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revision 1.1626 by jmc, Sun Mar 18 23:29:55 2012 UTC revision 1.1820 by jmc, Wed Feb 6 22:11:33 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/diagnostics:
8      - change default missing_value from UNSET_RL to -999.
9    o pkg/layers: improve vectorization of layers_fluxcalc.F, step 1
10      - split loops, make TatU/V 2D arrays. This along reduces the cpu time spent
11        in this routine by more than a factor of 3 on an NEC-SX8
12    o pkg/ecco:
13      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
14    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
15      - modifications for ALLOW_GENTIM2D_CONTROL
16      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
17      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
18      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
19      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
20    o model/src:
21      - account for moist thermodynamics in (dry) potential temperature equation;
22        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
23        and cpl_aim+ocn.
24      - also switch to standard compiler (gfortran, was using ifort previously)
25        for fizhi-cs experiments reference output.
26    o pkg/ctrl:
27      - 1st step toward generic time-varying control variable (2D) via CPP option
28        ALLOW_GENTIM2D_CONTROL
29      - note new namelist ctrl_nml_genarr in data.ctrl
30    o verification/global_ocean.cs32x15:
31      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
32        thsice calling sequence and update "output.icedyn.txt" output file.
33    o pkg/ptracers:
34      - from Ryan A.: code to allow to restart a tracer at regular time interval
35        specifying a reset frequency and a reset-phase (for each tracers).
36    o pkg/thsice:
37      - implement new sequence of calls for thsice+seaice:
38          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
39          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
40      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
41        in CPP_OPTIONS.h) to recover old sequence;
42      - update diagnostics for Intermediate State thsice diagnostics: now filled
43        just before advection (instead of just after advection in old sequence);
44      - update output of experiment offline_exf_seaice (standard test);
45      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
46        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
47    o pkg/aim_v23:
48      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
49      - use standard pkg/mdsio routines to read & write CO2 pickup file;
50      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
51      - Implement new sequence of calls for seaice advection (with thsice and
52        seaice diffusion): do ice advection after ice-Thermodynamic (previously
53        was done before); change aim_do_physics.F (split the bi,bj loops block);
54      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
55    o pkg/thsice:
56      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
57        where just seaice diffusion is used without seaice-dynamics.
58    
59    checkpoint64c (2013/01/18)
60    o pkg/seaice:
61      - add a parameter JFNKres_tFac that can replace JFNKres_t
62        (= JFNKres_tFac*JFNKresidual before JFNK solver)
63      - add a line search option to the JFNK solver
64      - move update of u/vIce and computation of initial residual into a separate
65        routine (same file); makes the code a little easier to read (?)
66      - the line search requires computation of the residual and for some reason
67        I cannot do the update of u/vIce at the beginning of the Newton loop
68        without changing the results, so we move computation of the new residual
69        also to the end of the Newton loop, even without the line search
70    o pkg/mdsio:
71      - write missing value (corresponding to undefined array value) to meta files;
72        skip this if missing value is one (UNSET_RL would be a better value for the
73        case of undefined missing value but it's current the default missing-value);
74        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
75    o pkg/exf & thsice:
76      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
77        diagnostics) even when SHORTWAVE_HEATING is #undef;
78    o verification/cfc_example:
79      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
80        illustrate how to use it).
81    o verification/offline_exf_seaice:
82      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
83        files to only one time-record.
84      in input.thermo: narrow the 2 bands of low initial ice-concentration near
85        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
86        snapshot output; same mcPheePiston value as in thsice with
87        surf-current=0.2m/s.
88      in input.thsice: similar set-up as in input.thermo (channel with same seaice
89        initial conditions).
90    o verification/cfc_example:
91      - update file "data" with more standard choice (default rotationPeriod,
92        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
93        set deltaTFreeSurf to deltaTtracer) and update the output.
94    o pkg/layers:
95      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
96      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
97    o verification/offline_exf_seaice:
98      - set all {field}period to zero for constant-in-time forcing (not tested
99        anywhere else).
100    o verification/offline_exf_seaice:
101      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
102      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
103    o model/src:
104      - implement Finite-Volume method for (hydrostatic) presure gradient
105        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
106    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
107      - In order to be compatible with the default EVP code, this requires changing
108        the EVP code around a little; and because any small change immediately
109        breaks the lab_sea.hb87 verification experiment, the reference output is
110        updated two times (each time the remaining aggrement was only 2 digits):
111        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
112        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
113        The adjoint test lab_sea.evp also needed to be updated.
114      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
115        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
116        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
117        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
118        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
119        kept obscure, because I need to test it a little more.
