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revision 1.1595 by gforget, Mon Feb 13 16:38:08 2012 UTC revision 1.1780 by mlosch, Wed Dec 12 22:45:01 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.  o pkg/seaice:
8    - switch to variable freezing point.    - first attempt at a multi-threaded fgmres solver for the JFNK solver:
9        introduce bi/bj loops and use global_sum_tile_rl instead of
10        mpi_allreduce in seaice_fgmres.F
11      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
12      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
13      - add a verification experiment for JFNK in offline_exf_seaice
14    o verification:
15      - change (for now, only fwd test) offline_exf_seaice experiment:
16        use a re-entrant channel with idealized costline (trapezoidal shape)
17        at southern boundary to explore seaice dynamics and thermodynamics
18        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
19        secondary test (input.thsice) use thermodynamics only with SST relaxation.
20      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
21    o pkg/exf:
22      - disable "sstExtrapol" when Nr=1
23    o verification:
24      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
25        to test pkg/cheapaml.
26    o pkg/aim_v23 & pkg/shap_filt:
27      - fix dissipation heating (erroneous gravity multiplication factor).
28    o pkg/seaice:
29      - remove unused field pressPre from jfnk solver
30      - rename two subroutines in seaice_preconditioner.F
31    o eesupp/src:
32       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
33    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
34       - remove wrong parts of the rhs and the lhs (were in there
35         because I did not understand the concept of this preconditioner)
36       - add an exchange between u- and v-sweep. This increases communication
37         by a factor of two but improves the convergence of jfnk. Ideally,
38         one would like the u- and v-sweep to be independent. So far within
39         undocumented ifdefs
40       - reorganize the extra computations for printing the residuals
41    o tools/genmake2:
42      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
43        since it's not necessary (and was preventing to use MNC in some cases).
44    
45    checkpoint64a (2012/11/16)
46    o pkg/autodiff:
47      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
48        autodiff_readparms.F no longer depends on calling order (within
49        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
50        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
51        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
52    o pkg/obcs:
53      - adding tidal velocity forcing capability to obcs
54        for usage example, see verification/seaice_obcs/input.tides
55    o pkg/seaice:
56      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
57        SEAICE_LSRrelaxU/V
58      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
59    o pkg/aim_v23:
60      - implement heating from friction (bottom friction and stratospheric drag).
61    o pkg/shap_filt:
62      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
63        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
64    o model/src:
65      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
66        time-constant addMass field from file (addMassFile);
67      - support for heating due to friction (and Kinetic Energy dissipation):
68        add option, run-time switch and 3-D field array + support code ; each pkg
69        or S/R can add heating contribution (if there is a sink of KE); the sum is
70        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
71    o pkg/seaice:
72      - complete merge of ITD code into seaice_growth.F
73        from MITgcm_contrib/torge/itd/code/
74        no verification so far, but Torge Martin tested
75        "1-D test case and Beaufort set up;
76        deliver okay results after 1 model year."
77      - complete merge of SEAICE_SIZE.h into all relevant routines
78      - move computation of eta at Z-points into calc_viscosities
79        + introduce global field etaZ
80        + add different methods for computing etaZ, for now the old
81          method (simple averages of eta to Z-points) is hardwired
82        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
83          seaice_preconditioner
84      - simplify computations for SEAICE_ZETA_SMOOTHREG
85      - seaice_preconditioner:
86        + replace one remaining press by pressLoc (mistake)
87        + adjust printing of residuals
88      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
89        + add (SEAICE.h) and rename some counters (initiliased in
90          seaice_init_fixed.F)
91        + add _BEGIN/END_MASTER (myThid)  around print statements
92        + print total number of iterations and failures over SEAICE_monFreq
93          interval to STDOUT
94      - move control over output-messages by fgmres to seaice_jfnk to save
95        some operations
96      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
97        in order to make restarts with sol .ne. zero (fgmres with restarts)
98        (seaice_jfnk.F, seaice_fgmres.F)
99      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
100        a serious convergence problem when open boundaries are involved
101    o pkg/ggl90: fix computation of control volumes for the case of
102      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
103      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
104    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
105    o pkg/autodiff
106      - Add inAdMode switch for SEAICEuseDYNAMICS:
107        SEAICEuseDYNAMICSinAdMode
108        (extend logic in ADAUTODIFF_INADMODE_SET)
109    o pkg/seaice
110      - Step 1 of merging ice-thickness distribution (ITD) code from
111        MITgcm_contrib/torge/itd/ (author: Torge Martin)
112        The code implements concept laid out in Thorndike et al. (1975);
113        code is enabled via CPP flag SEAICE_ITD
114        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
115        code is not complete yet!!
