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revision 1.1576 by jmc, Fri Jan 20 01:30:45 2012 UTC revision 1.1741 by jmc, Wed Sep 19 19:21:58 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 pkg/obcs:
8      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
9        index setting by master-thread. This fix multi-threads Pb in previous modifs.
10    o pkg/layers :
11      - add diagnostics to pkg/layers
12      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
13        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
14    o pkg/generic_advdiff/gad_implicit_r.F :
15      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
16    o pkg/seaice/seaice_growth.F:
17      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
18    o pkg/obcs:
19      - change default setting of OBCS_UVICE_OLD from defined to undef;
20      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
21        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
22      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
23      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
24        with Southern & Western OB at a tile edge (at least in a simple set-up).
25    o pkg/obcs:
26      - change settings of OB index in case OB coincides with tile edge (shared by
27        2 tiles), so that common OB location is registered by both tiles (instead of
28        only 1). However, for Southern and Western OB, index value = 0 is not
29        recognized as valid OB index (=default null value) and needs to be fixed.
30      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
31      - new parameter "OB_indexNone" for null index value (for now, still zero)
32        to replace hard-coded null index value of zero.
33    o pkg/exch2:
34      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
35        always check buffer-size (but outside the loop); move checking for valid
36        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
37        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
38    o pkg/ctrl (pack & unpack):
39      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
40        (locally defined) for different variables (+ remove the variable-specific
41        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
42        (to be extended to other local file names in ctrl.h).
43    o pkg/flt:
44      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
45    o pkg/mdsio:
46      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
47    o tools/genmake2:
48      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
49        (added by Alistair in version 1.51 for building without make depend);
50      - remove Header files list (H_SRC_FILES) from the dependence of targets
51         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
52        place in version 1.23): this save going through staf when unrelated header
53        file has been modified.
54       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
55        "make depend" step, still need to do "make links" before "make adtaf".
56    o eesupp/src (+ few pkg src files) & genmake2:
57      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
58      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
59      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
60         upper/lower case ; account for space between "#" and undef/define)
61    o pkg/flt (with exch2):
62      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
63      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
64    
65    checkpoint63s (2012/09/05)
66    o pkg/ecco:
67      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
68      - add more relevant #ifdef ALLOW_SMOOTH ones.
69      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
70    o pkg/ctrl:
71      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
72        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
73      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
74        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
75        ctrlSmoothCorrel3D (new).
76        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
77      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
78      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
79        controls when useAtmWind, and vice versa.
80      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
81      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
82          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
83      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
84          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
85      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
86        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
87    o pkg/smooth:
88      - remove un-necessary includes.
89      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
90        Those CPP options were never defined, and not necessary.
91    o model/src:
92      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
93      - standard treatment of useSMOOTH.
94    o pkg/autodiff:
95      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
96        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
97    o pkg/exch2:
98      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
99        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
100      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
101        and tiles to process mapping.
102      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
103        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
104        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
105        from w2_eeboot.F to w2_readparms.F.
106    o eesupp/src:
107      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
108        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
109        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
110      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
111        is defined (remove condition on usingMPI) to match cases where MPI_INIT
112        has been called.
113      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
114      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
115        (so that on 1 proc, get same myPid independently of usingMPI)
116      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
117        useCubedSphereExchange with EXCH-1 (safer).
118      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
119    o pkg/ggl90:
120      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
121        used in ALLOW_GGL90_SMOOTH code.
122    o pkg/flt:
123      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
124        floats at the Southern end of the domain).
125    o eesupp/inc:
126      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
127        but not used (and not to be used) anywhere, just for documentation.
128    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
129      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
130        a) can damage previously written records in any other multi-record files.
131        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
132    o tools/genmake2:
133      - define variable MAKE within Makefile and use it in place of 'make';
134      - update AD_CONFIG.h (if needed) before building any of the executable
135        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
136        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
137      - always print usual warning comment 'this file is automatically generated'
138        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
139    o pkg/cheapaml:
140      - updated to correspond to the code used in accepted paper (Nico Wienders).
141    o pkg/exf:
142        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
143        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
144        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
145    o pkg/exf, autodiff, ctrl, ecco and seaice:
146        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
147    o pkg/ctrl, ecco:
148        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
149        Depending on useAtmWind, one is inactive, and the other is active (see
150        exf_getffields.F/exf_getsurfacefluxes.F).