120    o pkg/cheapaml:
121      - fix few incorrect type (_RL/_RS) in subroutine calls.
122    o pkg/seaice:
123      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
124        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
125    o model/src:
126      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
127        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
128        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
129    o pkg/cheapaml:
130      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
131        update output of experiment cheapAML_box.
132      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
133        and set them only in one place (cheapaml_readparms.F).
134      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
135      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
136        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
137    o model/src/the_main_loop.F:
138      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
139    o pkg/seaice:
140      - remove legacy branch code.
141      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
142    o verification/*/code*/SEAICE_OPTIONS.h:
143      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
144        SEAICE_CAP_HEFF).
145    o pkg/cheapaml:
146      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
147        to load new forcing fields.
148      - add missing "_d 0" where it's needed; + some editing (improve indentation).
149      - remove switch to "-r8" compiler option (no longer needed) in verification
150        cheapAML_box, keep same output (small trucation error differences).
151    o verification/offline_exf_seaice:
152      - add thermodynamics only test.
153    o verification/cheapAML_box:
154      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
155        keep same output (same 14 digits for cg2d).
156      - switch on "-r8" compiler option (some numerical values are missing
157        the "_d 0") and update output (only 6 digits for cg2d were preserved).
158    
159    checkpoint64b (2012/12/24)
160    o pkg/cheapaml:
161      - remove un-used variables (Qnet,EmPmR) from pickup files.
162      - store tendency of advected variables into cheapaml pickup file
163        and fix the AB-2 restart.
164    o verification/offline_exf_seaice and lab_sea adjoint:
165      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
166      - switch to 4 time steps in offline, consistent with lab_sea.
167      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
168      - update results after change of experiment seaice.
169    o pkg/seaice:
170      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
171        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
172        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
173        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
174    o model/src:
175      - add run-time parameter to select CG2D solver minimum-residual solution
176        (in case of a poor convergence).
177    o pkg/seaice/seaice_lsr.F
178      - move calculation of matrix coefficients into new
179        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
180        file; the main purpose of this change is to be able to reuse the code
181        in S/R SEAICE_PRECONDITIONER
182      - modify the computation of the residual so that the mass of sea-ice
183        is not used twice; this simplifies the calculations, but since
184        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
185        not tested in testreport---this does not affect the testreport results.
186    o verification/seaice_obcs:
187      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
188        verification/lab_sea/input.salt_plume; changes results/output.txt*
189    o model/src:
190      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
191    o pkg/seaice:
192      - improve description of parameters in seaice_fgmres.F and start
193        cleaning up the code
194      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
195        second argument
196      - add a metric based on grid cell area to SEAICE_SCALPROD; update
197        results of offline_exf_seaice.dyn_jfnk
198      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
199    o pkg/aim_v23:
200      - fix an other bug in dissipation heating (grid-cell area was missing).
201    o model/src + pkg/seaice:
202      - add global (multi-tile) linear solver for pair of tri-diagonal system
203        along X and Y lines, respectively for U and V component.
204        Note: 1) MPI and cube-exchange not yet coded.
205            2) probably not accurate for poorly conditioned / large size problem.
206      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
207        default: not compiled and not used.
208    o pkg/seaice:
209      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
210        introduce bi/bj loops and use global_sum_tile_rl instead of
211        mpi_allreduce in seaice_fgmres.F
212      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
213      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
214      - add a verification experiment for JFNK in offline_exf_seaice
215    o verification:
216      - change (for now, only fwd test) offline_exf_seaice experiment:
217        use a re-entrant channel with idealized coastline (trapezoidal shape)
218        at southern boundary to explore seaice dynamics and thermodynamics
219        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
220        secondary test (input.thsice) use thermodynamics only with SST relaxation.
221      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
222    o pkg/exf:
223      - disable "sstExtrapol" when Nr=1
224    o verification:
225      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
226        to test pkg/cheapaml.
227    o pkg/aim_v23 & pkg/shap_filt:
228      - fix dissipation heating (erroneous gravity multiplication factor).
229    o pkg/seaice:
230      - remove unused field pressPre from jfnk solver
231      - rename two subroutines in seaice_preconditioner.F
232    o eesupp/src:
233       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
234    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
235       - remove wrong parts of the rhs and the lhs (were in there
236         because I did not understand the concept of this preconditioner)
237       - add an exchange between u- and v-sweep. This increases communication
238         by a factor of two but improves the convergence of jfnk. Ideally,
239         one would like the u- and v-sweep to be independent. So far within
240         undocumented ifdefs
241       - reorganize the extra computations for printing the residuals
242    o tools/genmake2:
243      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
244        since it's not necessary (and was preventing to use MNC in some cases).