116      - SEAICE_SIZE.h now included in almost all seaice routines
117    o verification (using seaice):
118      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
119        global_ocean.cs32x15.seaice ; update results.
120      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
121      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
122        offline_exf_seaice (previously compiling B-grid).
123    o pkg/exf:
124      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
125        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
126        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
127    o pkg/layers (adjust changes from Sept 19):
128      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
129        this allows to remove "layers_maxNum" dimension from all layers arrays.
130    o pkg/layers (adjust changes from Sept 19):
131      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
132      - snap-shot extended to all type of layers (not just the 1rst type);
133      - remove layers variables when corresponding CPP option is undef.
134    o pkg/layers:
135      - rename pkg/layers variable and add new output (layer exist & un-weighted
136        velocity in layer)
137    o pkg/seaice:
138      - simplify (?) ocean-drag coefficent computations by using
139        the same routine in all three solvers (saves some code lines)
140      - remove global fields DRAGA and DRAGS from C-grid code and
141        declare them locally in lsr.F (the only place where they are
142        still used)
143      - update AD output of lab_sea.evp (very sensitive anyway).
144    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
145      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
146      and SEAICEuseJFNK=.true. A few things to note:
147      - involves a FGMRES, that is parallel but very inefficient,
148        because of many scalar products (global sums) in the Gram-Schmidt
149        orthogonalization method. Needs to be replaced. Original code
150        from J.-F. Lemieux
151      - preconditioner for FGMRES is a stripped down version of LSOR
152      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
153        preconditioner. For the preconditioner, the default is set to 10.
154      - Jacobian times vector is computed with finite differences
155      - marginally related to JFNK-solver: add a smooth regularization for
156        zeta with tanh that will improve convergence (Lemieux and Tremblay,
157        2009) for any implicit solver (not implemented for EVP because EVP
158        does not need this regularization in the first place). Define
159        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
160    o eesupp/src:
161      - check in genmake2 that intrinsic S/R flush is available.
162      - add S/R to flush IO unit (if intrinsic S/R flush is available)
163      - flush standard & error msg unit before MPI termination
164      - if debugMode, flush IO unit after printing msg
165    o pkg/ctrl:
166      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
167        to ctrl_set_unpack_xyz.
168    
169    checkpoint64 (2012/10/09)
170    o pkg/shelfice
171      - in mom_fluxform.F, mom_vecinv.F:
172        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
173        Bug fix KappaRU -> KappaRV
174        does not change verification/isomip but may change other setups
175        (presumably constant KappaRU=KappaRV)
176      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
177    o pkg/obcs:
178      - fixed some indexing bugs in obcs_seaice_sponge.F
179      - added obcs relaxation subroutines for HSALT and HSNOW
180      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
181    o pkg/seaice:
182      - add "multicategory" parameterization for snow in analogy to ice,
183        default is off for now.
184    o pkg/obcs:
185      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
186        see verification/seaice_obcs/input.seaiceSponge for example application.
187      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
188        index setting by master-thread. This fix multi-threads Pb in previous modifs.
189    o pkg/layers :
190      - add diagnostics to pkg/layers
191      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
192        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
193    o pkg/generic_advdiff/gad_implicit_r.F :
194      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
195    o pkg/seaice/seaice_growth.F:
196      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
197    o pkg/obcs:
198      - change default setting of OBCS_UVICE_OLD from defined to undef;
199      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
200        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
201      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
202      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
203        with Southern & Western OB at a tile edge (at least in a simple set-up).
204    o pkg/obcs:
205      - change settings of OB index in case OB coincides with tile edge (shared by
206        2 tiles), so that common OB location is registered by both tiles (instead of
207        only 1). However, for Southern and Western OB, index value = 0 is not
208        recognized as valid OB index (=default null value) and needs to be fixed.
209      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
210      - new parameter "OB_indexNone" for null index value (for now, still zero)
211        to replace hard-coded null index value of zero.
212    o pkg/exch2:
213      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
214        always check buffer-size (but outside the loop); move checking for valid
215        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
216        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
217    o pkg/ctrl (pack & unpack):
218      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
219        (locally defined) for different variables (+ remove the variable-specific
220        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
221        (to be extended to other local file names in ctrl.h).