151    o tools/genmake2:
152      - improve error msg when failing in 2nd test of check_for_broken_Ff
153      - fix option '-makefile' short-name (-mf according to genmake2 -help)
154      - source local config file "genmake_local" just after processing the genmake2
155        command arguments (previously done before processing arg).
156    o pkg/grdchk:
157      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
158        to this routine from cost_final has been dropped in g_cost_final)
159      - improve printed information (more explicit msg, no longer using "print *,"
160         fix fcpertminus printed value).
161    o model/src:
162      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
163        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
164        this prevents getting cost-funct reset in adinitialise_varia recomputations.
165    o pkg/dic:
166      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
167        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
168    o pkg/grdchk:
169      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
170      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
171    o pkg/autodiff/ctrl/grdchk :
172      - attempt to sort out what works and what does not,
173        with regard to I/O, and to warn/stop accordingly.
174    o pkg/grdchk:
175      - attempt to fix grdchk in the case of useSingleCpuIO.
176      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
177       statements were moved from grdchk_main.F and into
178       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
179      - a global sum is applied to record numbers icvrec/layer
180       out of grdchk_loc so that they be passed to I/O routines.
181    o pkg/smooth:
182      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
183        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
184    o verification/testreport:
185      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
186      - can also use compressed (gzip) reference output file;
187      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
188        to be easier to collect by testreport.
189      - update existing TLM output (half out-of-date by more than 3 yrs).
190      - report NETCDF & LAPACK settings (from genmake2) in output dir.
191      - report run-time in each individual summary (previously only for AD test);
192        for TLM test, add also TAF version.
193      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
194    
195    checkpoint63r (2012/08/15)
196    o tools/genmake2:
197      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
198    o pkg/ecco/ecco_cost_final.F :
199      - fix fc print statements (to stdout and costfunction0000) so
200        that the printed value is always after the global sum.
201    o pkg/seaice/seaice_dynsolver.F :
202      - fix ice strength assymptote at SEAICE_area_max<1
203        (no change for the standard case of SEAICE_area_max=1)
204    o some cleaning:
205      - pkg source files: ensure that all *.F files from each pkg included the
206        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
207        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
208        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
209        includes;
210      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
211      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
212        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
213        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
214      - update option-file CPP_OPTIONS.h of all AD experiments:
215        * no longer include PACKAGES_CONFIG.h ;
216        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
217        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
218          including ECCO_CPPOPTIONS.h).
219    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
220      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
221        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
222        not necessary accurate).
223      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
224        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
225        deliberately break compilation (a remainder that it needs to be customized)
226      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
227      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
228      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
229    o tools/genamke2:
230      - check for lapack.
231    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
232      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
233        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
234        from both packages.
235      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
236      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
237      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
238        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
239    o pkg/cost : add comments to explain special and/or untested setups.
240    o pkg/exf:
241      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
242        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
243    o verification/*/code_ad:
244      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
245      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
246      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
247        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
248    o pkg/seaice :
249      - added possibility to change ice strength/PRESS0 relationship to
250        HEFF, according to the following run time parameters
251        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
252        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
253        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
254    o pkg/ggl90 :
255      - added run time flag mxlSurfFlag to include the code that ensure
256        mixing between first and second level (previously included as a comment)
257    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
258      - add test of newly added dumpAdByRec=T option where
259        we write all records to one file per variable.
260    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
261      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
262        to check that this code is ok with taf and compiles in adjoint.
263    o pkg/autodiff :
264      - added run time param dumpAdByRec : ad dump format switch.
265        If true then write all records to one file per variable.
266        Else write one file per record (remains the default).
267      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
268    o pkg/seaice:
269     - Added SEAICEuseTILT run time switch : if set to
270       false then omit the tilt term in seaice dynamics.
271     - Fix free drift calculation.
272    o pkg/shelfice:
273      When initializing SHELFICEDragQuadratic, set default to be
274      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
275      but retain option to set it independently
276      (inconsistenty spotted by Veronique Dansereau)
277    o eesupp/inc:
278      - in EEPARAMS.h, add real-type constant for some frequently used simple number
279         (0,1,2,1/2), with name explicitly referring to RS/RL type.
280    o model/src:
281      - move balancing of relaxation terms to new S/R balance_relax.F.
282    o pkg/autodiff:
283      re-write active I/O high-level (control) S/R:
284      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
285      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
286      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
287        MDS_READ/WRITE_FIELD); change loops to multi-threads.
288      - update and merge active_file_control_slice.flow into active_file_control.flow
289      - update the calls in lower level S/R (active_file.F, active_file_g.F and
290        active_file_ad.F) keeping the argument list and function unchanged.