245    
246    checkpoint64a (2012/11/16)
247    o pkg/autodiff:
248      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
249        autodiff_readparms.F no longer depends on calling order (within
250        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
251        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
252        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
253    o pkg/obcs:
254      - adding tidal velocity forcing capability to obcs
255        for usage example, see verification/seaice_obcs/input.tides
256    o pkg/seaice:
257      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
258        SEAICE_LSRrelaxU/V
259      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
260    o pkg/aim_v23:
261      - implement heating from friction (bottom friction and stratospheric drag).
262    o pkg/shap_filt:
263      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
264        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
265    o model/src:
266      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
267        time-constant addMass field from file (addMassFile);
268      - support for heating due to friction (and Kinetic Energy dissipation):
269        add option, run-time switch and 3-D field array + support code ; each pkg
270        or S/R can add heating contribution (if there is a sink of KE); the sum is
271        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
272    o pkg/seaice:
273      - complete merge of ITD code into seaice_growth.F
274        from MITgcm_contrib/torge/itd/code/
275        no verification so far, but Torge Martin tested
276        "1-D test case and Beaufort set up;
277        deliver okay results after 1 model year."
278      - complete merge of SEAICE_SIZE.h into all relevant routines
279      - move computation of eta at Z-points into calc_viscosities
280        + introduce global field etaZ
281        + add different methods for computing etaZ, for now the old
282          method (simple averages of eta to Z-points) is hardwired
283        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
284          seaice_preconditioner
285      - simplify computations for SEAICE_ZETA_SMOOTHREG
286      - seaice_preconditioner:
287        + replace one remaining press by pressLoc (mistake)
288        + adjust printing of residuals
289      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
290        + add (SEAICE.h) and rename some counters (initiliased in
291          seaice_init_fixed.F)
292        + add _BEGIN/END_MASTER (myThid)  around print statements
293        + print total number of iterations and failures over SEAICE_monFreq
294          interval to STDOUT
295      - move control over output-messages by fgmres to seaice_jfnk to save
296        some operations
297      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
298        in order to make restarts with sol .ne. zero (fgmres with restarts)
299        (seaice_jfnk.F, seaice_fgmres.F)
300      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
301        a serious convergence problem when open boundaries are involved
302    o pkg/ggl90: fix computation of control volumes for the case of
303      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
304      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
305    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
306    o pkg/autodiff
307      - Add inAdMode switch for SEAICEuseDYNAMICS:
308        SEAICEuseDYNAMICSinAdMode
309        (extend logic in ADAUTODIFF_INADMODE_SET)
310    o pkg/seaice
311      - Step 1 of merging ice-thickness distribution (ITD) code from
312        MITgcm_contrib/torge/itd/ (author: Torge Martin)
313        The code implements concept laid out in Thorndike et al. (1975);
314        code is enabled via CPP flag SEAICE_ITD
315        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
316        code is not complete yet!!
317      - SEAICE_SIZE.h now included in almost all seaice routines
318    o verification (using seaice):
319      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
320        global_ocean.cs32x15.seaice ; update results.
321      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
322      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
323        offline_exf_seaice (previously compiling B-grid).
324    o pkg/exf:
325      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
326        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
327        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
328    o pkg/layers (adjust changes from Sept 19):
329      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
330        this allows to remove "layers_maxNum" dimension from all layers arrays.
331    o pkg/layers (adjust changes from Sept 19):
332      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
333      - snap-shot extended to all type of layers (not just the 1rst type);
334      - remove layers variables when corresponding CPP option is undef.
335    o pkg/layers:
336      - rename pkg/layers variable and add new output (layer exist & un-weighted
337        velocity in layer)
338    o pkg/seaice:
339      - simplify (?) ocean-drag coefficent computations by using
340        the same routine in all three solvers (saves some code lines)
341      - remove global fields DRAGA and DRAGS from C-grid code and
342        declare them locally in lsr.F (the only place where they are
343        still used)
344      - update AD output of lab_sea.evp (very sensitive anyway).