222    o pkg/flt:
223      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
224    o pkg/mdsio:
225      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
226    o tools/genmake2:
227      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
228        (added by Alistair in version 1.51 for building without make depend);
229      - remove Header files list (H_SRC_FILES) from the dependence of targets
230         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
231        place in version 1.23): this save going through staf when unrelated header
232        file has been modified.
233       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
234        "make depend" step, still need to do "make links" before "make adtaf".
235    o eesupp/src (+ few pkg src files) & genmake2:
236      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
237      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
238      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
239         upper/lower case ; account for space between "#" and undef/define)
240    o pkg/flt (with exch2):
241      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
242      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
243    
244    checkpoint63s (2012/09/05)
245    o pkg/ecco:
246      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
247      - add more relevant #ifdef ALLOW_SMOOTH ones.
248      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
249    o pkg/ctrl:
250      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
251        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
252      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
253        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
254        ctrlSmoothCorrel3D (new).
255        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
256      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
257      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
258        controls when useAtmWind, and vice versa.
259      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
260      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
261          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
262      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
263          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
264      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
265        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
266    o pkg/smooth:
267      - remove un-necessary includes.
268      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
269        Those CPP options were never defined, and not necessary.
270    o model/src:
271      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
272      - standard treatment of useSMOOTH.
273    o pkg/autodiff:
274      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
275        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
276    o pkg/exch2:
277      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
278        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
279      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
280        and tiles to process mapping.
281      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
282        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
283        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
284        from w2_eeboot.F to w2_readparms.F.
285    o eesupp/src:
286      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
287        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
288        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
289      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
290        is defined (remove condition on usingMPI) to match cases where MPI_INIT
291        has been called.
292      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
293      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
294        (so that on 1 proc, get same myPid independently of usingMPI)
295      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
296        useCubedSphereExchange with EXCH-1 (safer).
297      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
298    o pkg/ggl90:
299      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
300        used in ALLOW_GGL90_SMOOTH code.
301    o pkg/flt:
302      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
303        floats at the Southern end of the domain).
304    o eesupp/inc:
305      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
306        but not used (and not to be used) anywhere, just for documentation.
307    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
308      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
309        a) can damage previously written records in any other multi-record files.
310        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
311    o tools/genmake2:
312      - define variable MAKE within Makefile and use it in place of 'make';
313      - update AD_CONFIG.h (if needed) before building any of the executable
314        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
315        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
316      - always print usual warning comment 'this file is automatically generated'
317        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
318    o pkg/cheapaml:
319      - updated to correspond to the code used in accepted paper (Nico Wienders).
320    o pkg/exf:
321        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
322        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
323        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
324    o pkg/exf, autodiff, ctrl, ecco and seaice:
325        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
326    o pkg/ctrl, ecco:
327        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
328        Depending on useAtmWind, one is inactive, and the other is active (see
329        exf_getffields.F/exf_getsurfacefluxes.F).
330    o tools/genmake2:
331      - improve error msg when failing in 2nd test of check_for_broken_Ff
332      - fix option '-makefile' short-name (-mf according to genmake2 -help)
333      - source local config file "genmake_local" just after processing the genmake2
334        command arguments (previously done before processing arg).
335    o pkg/grdchk:
336      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
337        to this routine from cost_final has been dropped in g_cost_final)
338      - improve printed information (more explicit msg, no longer using "print *,"
339         fix fcpertminus printed value).
340    o model/src:
341      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
342        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
343        this prevents getting cost-funct reset in adinitialise_varia recomputations.
344    o pkg/dic:
345      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
346        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
347    o pkg/grdchk:
348      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
349      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
350    o pkg/autodiff/ctrl/grdchk :
351      - attempt to sort out what works and what does not,
352        with regard to I/O, and to warn/stop accordingly.
353    o pkg/grdchk:
354      - attempt to fix grdchk in the case of useSingleCpuIO.
355      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
356       statements were moved from grdchk_main.F and into
357       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
358      - a global sum is applied to record numbers icvrec/layer
359       out of grdchk_loc so that they be passed to I/O routines.
360    o pkg/smooth:
361      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
362        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
363    o verification/testreport:
364      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
365      - can also use compressed (gzip) reference output file;
366      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
367        to be easier to collect by testreport.