291      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
292        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
293      - new low-level active I/O routines, one for each type (RL/RS), for active var
294        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
295        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
296        right type.
297    o autodiff and RS=real*4:
298      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
299        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
300      - change argument type of 3-D mask argument to _RS to match type in the call
301        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
302    o pkg/thsice:
303      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
304      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
305        fresh-water flux: uniform correction or proportional to local precip.
306    o pkg/ctrl:
307      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
308      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
309                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
310      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
311    
312    checkpoint63q (2012/07/30)
313    o pkg/autodiff:
314      note about monitor and snap-shot of ad-variables:
315      a) need to apply ADEXCH before monitor or output of ad-vars to include
316       overlap contributions (was done for adjDump but missing for monitor).
317      b) since ADEXCH implies adding overlap values to interior array, machine
318       truncation error is expected when adding an ADEXCH call in the middle of
319       the time-stepping (although mathematically identical).
320      modifs:
321      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
322        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
323      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
324        apply ADEXCH before monitor or snap-shot of ad-variables:
325           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
326      - implement new method (copy+adexch) for snap-shot and monitor of main model
327        ad-vars (initially not used by default -> output unchanged).
328      - change default (set to 2) to use new method and update few output_adm.txt
329        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
330        and both tutorial_tracer_adjsens tests).
331      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
332        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
333    o pkg/ctrl:
334      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
335      generic control variables via
336      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
337      Only required customization should be S/R ctrl_map_ini_genarr.F
338      (routine in repository contains example)
339    o pkg/exf:
340      - fix and refine checking of surface-relaxation setting when using EXF
341    o verification (adjoint exp):
342      - reduce length of simulation by half for experiment global_ocean.cs32x15
343        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
344    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
345      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
346        of KE that can occur with aggressive optimization
347      + put quadratic bottom drag calculation in separated loops (only done if
348        using bottomDragQuadratic)
349    o model/src: CG2D_NSA
350      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
351         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
352      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
353         change cg2d residual target to be expressed in Wunits (=> do not normalise
354         RHS ; this fix global_max Pb with TAF); update output.
355    o verification/tutorial_tracer_adjsens:
356       improve parameter consistency (and get rid of warnings):
357       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
358       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
359       - use staggerTimeStep (for stability) in som81; use default rotation period.
360    o pkg/exch2:
361      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
362        reset to 0 = 1 long line in X)
363    o pkg/mdsio:
364      - fix reading of dimensions from meta file for large-size domain
365    o model/src:
366      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
367      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
368        Cubed-Sphere Exch with CS-corners inside the domain;
369        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
370        globalArea and to set hasWetCSCorners.
371      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
372        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
373      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
374        useCDscheme and useCubedSphereExchange).
375    o pkg/seaice/seaice_growth.F :
376      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
377        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
378        when the previous code was not correct.
379      - in all cases diagnoze the boundary condition mismatch to SIaaflux
380      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
381        that term to QNET (essentially to set the melt/freeze water to 0degC).
382        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
383    o verification/global_ocean.cs32x15/input.seaice :
384      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
385      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
386      - update results (output.seaice.txt) accordingly.
387    o verification/lab_sea/input/data.seaice :
388      - remove SEAICEheatConsFix, which is now be tested
389        in global_ocean.cs32x15. The presently coded fix
390        is only consistent with real fresh water + nlfs.
391      - update results (output.txt) accordingly.
392    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
393    o AD_CONFIG.h file:
394      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
395      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
396        add it explicitly in each fortran src file where it is needed.
397        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
398        thus introducing potentially wrong dependency; therefore, better to include
399        it only where it's really needed, and after any other included OPTIONS file
400        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
401        or ALLOW_TANGENTLINEAR_RUN).
402    
403    checkpoint63p (2012/07/06)
404    o pkg/autodiff:
405      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
406      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
407        which are now read from new parameter file "data.autodiff" (inAdExact
408        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
409      - add file "data.autodiff" in all verification/*/input_ad/ directories.