345    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
346      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
347      and SEAICEuseJFNK=.true. A few things to note:
348      - involves a FGMRES, that is parallel but very inefficient,
349        because of many scalar products (global sums) in the Gram-Schmidt
350        orthogonalization method. Needs to be replaced. Original code
351        from J.-F. Lemieux
352      - preconditioner for FGMRES is a stripped down version of LSOR
353      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
354        preconditioner. For the preconditioner, the default is set to 10.
355      - Jacobian times vector is computed with finite differences
356      - marginally related to JFNK-solver: add a smooth regularization for
357        zeta with tanh that will improve convergence (Lemieux and Tremblay,
358        2009) for any implicit solver (not implemented for EVP because EVP
359        does not need this regularization in the first place). Define
360        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
361    o eesupp/src:
362      - check in genmake2 that intrinsic S/R flush is available.
363      - add S/R to flush IO unit (if intrinsic S/R flush is available)
364      - flush standard & error msg unit before MPI termination
365      - if debugMode, flush IO unit after printing msg
366    o pkg/ctrl:
367      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
368        to ctrl_set_unpack_xyz.
369    
370    checkpoint64 (2012/10/09)
371    o pkg/shelfice
372      - in mom_fluxform.F, mom_vecinv.F:
373        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
374        Bug fix KappaRU -> KappaRV
375        does not change verification/isomip but may change other setups
376        (presumably constant KappaRU=KappaRV)
377      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
378    o pkg/obcs:
379      - fixed some indexing bugs in obcs_seaice_sponge.F
380      - added obcs relaxation subroutines for HSALT and HSNOW
381      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
382    o pkg/seaice:
383      - add "multicategory" parameterization for snow in analogy to ice,
384        default is off for now.
385    o pkg/obcs:
386      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
387        see verification/seaice_obcs/input.seaiceSponge for example application.
388      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
389        index setting by master-thread. This fix multi-threads Pb in previous modifs.
390    o pkg/layers :
391      - add diagnostics to pkg/layers
392      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
393        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
394    o pkg/generic_advdiff/gad_implicit_r.F :
395      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
396    o pkg/seaice/seaice_growth.F:
397      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
398    o pkg/obcs:
399      - change default setting of OBCS_UVICE_OLD from defined to undef;
400      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
401        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
402      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
403      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
404        with Southern & Western OB at a tile edge (at least in a simple set-up).
405    o pkg/obcs:
406      - change settings of OB index in case OB coincides with tile edge (shared by
407        2 tiles), so that common OB location is registered by both tiles (instead of
408        only 1). However, for Southern and Western OB, index value = 0 is not
409        recognized as valid OB index (=default null value) and needs to be fixed.
410      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
411      - new parameter "OB_indexNone" for null index value (for now, still zero)
412        to replace hard-coded null index value of zero.
413    o pkg/exch2:
414      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
415        always check buffer-size (but outside the loop); move checking for valid
416        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
417        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
418    o pkg/ctrl (pack & unpack):
419      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
420        (locally defined) for different variables (+ remove the variable-specific
421        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
422        (to be extended to other local file names in ctrl.h).
423    o pkg/flt:
424      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
425    o pkg/mdsio:
426      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
427    o tools/genmake2:
428      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
429        (added by Alistair in version 1.51 for building without make depend);
430      - remove Header files list (H_SRC_FILES) from the dependence of targets
431         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
432        place in version 1.23): this save going through staf when unrelated header
433        file has been modified.
434       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
435        "make depend" step, still need to do "make links" before "make adtaf".
436    o eesupp/src (+ few pkg src files) & genmake2:
437      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
438      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
439      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
440         upper/lower case ; account for space between "#" and undef/define)
441    o pkg/flt (with exch2):
442      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
443      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
444    
445    checkpoint63s (2012/09/05)
446    o pkg/ecco:
447      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
448      - add more relevant #ifdef ALLOW_SMOOTH ones.
449      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
450    o pkg/ctrl:
451      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
452        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
453      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
454        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
455        ctrlSmoothCorrel3D (new).
456        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
457      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
458      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
459        controls when useAtmWind, and vice versa.
460      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
461      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
462          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
463      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
464          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
465      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
466        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
467    o pkg/smooth:
468      - remove un-necessary includes.
469      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
470        Those CPP options were never defined, and not necessary.
471    o model/src:
472      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
473      - standard treatment of useSMOOTH.
474    o pkg/autodiff:
475      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
476        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
477    o pkg/exch2:
478      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
479        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
480      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
481        and tiles to process mapping.
482      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
483        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
484        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
485        from w2_eeboot.F to w2_readparms.F.