368      - update existing TLM output (half out-of-date by more than 3 yrs).
369      - report NETCDF & LAPACK settings (from genmake2) in output dir.
370      - report run-time in each individual summary (previously only for AD test);
371        for TLM test, add also TAF version.
372      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
373    
374    checkpoint63r (2012/08/15)
375    o tools/genmake2:
376      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
377    o pkg/ecco/ecco_cost_final.F :
378      - fix fc print statements (to stdout and costfunction0000) so
379        that the printed value is always after the global sum.
380    o pkg/seaice/seaice_dynsolver.F :
381      - fix ice strength assymptote at SEAICE_area_max<1
382        (no change for the standard case of SEAICE_area_max=1)
383    o some cleaning:
384      - pkg source files: ensure that all *.F files from each pkg included the
385        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
386        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
387        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
388        includes;
389      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
390      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
391        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
392        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
393      - update option-file CPP_OPTIONS.h of all AD experiments:
394        * no longer include PACKAGES_CONFIG.h ;
395        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
396        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
397          including ECCO_CPPOPTIONS.h).
398    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
399      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
400        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
401        not necessary accurate).
402      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
403        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
404        deliberately break compilation (a remainder that it needs to be customized)
405      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
406      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
407      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
408    o tools/genamke2:
409      - check for lapack.
410    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
411      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
412        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
413        from both packages.
414      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
415      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
416      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
417        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
418    o pkg/cost : add comments to explain special and/or untested setups.
419    o pkg/exf:
420      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
421        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
422    o verification/*/code_ad:
423      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
424      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
425      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
426        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
427    o pkg/seaice :
428      - added possibility to change ice strength/PRESS0 relationship to
429        HEFF, according to the following run time parameters
430        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
431        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
432        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
433    o pkg/ggl90 :
434      - added run time flag mxlSurfFlag to include the code that ensure
435        mixing between first and second level (previously included as a comment)
436    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
437      - add test of newly added dumpAdByRec=T option where
438        we write all records to one file per variable.
439    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
440      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
441        to check that this code is ok with taf and compiles in adjoint.
442    o pkg/autodiff :
443      - added run time param dumpAdByRec : ad dump format switch.
444        If true then write all records to one file per variable.
445        Else write one file per record (remains the default).
446      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
447    o pkg/seaice:
448     - Added SEAICEuseTILT run time switch : if set to
449       false then omit the tilt term in seaice dynamics.
450     - Fix free drift calculation.
451    o pkg/shelfice:
452      When initializing SHELFICEDragQuadratic, set default to be
453      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
454      but retain option to set it independently
455      (inconsistenty spotted by Veronique Dansereau)
456    o eesupp/inc:
457      - in EEPARAMS.h, add real-type constant for some frequently used simple number
458         (0,1,2,1/2), with name explicitly referring to RS/RL type.
459    o model/src:
460      - move balancing of relaxation terms to new S/R balance_relax.F.
461    o pkg/autodiff:
462      re-write active I/O high-level (control) S/R:
463      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
464      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
465      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
466        MDS_READ/WRITE_FIELD); change loops to multi-threads.
467      - update and merge active_file_control_slice.flow into active_file_control.flow
468      - update the calls in lower level S/R (active_file.F, active_file_g.F and
469        active_file_ad.F) keeping the argument list and function unchanged.
470      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
471        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
472      - new low-level active I/O routines, one for each type (RL/RS), for active var
473        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
474        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
475        right type.
476    o autodiff and RS=real*4:
477      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
478        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
479      - change argument type of 3-D mask argument to _RS to match type in the call
480        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
481    o pkg/thsice:
482      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
483      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
484        fresh-water flux: uniform correction or proportional to local precip.
485    o pkg/ctrl:
486      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
487      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
488                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
489      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
490    
491    checkpoint63q (2012/07/30)
492    o pkg/autodiff:
493      note about monitor and snap-shot of ad-variables:
494      a) need to apply ADEXCH before monitor or output of ad-vars to include
495       overlap contributions (was done for adjDump but missing for monitor).
496      b) since ADEXCH implies adding overlap values to interior array, machine
497       truncation error is expected when adding an ADEXCH call in the middle of
498       the time-stepping (although mathematically identical).