410      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
411        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
412    o verification/tutorial_tracer_adjsens/
413      - add extra sub-verification which uses "SOM" advection scheme
414        (2nd Order-Moment Advection Scheme, Prather Limiter) with
415          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
416        and in data:
417          multiDimAdvection=.TRUE.,
418          tempAdvScheme=81,
419          saltAdvScheme=81,
420    o model/src:
421      - introduce ALLOW_BALANCE_RELAX which allow the removal
422       of the global mean of relaxation terms by setting
423       balanceThetaClimRelax and balanceSaltClimRelax
424      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
425       This case is now treated appropriately in seaice_growth.F
426    o pkg/seaice:
427      - do balanceEmPmR and balanceQnet based on the net fluxes
428        (SItflux) that enter the ocean+ice system rather than QNET
429        and EMPMR. Works best in real fresh water.
430      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
431        out of the diagnotics bloc, and stored in global arrays.
432    
433    checkpoint63o (2012/06/29)
434    o vertical mixing schemes:
435      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
436      - replace computation of density (in Function STATE1, opps_calc.F) by a call
437        to S/R FIND_RHO_SCALAR
438      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
439        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
440        affects output (vermix.ggl90) at truncation level.
441    o testreport:
442      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
443        (nSx,nSy) for the number of threads (from eedata.mth)
444    o model/src:
445      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
446        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
447    o verification/tutorial_tracer_adjsens/
448      - compile with ALLOW_CG2D_NSA
449      - run with nonlinFreeSurf=3
450      - update reference output_adm.txt
451    o tools/genmake2:
452      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
453        refine usePROFILES switching off (only when NetCDF is not available).
454    o verification (atmospheric set-up):
455      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
456    o pkg/profiles : refine profiles and files handling.
457    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
458    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
459      - changes to use model/src/the_main_loop.F rather than the ecco version
460        in ecco type adjoint runs.
461    o model/src:
462      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
463      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
464      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
465    o model/src:
466      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
467        update output of test experiment bottom_ctrl_5x5.
468    o pkg/generic_advdiff:
469      - implement vertical bi-harmonic diffusion (for now, only for T & S and
470        only explicitly).
471    o verification/bottom_ctrl_5x5/
472      update reference output (results changed quite some time ago,
473      not sure when; but new reference results look ok in terms of grdchk)
474    o verification/1D_ocean_ice_column/
475      For verification purposes, the exact adjoint rather than an approx.
476      should be used (e.g., to comare against F.D. or TLM).
477      removed autodiff_inadmode*_ad.F routines in code_ad/
478      Update results/ accordingly.
479    o pkg/cal:
480      - change cal_getdate.F so that output date is function of input time only
481        (less ambiguous, not mixed up with input iteration number).
482      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
483    o pkg/diagnostics:
484      - implement calendarDumps also for stats-diags
485      - implement calendarDumps also for snap-shot output (negative freq)
486      - for now, ignores calendarDumps if non-zero phase-lag.
487    
488    checkpoint63n (2012/06/04)
489    o model/src:
490      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
491        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
492      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
493        similar to calc_r_star.F); update results of experiment internal_wave and
494        tutorial_global_oce_in_p (affected @ truncation level).
495    o pkg/shelfice:
496      - add parameterisation of advective-diffusive flux into the ice shelf
497        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
498      - simply eps3/3a computation
499    o eesupp:
500     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
501       between tiles, just fill-in edges assuming locally periodic subdomain) and
502       add corresponding exchange subroutines (EXCH0);
503     - new CG-solver version (_EX0) for disconnected-tiles special case.
504    o model/src (CG-solvers):
505     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
506       (similar final residual output and max-Iter number as with standard version);
507     - allows to store and use lowest-residual solution (standard & _SR versions);
508     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
509     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
510    o eesup/src:
511     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
512       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
513    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
514    
515    checkpoint63m (2012/04/27)
516    o pkg/shelfice:
517     - account for partical cells in surface level below ice-shelf for hydrostatic
518       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
519    o ad test experiments:
520     - update and rename to "ad_optfile.local" local AD-optfile specific to a
521       particular adjoint verification experiment (in verification/*/code_ad/)
522    o pkg/seaice & pkg/exf:
523     - Part two of ECCO-CLIVAR code merges.
524       Completes merge of seaice area relax. code.
525       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
526       to be set in EXF_OPTIONS.h since this pkg controls its I/O
527       (and avoids second CPP option in SEAICE_OPTIONS.h)
528     - change default value of costIceStart & costIceEnd to a valid date.
529     - add snowPrecip to HSNOW in seaice_growth
530    o pkg/ptracers:
531     - move ptracers summary and setup check into separated S/R ; add a check for
532       valid PTRACERS_Iter0 value (error+stop or just warning).