486    o eesupp/src:
487      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
488        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
489        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
490      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
491        is defined (remove condition on usingMPI) to match cases where MPI_INIT
492        has been called.
493      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
494      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
495        (so that on 1 proc, get same myPid independently of usingMPI)
496      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
497        useCubedSphereExchange with EXCH-1 (safer).
498      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
499    o pkg/ggl90:
500      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
501        used in ALLOW_GGL90_SMOOTH code.
502    o pkg/flt:
503      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
504        floats at the Southern end of the domain).
505    o eesupp/inc:
506      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
507        but not used (and not to be used) anywhere, just for documentation.
508    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
509      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
510        a) can damage previously written records in any other multi-record files.
511        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
512    o tools/genmake2:
513      - define variable MAKE within Makefile and use it in place of 'make';
514      - update AD_CONFIG.h (if needed) before building any of the executable
515        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
516        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
517      - always print usual warning comment 'this file is automatically generated'
518        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
519    o pkg/cheapaml:
520      - updated to correspond to the code used in accepted paper (Nico Wienders).
521    o pkg/exf:
522        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
523        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
524        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
525    o pkg/exf, autodiff, ctrl, ecco and seaice:
526        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
527    o pkg/ctrl, ecco:
528        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
529        Depending on useAtmWind, one is inactive, and the other is active (see
530        exf_getffields.F/exf_getsurfacefluxes.F).
531    o tools/genmake2:
532      - improve error msg when failing in 2nd test of check_for_broken_Ff
533      - fix option '-makefile' short-name (-mf according to genmake2 -help)
534      - source local config file "genmake_local" just after processing the genmake2
535        command arguments (previously done before processing arg).
536    o pkg/grdchk:
537      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
538        to this routine from cost_final has been dropped in g_cost_final)
539      - improve printed information (more explicit msg, no longer using "print *,"
540         fix fcpertminus printed value).
541    o model/src:
542      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
543        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
544        this prevents getting cost-funct reset in adinitialise_varia recomputations.
545    o pkg/dic:
546      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
547        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
548    o pkg/grdchk:
549      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
550      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
551    o pkg/autodiff/ctrl/grdchk :
552      - attempt to sort out what works and what does not,
553        with regard to I/O, and to warn/stop accordingly.
554    o pkg/grdchk:
555      - attempt to fix grdchk in the case of useSingleCpuIO.
556      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
557       statements were moved from grdchk_main.F and into
558       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
559      - a global sum is applied to record numbers icvrec/layer
560       out of grdchk_loc so that they be passed to I/O routines.
561    o pkg/smooth:
562      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
563        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
564    o verification/testreport:
565      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
566      - can also use compressed (gzip) reference output file;
567      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
568        to be easier to collect by testreport.
569      - update existing TLM output (half out-of-date by more than 3 yrs).
570      - report NETCDF & LAPACK settings (from genmake2) in output dir.
571      - report run-time in each individual summary (previously only for AD test);
572        for TLM test, add also TAF version.
573      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
574    
575    checkpoint63r (2012/08/15)
576    o tools/genmake2:
577      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
578    o pkg/ecco/ecco_cost_final.F :
579      - fix fc print statements (to stdout and costfunction0000) so
580        that the printed value is always after the global sum.
581    o pkg/seaice/seaice_dynsolver.F :
582      - fix ice strength assymptote at SEAICE_area_max<1
583        (no change for the standard case of SEAICE_area_max=1)
584    o some cleaning:
585      - pkg source files: ensure that all *.F files from each pkg included the
586        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
587        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
588        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
589        includes;
590      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
591      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
592        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
593        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
594      - update option-file CPP_OPTIONS.h of all AD experiments:
595        * no longer include PACKAGES_CONFIG.h ;
596        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
597        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
598          including ECCO_CPPOPTIONS.h).
599    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
600      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
601        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
602        not necessary accurate).
603      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
604        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
605        deliberately break compilation (a remainder that it needs to be customized)
606      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
607      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
608      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
609    o tools/genamke2:
610      - check for lapack.
611    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
612      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
613        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
614        from both packages.
615      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
616      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
617      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
618        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
619    o pkg/cost : add comments to explain special and/or untested setups.
620    o pkg/exf:
621      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
622        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
623    o verification/*/code_ad:
624      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
625      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
626      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
627        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
628    o pkg/seaice :
629      - added possibility to change ice strength/PRESS0 relationship to
630        HEFF, according to the following run time parameters
631        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
632        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
633        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
634    o pkg/ggl90 :
635      - added run time flag mxlSurfFlag to include the code that ensure
636        mixing between first and second level (previously included as a comment)
637    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
638      - add test of newly added dumpAdByRec=T option where
639        we write all records to one file per variable.