499      modifs:
500      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
501        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
502      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
503        apply ADEXCH before monitor or snap-shot of ad-variables:
504           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
505      - implement new method (copy+adexch) for snap-shot and monitor of main model
506        ad-vars (initially not used by default -> output unchanged).
507      - change default (set to 2) to use new method and update few output_adm.txt
508        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
509        and both tutorial_tracer_adjsens tests).
510      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
511        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
512    o pkg/ctrl:
513      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
514      generic control variables via
515      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
516      Only required customization should be S/R ctrl_map_ini_genarr.F
517      (routine in repository contains example)
518    o pkg/exf:
519      - fix and refine checking of surface-relaxation setting when using EXF
520    o verification (adjoint exp):
521      - reduce length of simulation by half for experiment global_ocean.cs32x15
522        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
523    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
524      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
525        of KE that can occur with aggressive optimization
526      + put quadratic bottom drag calculation in separated loops (only done if
527        using bottomDragQuadratic)
528    o model/src: CG2D_NSA
529      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
530         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
531      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
532         change cg2d residual target to be expressed in Wunits (=> do not normalise
533         RHS ; this fix global_max Pb with TAF); update output.
534    o verification/tutorial_tracer_adjsens:
535       improve parameter consistency (and get rid of warnings):
536       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
537       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
538       - use staggerTimeStep (for stability) in som81; use default rotation period.
539    o pkg/exch2:
540      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
541        reset to 0 = 1 long line in X)
542    o pkg/mdsio:
543      - fix reading of dimensions from meta file for large-size domain
544    o model/src:
545      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
546      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
547        Cubed-Sphere Exch with CS-corners inside the domain;
548        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
549        globalArea and to set hasWetCSCorners.
550      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
551        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
552      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
553        useCDscheme and useCubedSphereExchange).
554    o pkg/seaice/seaice_growth.F :
555      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
556        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
557        when the previous code was not correct.
558      - in all cases diagnoze the boundary condition mismatch to SIaaflux
559      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
560        that term to QNET (essentially to set the melt/freeze water to 0degC).
561        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
562    o verification/global_ocean.cs32x15/input.seaice :
563      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
564      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
565      - update results (output.seaice.txt) accordingly.
566    o verification/lab_sea/input/data.seaice :
567      - remove SEAICEheatConsFix, which is now be tested
568        in global_ocean.cs32x15. The presently coded fix
569        is only consistent with real fresh water + nlfs.
570      - update results (output.txt) accordingly.
571    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
572    o AD_CONFIG.h file:
573      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
574      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
575        add it explicitly in each fortran src file where it is needed.
576        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
577        thus introducing potentially wrong dependency; therefore, better to include
578        it only where it's really needed, and after any other included OPTIONS file
579        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
580        or ALLOW_TANGENTLINEAR_RUN).
581    
582    checkpoint63p (2012/07/06)
583    o pkg/autodiff:
584      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
585      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
586        which are now read from new parameter file "data.autodiff" (inAdExact
587        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
588      - add file "data.autodiff" in all verification/*/input_ad/ directories.
589      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
590        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
591    o verification/tutorial_tracer_adjsens/
592      - add extra sub-verification which uses "SOM" advection scheme
593        (2nd Order-Moment Advection Scheme, Prather Limiter) with
594          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
595        and in data:
596          multiDimAdvection=.TRUE.,
597          tempAdvScheme=81,
598          saltAdvScheme=81,
599    o model/src:
600      - introduce ALLOW_BALANCE_RELAX which allow the removal
601       of the global mean of relaxation terms by setting
602       balanceThetaClimRelax and balanceSaltClimRelax
603      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
604       This case is now treated appropriately in seaice_growth.F
605    o pkg/seaice:
606      - do balanceEmPmR and balanceQnet based on the net fluxes
607        (SItflux) that enter the ocean+ice system rather than QNET
608        and EMPMR. Works best in real fresh water.
609      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
610        out of the diagnotics bloc, and stored in global arrays.
611    
612    checkpoint63o (2012/06/29)
613    o vertical mixing schemes:
614      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
615      - replace computation of density (in Function STATE1, opps_calc.F) by a call
616        to S/R FIND_RHO_SCALAR
617      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
618        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
619        affects output (vermix.ggl90) at truncation level.
620    o testreport:
621      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
622        (nSx,nSy) for the number of threads (from eedata.mth)
623    o model/src:
624      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
625        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
626    o verification/tutorial_tracer_adjsens/
627      - compile with ALLOW_CG2D_NSA
628      - run with nonlinFreeSurf=3
629      - update reference output_adm.txt
630    o tools/genmake2:
631      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
632        refine usePROFILES switching off (only when NetCDF is not available).
