       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
830    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
831    
832    checkpoint63m (2012/04/27)
833    o pkg/shelfice:
834     - account for partical cells in surface level below ice-shelf for hydrostatic
835       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
836    o ad test experiments:
837     - update and rename to "ad_optfile.local" local AD-optfile specific to a
838       particular adjoint verification experiment (in verification/*/code_ad/)
839    o pkg/seaice & pkg/exf:
840     - Part two of ECCO-CLIVAR code merges.
841       Completes merge of seaice area relax. code.
842       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
843       to be set in EXF_OPTIONS.h since this pkg controls its I/O
844       (and avoids second CPP option in SEAICE_OPTIONS.h)
845     - change default value of costIceStart & costIceEnd to a valid date.
846     - add snowPrecip to HSNOW in seaice_growth
847    o pkg/ptracers:
848     - move ptracers summary and setup check into separated S/R ; add a check for
849       valid PTRACERS_Iter0 value (error+stop or just warning).
850    o pkg/cal (+ pkg/ecco):
851     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
852       as input; and for AD, unless both are not differentiable (e.g., k index)).
853    o model/src:
854     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
855       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
856       temporary set to usingZCoords value (to be changed to F when using shelfice).
857     - hydrostatic pressure: implement partial cell near the surface also for
858       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
859       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
860    o pkg/ctrl/ctrl_init.F:
861     - add a formal parameter to s/r ctrl_init_rec to print
862       xx_$(ctrl_valiable)_file for easier debugging
863     - move call of cal_* routines into the if-block where they are really
864       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
865       to specify a startdate
866    o pkg/seaice:
867     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
868       global_ocean.cs32x15/code versions).
869     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
870       verification experiment global_ocean.cs32x15.seaice and update results.
871    o pkg/exf:
872     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
873       (according to useExfYearlyFields).
874    o pkg/cal:
875     - move calendar setting & summary (previously in cal_readparams.F) into new
876       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
877       length of the simulation is set (after SET_PARMS call); This is an attempt
878       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
879     - For safety: keep a record of pkg/cal parameter settings status
880               to allow to STOP if one pkg/cal S/R is called too early.
881     - add a stop in all basic pkg/cal subroutines if called before setting is done.
882     - modify cal_getdate.F: stop when nothing was returned;
883       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
884       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
885    
886    checkpoint63l (2012/04/04)
887    o pkg/bbl:
888      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
889        update global_with_exf output.yearly.txt file.
890    o pkg/cal:
891      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
892      - remove 2 unsused and very short (1 line only) functions ;
893      - remove unsused subroutines from AD-Diff list.
894    o model/src:
895      - start to implement clean wait to stop in initialization S/R (config_check.F,
896         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
897    o folowing PRINT_MESSAGE changes:
898      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
899  o pkg/bbl:  o pkg/bbl:
900    - modification so it can work with z*    - modification so it can work with z*
901    - replace deltaT with dTtracerLev(k) for asynchronous time stepping    - replace deltaT with dTtracerLev(k) for asynchronous time stepping
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