533    o pkg/cal (+ pkg/ecco):
534     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
535       as input; and for AD, unless both are not differentiable (e.g., k index)).
536    o model/src:
537     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
538       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
539       temporary set to usingZCoords value (to be changed to F when using shelfice).
540     - hydrostatic pressure: implement partial cell near the surface also for
541       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
542       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
543    o pkg/ctrl/ctrl_init.F:
544     - add a formal parameter to s/r ctrl_init_rec to print
545       xx_$(ctrl_valiable)_file for easier debugging
546     - move call of cal_* routines into the if-block where they are really
547       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
548       to specify a startdate
549    o pkg/seaice:
550     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
551       global_ocean.cs32x15/code versions).
552     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
553       verification experiment global_ocean.cs32x15.seaice and update results.
554    o pkg/exf:
555     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
556       (according to useExfYearlyFields).
557    o pkg/cal:
558     - move calendar setting & summary (previously in cal_readparams.F) into new
559       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
560       length of the simulation is set (after SET_PARMS call); This is an attempt
561       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
562     - For safety: keep a record of pkg/cal parameter settings status
563               to allow to STOP if one pkg/cal S/R is called too early.
564     - add a stop in all basic pkg/cal subroutines if called before setting is done.
565     - modify cal_getdate.F: stop when nothing was returned;
566       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
567       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
568    
569    checkpoint63l (2012/04/04)
570    o pkg/bbl:
571      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
572        update global_with_exf output.yearly.txt file.
573    o pkg/cal:
574      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
575      - remove 2 unsused and very short (1 line only) functions ;
576      - remove unsused subroutines from AD-Diff list.
577    o model/src:
578      - start to implement clean wait to stop in initialization S/R (config_check.F,
579         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
580    o folowing PRINT_MESSAGE changes:
581      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
582    o pkg/bbl:
583      - modification so it can work with z*
584      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
585      - global_with_exf/input.yearly verification; changes output.yearly.txt
586    o eesupp/src:
587      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
588        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
589      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
590        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
591      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
592      - when using MPI, always set usingMPI=T ; set default accordingly and stop
593        if not consistent.
594      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
595        argument is zero (in case called within single-thread section).
596    o pkg/fizhi:
597        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
598        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
599    o pkg/exch2:
600      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
601        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
602      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
603        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
604        with bad ones coming from a not-yet-updated halo.
605        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
606    o pkg/frazil:
607        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
608        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
609    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
610    o verification/lab_sea
611      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
612      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
613      * nTimeSteps 3 -> 4
614      * changed reference output accordingly
615    o pkg/ctrl:
616      * fix ctrl_get_gen for xx_sst, xx_sss
617    o pkg/fizhi:
618      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
619        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
620      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
621        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
622        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
623    o pkg/gmredi:
624      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
625    o pkg/fizhi:
626      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
627        (old)aces open64 tuv test.
628    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
629    o pkg/mom_vecinv:
630      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
631        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
632        with non-lin free-surf).
633    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
634      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
635      some compilers (gfortran 4.6.0 on MacOS)
636    o momentum:
637      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
638        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
639        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
640    
641    checkpoint63k (2012/03/17)
642    o model/src:
643       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
644         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
645       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
646         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
647    o model/src: solve_*diagonal.F
648       - replace division with multiplication by inverse (similar to original version)
649         update output of AD exp. global_ocean.90x40x15.
650       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
651         to enable the use of the vectorized & differentiable solve_tridiagonal.F
652       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
653         vertical advection (to get solve_tridiagonal tested in AD mode).
654    o pkg/seaice: ECCO-CLIVAR merge:
655      1. seaice AREA relaxation
656         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
657         * runtime flag: SEAICE_tauAreaObsRelax
658      2. modified global mean cost imbalance code: CPP option
659          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
660    o another iteration on solve_*diagonal.F
661       Make choices independent of AUTODIFF
662       Default will be the adjoinable vectorized version.
663       Alternative choices are:
664       * non-adjoinable original version with low memory footprint:
665         #define SOLVE_DIAGONAL_LOWMEMORY
666       * still adjoinable but does not vectorize (k as inner-most loop):
667         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
668    o testreport
669     - add option to use a home made wrapper around "make"
670     - remove MITGCM_IEEE env. variable (no longer active)
671    o pkg/shelfice
672     - improve computation of friction velocity for velocity dependent
673       exchange coefficients: include velocities into SHELFICEBoundaryLayer
674       block to average velocities vertically
675     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
676    o Modify diagonal solvers, now three versions (upon request):
677      #ifndef SOLVE_DIAGONAL_AUTODIFF
678        1. default version (dating back a while ago)
679      #else /* def SOLVE_DIAGONAL_AUTODIFF */
680      # ifdef SOLVE_DIAGONAL_KINNER
681        2. adjoinable version with k-innermost loop (G. Forget)
682      # else
683        3. adjoinable vectorized version of 2.