633    o verification (atmospheric set-up):
634      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
635    o pkg/profiles : refine profiles and files handling.
636    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
637    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
638      - changes to use model/src/the_main_loop.F rather than the ecco version
639        in ecco type adjoint runs.
640    o model/src:
641      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
642      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
643      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
644    o model/src:
645      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
646        update output of test experiment bottom_ctrl_5x5.
647    o pkg/generic_advdiff:
648      - implement vertical bi-harmonic diffusion (for now, only for T & S and
649        only explicitly).
650    o verification/bottom_ctrl_5x5/
651      update reference output (results changed quite some time ago,
652      not sure when; but new reference results look ok in terms of grdchk)
653    o verification/1D_ocean_ice_column/
654      For verification purposes, the exact adjoint rather than an approx.
655      should be used (e.g., to comare against F.D. or TLM).
656      removed autodiff_inadmode*_ad.F routines in code_ad/
657      Update results/ accordingly.
658    o pkg/cal:
659      - change cal_getdate.F so that output date is function of input time only
660        (less ambiguous, not mixed up with input iteration number).
661      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
662    o pkg/diagnostics:
663      - implement calendarDumps also for stats-diags
664      - implement calendarDumps also for snap-shot output (negative freq)
665      - for now, ignores calendarDumps if non-zero phase-lag.
666    
667    checkpoint63n (2012/06/04)
668    o model/src:
669      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
670        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
671      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
672        similar to calc_r_star.F); update results of experiment internal_wave and
673        tutorial_global_oce_in_p (affected @ truncation level).
674    o pkg/shelfice:
675      - add parameterisation of advective-diffusive flux into the ice shelf
676        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
677      - simply eps3/3a computation
678    o eesupp:
679     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
680       between tiles, just fill-in edges assuming locally periodic subdomain) and
681       add corresponding exchange subroutines (EXCH0);
682     - new CG-solver version (_EX0) for disconnected-tiles special case.
683    o model/src (CG-solvers):
684     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
685       (similar final residual output and max-Iter number as with standard version);
686     - allows to store and use lowest-residual solution (standard & _SR versions);
687     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
688     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
689    o eesup/src:
690     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
691       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
692    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
693    
694    checkpoint63m (2012/04/27)
695    o pkg/shelfice:
696     - account for partical cells in surface level below ice-shelf for hydrostatic
697       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
698    o ad test experiments:
699     - update and rename to "ad_optfile.local" local AD-optfile specific to a
700       particular adjoint verification experiment (in verification/*/code_ad/)
701    o pkg/seaice & pkg/exf:
702     - Part two of ECCO-CLIVAR code merges.
703       Completes merge of seaice area relax. code.
704       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
705       to be set in EXF_OPTIONS.h since this pkg controls its I/O
706       (and avoids second CPP option in SEAICE_OPTIONS.h)
707     - change default value of costIceStart & costIceEnd to a valid date.
708     - add snowPrecip to HSNOW in seaice_growth
709    o pkg/ptracers:
710     - move ptracers summary and setup check into separated S/R ; add a check for
711       valid PTRACERS_Iter0 value (error+stop or just warning).
712    o pkg/cal (+ pkg/ecco):
713     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
714       as input; and for AD, unless both are not differentiable (e.g., k index)).
715    o model/src:
716     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
717       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
718       temporary set to usingZCoords value (to be changed to F when using shelfice).
719     - hydrostatic pressure: implement partial cell near the surface also for
720       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
721       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
722    o pkg/ctrl/ctrl_init.F:
723     - add a formal parameter to s/r ctrl_init_rec to print
724       xx_$(ctrl_valiable)_file for easier debugging
725     - move call of cal_* routines into the if-block where they are really
726       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
727       to specify a startdate
728    o pkg/seaice:
729     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
730       global_ocean.cs32x15/code versions).
731     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
732       verification experiment global_ocean.cs32x15.seaice and update results.
733    o pkg/exf:
734     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
735       (according to useExfYearlyFields).
736    o pkg/cal:
737     - move calendar setting & summary (previously in cal_readparams.F) into new
738       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
739       length of the simulation is set (after SET_PARMS call); This is an attempt
740       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
741     - For safety: keep a record of pkg/cal parameter settings status
742               to allow to STOP if one pkg/cal S/R is called too early.