640    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
641      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
642        to check that this code is ok with taf and compiles in adjoint.
643    o pkg/autodiff :
644      - added run time param dumpAdByRec : ad dump format switch.
645        If true then write all records to one file per variable.
646        Else write one file per record (remains the default).
647      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
648    o pkg/seaice:
649     - Added SEAICEuseTILT run time switch : if set to
650       false then omit the tilt term in seaice dynamics.
651     - Fix free drift calculation.
652    o pkg/shelfice:
653      When initializing SHELFICEDragQuadratic, set default to be
654      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
655      but retain option to set it independently
656      (inconsistenty spotted by Veronique Dansereau)
657    o eesupp/inc:
658      - in EEPARAMS.h, add real-type constant for some frequently used simple number
659         (0,1,2,1/2), with name explicitly referring to RS/RL type.
660    o model/src:
661      - move balancing of relaxation terms to new S/R balance_relax.F.
662    o pkg/autodiff:
663      re-write active I/O high-level (control) S/R:
664      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
665      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
666      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
667        MDS_READ/WRITE_FIELD); change loops to multi-threads.
668      - update and merge active_file_control_slice.flow into active_file_control.flow
669      - update the calls in lower level S/R (active_file.F, active_file_g.F and
670        active_file_ad.F) keeping the argument list and function unchanged.
671      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
672        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
673      - new low-level active I/O routines, one for each type (RL/RS), for active var
674        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
675        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
676        right type.
677    o autodiff and RS=real*4:
678      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
679        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
680      - change argument type of 3-D mask argument to _RS to match type in the call
681        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
682    o pkg/thsice:
683      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
684      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
685        fresh-water flux: uniform correction or proportional to local precip.
686    o pkg/ctrl:
687      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
688      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
689                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
690      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
691    
692    checkpoint63q (2012/07/30)
693    o pkg/autodiff:
694      note about monitor and snap-shot of ad-variables:
695      a) need to apply ADEXCH before monitor or output of ad-vars to include
696       overlap contributions (was done for adjDump but missing for monitor).
697      b) since ADEXCH implies adding overlap values to interior array, machine
698       truncation error is expected when adding an ADEXCH call in the middle of
699       the time-stepping (although mathematically identical).
700      modifs:
701      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
702        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
703      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
704        apply ADEXCH before monitor or snap-shot of ad-variables:
705           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
706      - implement new method (copy+adexch) for snap-shot and monitor of main model
707        ad-vars (initially not used by default -> output unchanged).
708      - change default (set to 2) to use new method and update few output_adm.txt
709        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
710        and both tutorial_tracer_adjsens tests).
711      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
712        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
713    o pkg/ctrl:
714      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
715      generic control variables via
716      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
717      Only required customization should be S/R ctrl_map_ini_genarr.F
718      (routine in repository contains example)
719    o pkg/exf:
720      - fix and refine checking of surface-relaxation setting when using EXF
721    o verification (adjoint exp):
722      - reduce length of simulation by half for experiment global_ocean.cs32x15
723        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
724    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
725      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
726        of KE that can occur with aggressive optimization
727      + put quadratic bottom drag calculation in separated loops (only done if
728        using bottomDragQuadratic)
729    o model/src: CG2D_NSA
730      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
731         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
732      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
733         change cg2d residual target to be expressed in Wunits (=> do not normalise
734         RHS ; this fix global_max Pb with TAF); update output.
735    o verification/tutorial_tracer_adjsens:
736       improve parameter consistency (and get rid of warnings):
737       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
738       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
739       - use staggerTimeStep (for stability) in som81; use default rotation period.
740    o pkg/exch2:
741      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
742        reset to 0 = 1 long line in X)
743    o pkg/mdsio:
744      - fix reading of dimensions from meta file for large-size domain
745    o model/src:
746      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
747      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
748        Cubed-Sphere Exch with CS-corners inside the domain;
749        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
750        globalArea and to set hasWetCSCorners.
751      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
752        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
753      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
754        useCDscheme and useCubedSphereExchange).
755    o pkg/seaice/seaice_growth.F :
756      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
757        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
758        when the previous code was not correct.
759      - in all cases diagnoze the boundary condition mismatch to SIaaflux
760      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
761        that term to QNET (essentially to set the melt/freeze water to 0degC).