684      # endif
685      #endif /* SOLVE_DIAGONAL_AUTODIFF */
686      All flags are currently set within routines, but could/should be moved to CPP-options.
687      Array bounds for 1. are as before, for 2.,3. cover the entire domain
688      (could be changed for 1. too).
689    o verification/lab_sea (fwd):
690      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
691        use 7 categories (except hb87), new solve4temp params (except salt_plume),
692        constant salinity (=4) or variable salinity (salt_plume) done through
693        SItracer.
694    o pkg/seaice:
695      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
696      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
697         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
698        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
699        SEAICE_freeze got retired) but already better than previously with
700        SEAICE_freeze=123456.7 deg.C;
701      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
702        (safer multi-threaded setting); always set SEAICEuseEVP;
703      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
704        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
705        stop if multiple specifications for the same coeff; make sure default
706        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
707    o pkg/obcs:
708      - allow to switch to upwind 1rst order advection scheme for the advective
709        flux computation at the open-boundary; disabled for adjoint built.
710    o pkg/ptracers:
711      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
712      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
713      - add parameter to decide when to start a tracer; use internal flag to
714        know which tracer to step-forward; switch this internal flag at the top
715        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
716        for adjoint built.
717    o pkg/seaice:
718      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
719      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
720      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
721    o pkg/ecco:
722      - fix writing of output file DiagnosCost_ClimSalt/Theta
723        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
724    o pkg/seaice:
725      - add missing initialisation of COR_ICE array in dynsolver.F
726      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
727        compiled either way, and is tested in all exps (multidim was only tested
728        in lab_sea ad before).
729      - cosmetic change to prepare for future addition of ITD. no change to results.
730        no defaults change.
731      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
732      - by lack of adequate verification experiments, I further used custom versions
733        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
734        should be correct.
735      - avoid recomputations in ad.
736    o array initialisation in adjoint mode:
737      1) pkg/mom_common/mom_calc_ke.F:
738        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
739        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
740        part this initialisation is gone, resulting in Floating Point Exception
741        (caught by open64 compiler with debug option).
742      2) model/src/convective_weights.F
743        set output convectCount over the full array range (instead of doing
744        an update): this fix a similar issue when called within recomputation (adjoint)
745        which could by-pass the initialisation (normally done in the caller S/R).
746    o pkg/seaice:
747      - final version of turbulent flux params, as agreed at MIT ice meet:
748           SEAICE_mcPheePiston (default is ~ 0.000875)
749           SEAICE_mcPheeTaper (default is 0.)
750           SEAICE_frazilFrac (defualt is 1.)
751           SEAICE_mcPheeStepFunc (default is false)
752      - changes results at trunction error level
753      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
754    o added pkg/frazil:
755      - see frazil_description.tex for details
756      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
757    o pkg/shelfice/shelfice_thermodynamics.F
758      - fix exponents for velocity dependent exchange coefficients: change
759        from 2/3(=0) to 0.66666666666666667
760      - move computation of velocity dependent exchange coefficients into
761        separate loop, so that it applies to both thermodynamics
762      - move some divisions by constants out of loops
763    
764    checkpoint63j (2012/02/16)
765    o pkg/seaice:
766      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
767      - SItracer:  added run time params, and allow coupling to ocn salinity.
768    o pkg/seaice: remove (almost) all divisions by constants within loops
769      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
770      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
771      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
772      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
773    o pkg/seaice :
774      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
775        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
776      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
777      - add permanent SItflux diag that corresponds to TFLUX but includes
778        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
779      - allow activation/testing of a fix for suspected missing term in
780        ocn-ice heat budget (to be confirmed). To test this, you want to
781        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
782        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
783      - no change in results, fwd or ad.
784    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
785      - switch to variable freezing point.
786           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
787      - bug fix : the sublimation term that was missing is now activated.