743     - add a stop in all basic pkg/cal subroutines if called before setting is done.
744     - modify cal_getdate.F: stop when nothing was returned;
745       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
746       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
747    
748    checkpoint63l (2012/04/04)
749    o pkg/bbl:
750      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
751        update global_with_exf output.yearly.txt file.
752    o pkg/cal:
753      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
754      - remove 2 unsused and very short (1 line only) functions ;
755      - remove unsused subroutines from AD-Diff list.
756    o model/src:
757      - start to implement clean wait to stop in initialization S/R (config_check.F,
758         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
759    o folowing PRINT_MESSAGE changes:
760      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
761    o pkg/bbl:
762      - modification so it can work with z*
763      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
764      - global_with_exf/input.yearly verification; changes output.yearly.txt
765    o eesupp/src:
766      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
767        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
768      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
769        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
770      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
771      - when using MPI, always set usingMPI=T ; set default accordingly and stop
772        if not consistent.
773      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
774        argument is zero (in case called within single-thread section).
775    o pkg/fizhi:
776        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
777        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
778    o pkg/exch2:
779      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
780        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
781      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
782        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
783        with bad ones coming from a not-yet-updated halo.
784        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
785    o pkg/frazil:
786        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
787        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
788    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
789    o verification/lab_sea
790      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
791      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
792      * nTimeSteps 3 -> 4
793      * changed reference output accordingly
794    o pkg/ctrl:
795      * fix ctrl_get_gen for xx_sst, xx_sss
796    o pkg/fizhi:
797      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
798        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
799      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
800        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
801        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
802    o pkg/gmredi:
803      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
804    o pkg/fizhi:
805      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
806        (old)aces open64 tuv test.
807    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
808    o pkg/mom_vecinv:
809      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
810        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
811        with non-lin free-surf).
812    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
813      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
814      some compilers (gfortran 4.6.0 on MacOS)
815    o momentum:
816      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
817        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
818        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
819    
820    checkpoint63k (2012/03/17)
821    o model/src:
822       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
823         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
824       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
825         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
826    o model/src: solve_*diagonal.F
827       - replace division with multiplication by inverse (similar to original version)
828         update output of AD exp. global_ocean.90x40x15.
829       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
830         to enable the use of the vectorized & differentiable solve_tridiagonal.F
831       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
832         vertical advection (to get solve_tridiagonal tested in AD mode).
833    o pkg/seaice: ECCO-CLIVAR merge:
834      1. seaice AREA relaxation
835         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
836         * runtime flag: SEAICE_tauAreaObsRelax
837      2. modified global mean cost imbalance code: CPP option
838          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
839    o another iteration on solve_*diagonal.F
840       Make choices independent of AUTODIFF
841       Default will be the adjoinable vectorized version.
842       Alternative choices are:
843       * non-adjoinable original version with low memory footprint:
844         #define SOLVE_DIAGONAL_LOWMEMORY
845       * still adjoinable but does not vectorize (k as inner-most loop):
846         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
847    o testreport
848     - add option to use a home made wrapper around "make"
849     - remove MITGCM_IEEE env. variable (no longer active)
850    o pkg/shelfice
851     - improve computation of friction velocity for velocity dependent
852       exchange coefficients: include velocities into SHELFICEBoundaryLayer
853       block to average velocities vertically
854     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
855    o Modify diagonal solvers, now three versions (upon request):
856      #ifndef SOLVE_DIAGONAL_AUTODIFF
857        1. default version (dating back a while ago)
858      #else /* def SOLVE_DIAGONAL_AUTODIFF */
859      # ifdef SOLVE_DIAGONAL_KINNER
860        2. adjoinable version with k-innermost loop (G. Forget)
861      # else
862        3. adjoinable vectorized version of 2.
863      # endif
864      #endif /* SOLVE_DIAGONAL_AUTODIFF */
865      All flags are currently set within routines, but could/should be moved to CPP-options.
866      Array bounds for 1. are as before, for 2.,3. cover the entire domain
867      (could be changed for 1. too).