762        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
763    o verification/global_ocean.cs32x15/input.seaice :
764      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
765      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
766      - update results (output.seaice.txt) accordingly.
767    o verification/lab_sea/input/data.seaice :
768      - remove SEAICEheatConsFix, which is now be tested
769        in global_ocean.cs32x15. The presently coded fix
770        is only consistent with real fresh water + nlfs.
771      - update results (output.txt) accordingly.
772    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
773    o AD_CONFIG.h file:
774      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
775      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
776        add it explicitly in each fortran src file where it is needed.
777        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
778        thus introducing potentially wrong dependency; therefore, better to include
779        it only where it's really needed, and after any other included OPTIONS file
780        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
781        or ALLOW_TANGENTLINEAR_RUN).
782    
783    checkpoint63p (2012/07/06)
784    o pkg/autodiff:
785      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
786      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
787        which are now read from new parameter file "data.autodiff" (inAdExact
788        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
789      - add file "data.autodiff" in all verification/*/input_ad/ directories.
790      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
791        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
792    o verification/tutorial_tracer_adjsens/
793      - add extra sub-verification which uses "SOM" advection scheme
794        (2nd Order-Moment Advection Scheme, Prather Limiter) with
795          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
796        and in data:
797          multiDimAdvection=.TRUE.,
798          tempAdvScheme=81,
799          saltAdvScheme=81,
800    o model/src:
801      - introduce ALLOW_BALANCE_RELAX which allow the removal
802       of the global mean of relaxation terms by setting
803       balanceThetaClimRelax and balanceSaltClimRelax
804      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
805       This case is now treated appropriately in seaice_growth.F
806    o pkg/seaice:
807      - do balanceEmPmR and balanceQnet based on the net fluxes
808        (SItflux) that enter the ocean+ice system rather than QNET
809        and EMPMR. Works best in real fresh water.
810      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
811        out of the diagnotics bloc, and stored in global arrays.
812    
813    checkpoint63o (2012/06/29)
814    o vertical mixing schemes:
815      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
816      - replace computation of density (in Function STATE1, opps_calc.F) by a call
817        to S/R FIND_RHO_SCALAR
818      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
819        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
820        affects output (vermix.ggl90) at truncation level.
821    o testreport:
822      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
823        (nSx,nSy) for the number of threads (from eedata.mth)
824    o model/src:
825      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
826        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
827    o verification/tutorial_tracer_adjsens/
828      - compile with ALLOW_CG2D_NSA
829      - run with nonlinFreeSurf=3
830      - update reference output_adm.txt
831    o tools/genmake2:
832      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
833        refine usePROFILES switching off (only when NetCDF is not available).
834    o verification (atmospheric set-up):
835      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
836    o pkg/profiles : refine profiles and files handling.
837    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
838    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
839      - changes to use model/src/the_main_loop.F rather than the ecco version
840        in ecco type adjoint runs.
841    o model/src:
842      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
843      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
844      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
845    o model/src:
846      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
847        update output of test experiment bottom_ctrl_5x5.
848    o pkg/generic_advdiff:
849      - implement vertical bi-harmonic diffusion (for now, only for T & S and
850        only explicitly).
851    o verification/bottom_ctrl_5x5/
852      update reference output (results changed quite some time ago,
853      not sure when; but new reference results look ok in terms of grdchk)
854    o verification/1D_ocean_ice_column/
855      For verification purposes, the exact adjoint rather than an approx.
856      should be used (e.g., to comare against F.D. or TLM).
857      removed autodiff_inadmode*_ad.F routines in code_ad/
858      Update results/ accordingly.
859    o pkg/cal:
860      - change cal_getdate.F so that output date is function of input time only
861        (less ambiguous, not mixed up with input iteration number).
862      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
863    o pkg/diagnostics:
864      - implement calendarDumps also for stats-diags
865      - implement calendarDumps also for snap-shot output (negative freq)
866      - for now, ignores calendarDumps if non-zero phase-lag.
867    
868    checkpoint63n (2012/06/04)
869    o model/src:
870      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
871        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
872      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
873        similar to calc_r_star.F); update results of experiment internal_wave and
874        tutorial_global_oce_in_p (affected @ truncation level).
875    o pkg/shelfice:
876      - add parameterisation of advective-diffusive flux into the ice shelf
877        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
878      - simply eps3/3a computation
879    o eesupp:
880     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
881       between tiles, just fill-in edges assuming locally periodic subdomain) and
882       add corresponding exchange subroutines (EXCH0);
883     - new CG-solver version (_EX0) for disconnected-tiles special case.