788           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
789      - bug fix : flooding sign term for SIsal0.NE.0.
790           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
791    o pkg/seaice:
792      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
793        is now the default, and the old default constant freezing point is recovered
794        with SEAICE_tempFrz0    = -1.96,
795             SEAICE_dTempFrz_dS = 0.,
796      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
797      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
798      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
799        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
800      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
801        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
802      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
803        seaice_growth r149 for legacy branch (no results change).
804      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
805        from I. Fenty).
806      - results did not change except for global_ocean.cs32x15, mostly due to the
807        switch to variable freezing point (see above item for detail).
808    o pkg/thsice:
809      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
810        seawater freezing in thsice_calc_thickn (not used).
811    o pkg/seaice: turbulent flux term specification via run time params.
812      - replace CPP switches with run time switches to facilitate testing
813      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
814                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
815      - added runtime parameter : SEAICEturbFluxFormula
816      - move Mcphee constants to SEAICE_PARAMS.h
817      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
818                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
819                 remove seaice_summary call (moved to seaice_init_fixed)
820      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
821        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
822      - seaice_summary.F : add missing report of read turbulent flux term set up
823                           and SITRACER.
824      - seaice_check.F : check range; inform and stop if retired CPPs are used
825                         (incl. SEAICE_AGE).
826      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
827             CPP switch, same computation as before for the different options.
828      - change results at the truncation level.
829    o pkg/seaice:
830      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
831        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
832        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
833      - update verification/*/input*/data.seaice:
834        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
835        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
836        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
837        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
838    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
839      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
840        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
841        difference in results only due to machine truncation.
842      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
843        MaykutPolySatVap; keep MIN_LWDOWN.
844      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
845      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
846        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
847    o pkg/salt_plume:
848      - isolate saltPlumeFlux array exch into a specific S/R called from
849        do_oceanic_phys.F
850      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
851    o verification:
852      - move untested set-up to MITgcm_contrib/verification_other.
853    o pkg/seaice:
854      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
855    o pkg/seaice:
856      - seaice_solve4temp.F (keeping results unchanged):
857        * add 2 future run-time params to select which saturation vapor pressure
858          formula is used and how post-iteration fluxes are set.
859          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
860        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
861          the linearized expression to stay consistent with tsurf finding.
862      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
863        can be < 0.
864    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
865      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
866        conductive heat flux F_c , and add it explicitly when updating tsurf as
867        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
868        so that now F_ia has a consistent meaning through the entire routine.
869        This causes differences at truncation level: update output of fwd exp.
870        global_ocean.cs32x15.seaice.
871    o pkg/seaice:
872      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
873        of arrays, sign/direction of fluxes; no effect on results.
874      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
875        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
876        note: this should have been done before changing celsius2K default.
877      - to keep results unchanged, add back old value of celsius2K in verification
878        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
879      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
880        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
881        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
882        freezing temp is consistent with value in seaice_growth.F ; this causes
883        differences at machine truncation level: update lab_sea AD output (3/4).
884    o pkg/seaice:
885      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
886        and climsst/sss even when using seaice (to prevent calculation that might
887        use SST on land); does not affect any verification exp.
888      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
889        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
890    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
891      over land (non-legacy code)
892    o vectorize salt_plume package:
893      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
894      - this code computes plumebk everywhere (also over land), thus requires
895        code to avoid divisions by zero and catch the case of kLev=Nr.
896      - efficiency of salt_plume_frac is still sub-optimal
897    o tools (genmake2):
898      - fix makefile NAME specification (option: -makefile NAME) by adding
899        "-f $MAKEFILE" in few places where it was missing including makedepend
900        command (contribution from Paul).
901    
902    checkpoint63i (2012/01/24)
903    o model/src:
904      - add factorized versions of some EOS code to find_rho.F,
905        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
906    o model/src:
907      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
908      - change default celsius2K from 273.16 to 273.15
909      - to keep results unchanged, add back old value of celsius2K in verification
910        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
911         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
912    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
913      to make TAF generate vectorizable code
914    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
915       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
916       have flags that do this more efficiently.
917    o pkg/diagnostics/diagstats_calc.F
918      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
919  o pkg/obcs (with exch2):  o pkg/obcs (with exch2):
920    - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)    - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
921      and remove code (in obcs_readparms.F) which was based on EXCH of indices      and remove code (in obcs_readparms.F) which was based on EXCH of indices
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