868    o verification/lab_sea (fwd):
869      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
870        use 7 categories (except hb87), new solve4temp params (except salt_plume),
871        constant salinity (=4) or variable salinity (salt_plume) done through
872        SItracer.
873    o pkg/seaice:
874      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
875      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
876         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
877        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
878        SEAICE_freeze got retired) but already better than previously with
879        SEAICE_freeze=123456.7 deg.C;
880      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
881        (safer multi-threaded setting); always set SEAICEuseEVP;
882      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
883        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
884        stop if multiple specifications for the same coeff; make sure default
885        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
886    o pkg/obcs:
887      - allow to switch to upwind 1rst order advection scheme for the advective
888        flux computation at the open-boundary; disabled for adjoint built.
889    o pkg/ptracers:
890      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
891      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
892      - add parameter to decide when to start a tracer; use internal flag to
893        know which tracer to step-forward; switch this internal flag at the top
894        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
895        for adjoint built.
896    o pkg/seaice:
897      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
898      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
899      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
900    o pkg/ecco:
901      - fix writing of output file DiagnosCost_ClimSalt/Theta
902        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
903    o pkg/seaice:
904      - add missing initialisation of COR_ICE array in dynsolver.F
905      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
906        compiled either way, and is tested in all exps (multidim was only tested
907        in lab_sea ad before).
908      - cosmetic change to prepare for future addition of ITD. no change to results.
909        no defaults change.
910      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
911      - by lack of adequate verification experiments, I further used custom versions
912        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
913        should be correct.
914      - avoid recomputations in ad.
915    o array initialisation in adjoint mode:
916      1) pkg/mom_common/mom_calc_ke.F:
917        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
918        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
919        part this initialisation is gone, resulting in Floating Point Exception
920        (caught by open64 compiler with debug option).
921      2) model/src/convective_weights.F
922        set output convectCount over the full array range (instead of doing
923        an update): this fix a similar issue when called within recomputation (adjoint)
924        which could by-pass the initialisation (normally done in the caller S/R).
925    o pkg/seaice:
926      - final version of turbulent flux params, as agreed at MIT ice meet:
927           SEAICE_mcPheePiston (default is ~ 0.000875)
928           SEAICE_mcPheeTaper (default is 0.)
929           SEAICE_frazilFrac (defualt is 1.)
930           SEAICE_mcPheeStepFunc (default is false)
931      - changes results at trunction error level
932      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
933    o added pkg/frazil:
934      - see frazil_description.tex for details
935      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
936    o pkg/shelfice/shelfice_thermodynamics.F
937      - fix exponents for velocity dependent exchange coefficients: change
938        from 2/3(=0) to 0.66666666666666667
939      - move computation of velocity dependent exchange coefficients into
940        separate loop, so that it applies to both thermodynamics
941      - move some divisions by constants out of loops
942    
943    checkpoint63j (2012/02/16)
944    o pkg/seaice:
945      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
946      - SItracer:  added run time params, and allow coupling to ocn salinity.
947    o pkg/seaice: remove (almost) all divisions by constants within loops
948      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
949      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
950      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
951      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
952    o pkg/seaice :
953      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
954        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
955      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
956      - add permanent SItflux diag that corresponds to TFLUX but includes
957        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
958      - allow activation/testing of a fix for suspected missing term in
959        ocn-ice heat budget (to be confirmed). To test this, you want to
960        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
961        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
962      - no change in results, fwd or ad.
963    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
964      - switch to variable freezing point.
965         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
966    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
967         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
968    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
969         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
970  o pkg/seaice:  o pkg/seaice:
971    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
972   is now the default, and the old default constant freezing point is recovered with      is now the default, and the old default constant freezing point is recovered
973   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
974   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
975    - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.    - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
976    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
977    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
978   activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.      activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
979    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
980   was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).      was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
981    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
982   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
983    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
984    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
985    to variable freezing point (see above item for detail).    - results did not change except for global_ocean.cs32x15, mostly due to the
986        switch to variable freezing point (see above item for detail).
987  o pkg/thsice:  o pkg/thsice:
988    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
989      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
990  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
991    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
992    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
993                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
994    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
995    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
996    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
997      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
998      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
999    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
1000      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
1001    - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).    - seaice_summary.F : add missing report of read turbulent flux term set up
1002    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
1003      - seaice_check.F : check range; inform and stop if retired CPPs are used
1004                         (incl. SEAICE_AGE).
1005    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
1006          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
1007    - change results at the truncation level.    - change results at the truncation level.
1008  o pkg/seaice:  o pkg/seaice:
1009    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
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