884    o model/src (CG-solvers):
885     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
886       (similar final residual output and max-Iter number as with standard version);
887     - allows to store and use lowest-residual solution (standard & _SR versions);
888     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
889     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
890    o eesup/src:
891     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
892       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
893    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
894    
895    checkpoint63m (2012/04/27)
896    o pkg/shelfice:
897     - account for partical cells in surface level below ice-shelf for hydrostatic
898       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
899    o ad test experiments:
900     - update and rename to "ad_optfile.local" local AD-optfile specific to a
901       particular adjoint verification experiment (in verification/*/code_ad/)
902    o pkg/seaice & pkg/exf:
903     - Part two of ECCO-CLIVAR code merges.
904       Completes merge of seaice area relax. code.
905       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
906       to be set in EXF_OPTIONS.h since this pkg controls its I/O
907       (and avoids second CPP option in SEAICE_OPTIONS.h)
908     - change default value of costIceStart & costIceEnd to a valid date.
909     - add snowPrecip to HSNOW in seaice_growth
910    o pkg/ptracers:
911     - move ptracers summary and setup check into separated S/R ; add a check for
912       valid PTRACERS_Iter0 value (error+stop or just warning).
913    o pkg/cal (+ pkg/ecco):
914     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
915       as input; and for AD, unless both are not differentiable (e.g., k index)).
916    o model/src:
917     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
918       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
919       temporary set to usingZCoords value (to be changed to F when using shelfice).
920     - hydrostatic pressure: implement partial cell near the surface also for
921       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
922       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
923    o pkg/ctrl/ctrl_init.F:
924     - add a formal parameter to s/r ctrl_init_rec to print
925       xx_$(ctrl_valiable)_file for easier debugging
926     - move call of cal_* routines into the if-block where they are really
927       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
928       to specify a startdate
929    o pkg/seaice:
930     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
931       global_ocean.cs32x15/code versions).
932     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
933       verification experiment global_ocean.cs32x15.seaice and update results.
934    o pkg/exf:
935     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
936       (according to useExfYearlyFields).
937    o pkg/cal:
938     - move calendar setting & summary (previously in cal_readparams.F) into new
939       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
940       length of the simulation is set (after SET_PARMS call); This is an attempt
941       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
942     - For safety: keep a record of pkg/cal parameter settings status
943               to allow to STOP if one pkg/cal S/R is called too early.
944     - add a stop in all basic pkg/cal subroutines if called before setting is done.
945     - modify cal_getdate.F: stop when nothing was returned;
946       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
947       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
948    
949    checkpoint63l (2012/04/04)
950    o pkg/bbl:
951      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
952        update global_with_exf output.yearly.txt file.
953    o pkg/cal:
954      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
955      - remove 2 unsused and very short (1 line only) functions ;
956      - remove unsused subroutines from AD-Diff list.
957    o model/src:
958      - start to implement clean wait to stop in initialization S/R (config_check.F,
959         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
960    o folowing PRINT_MESSAGE changes:
961      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
962    o pkg/bbl:
963      - modification so it can work with z*
964      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
965      - global_with_exf/input.yearly verification; changes output.yearly.txt
966    o eesupp/src:
967      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
968        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
969      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
970        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
971      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
972      - when using MPI, always set usingMPI=T ; set default accordingly and stop
973        if not consistent.
974      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
975        argument is zero (in case called within single-thread section).
976    o pkg/fizhi:
977        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
978        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
979    o pkg/exch2:
980      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
981        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
982      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
983        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
984        with bad ones coming from a not-yet-updated halo.
985        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
986    o pkg/frazil:
987        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
988        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
989    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
990    o verification/lab_sea
991      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
992      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
993      * nTimeSteps 3 -> 4
994      * changed reference output accordingly
995    o pkg/ctrl:
996      * fix ctrl_get_gen for xx_sst, xx_sss
997    o pkg/fizhi:
998      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
999        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1000      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1001        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1002        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1003    o pkg/gmredi:
1004      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1005    o pkg/fizhi:
1006      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1007        (old)aces open64 tuv test.
1008    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1009    o pkg/mom_vecinv:
1010      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1011        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1012        with non-lin free-surf).
1013    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1014      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1015      some compilers (gfortran 4.6.0 on MacOS)
1016  o momentum:  o momentum:
1017    - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM    - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1018      & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised      & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
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