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revision 1.1533 by jmc, Thu Nov 10 21:04:47 2011 UTC revision 1.1739 by jmc, Tue Sep 18 21:26:19 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      - change default setting of OBCS_UVICE_OLD from defined to undef;
9      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
10        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
11      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
12      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
13        with Southern & Western OB at a tile edge (at least in a simple set-up).
14    o pkg/obcs:
15      - change settings of OB index in case OB coincides with tile edge (shared by
16        2 tiles), so that common OB location is registered by both tiles (instead of
17        only 1). However, for Southern and Western OB, index value = 0 is not
18        recognized as valid OB index (=default null value) and needs to be fixed.
19      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
20      - new parameter "OB_indexNone" for null index value (for now, still zero)
21        to replace hard-coded null index value of zero.
22    o pkg/exch2:
23      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
24        always check buffer-size (but outside the loop); move checking for valid
25        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
26        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
27    o pkg/ctrl (pack & unpack):
28      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
29        (locally defined) for different variables (+ remove the variable-specific
30        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
31        (to be extended to other local file names in ctrl.h).
32    o pkg/flt:
33      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
34    o pkg/mdsio:
35      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
36    o tools/genmake2:
37      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
38        (added by Alistair in version 1.51 for building without make depend);
39      - remove Header files list (H_SRC_FILES) from the dependence of targets
40         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
41        place in version 1.23): this save going through staf when unrelated header
42        file has been modified.
43       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
44        "make depend" step, still need to do "make links" before "make adtaf".
45    o eesupp/src (+ few pkg src files) & genmake2:
46      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
47      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
48      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
49         upper/lower case ; account for space between "#" and undef/define)
50    o pkg/flt (with exch2):
51      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
52      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
53    
54    checkpoint63s (2012/09/05)
55    o pkg/ecco:
56      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
57      - add more relevant #ifdef ALLOW_SMOOTH ones.
58      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
59    o pkg/ctrl:
60      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
61        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
62      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
63        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
64        ctrlSmoothCorrel3D (new).
65        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
66      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
67      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
68        controls when useAtmWind, and vice versa.
69      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
70      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
71          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
72      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
73          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
74      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
75        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
76    o pkg/smooth:
77      - remove un-necessary includes.
78      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
79        Those CPP options were never defined, and not necessary.
80    o model/src:
81      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
82      - standard treatment of useSMOOTH.
83    o pkg/autodiff:
84      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
85        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
86    o pkg/exch2:
87      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
88        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
89      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
90        and tiles to process mapping.
91      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
92        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
93        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
94        from w2_eeboot.F to w2_readparms.F.
95    o eesupp/src:
96      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
97        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
98        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
99      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
100        is defined (remove condition on usingMPI) to match cases where MPI_INIT
101        has been called.
102      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
103      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
104        (so that on 1 proc, get same myPid independently of usingMPI)
105      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
106        useCubedSphereExchange with EXCH-1 (safer).
107      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
108    o pkg/ggl90:
109      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
110        used in ALLOW_GGL90_SMOOTH code.
111    o pkg/flt:
112      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
113        floats at the Southern end of the domain).
114    o eesupp/inc:
115      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
116        but not used (and not to be used) anywhere, just for documentation.
117    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
118      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
119        a) can damage previously written records in any other multi-record files.
120        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
121    o tools/genmake2:
122      - define variable MAKE within Makefile and use it in place of 'make';
123      - update AD_CONFIG.h (if needed) before building any of the executable
124        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
125        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
126      - always print usual warning comment 'this file is automatically generated'
127        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
128    o pkg/cheapaml:
129      - updated to correspond to the code used in accepted paper (Nico Wienders).
130    o pkg/exf:
131        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
132        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
133        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
134    o pkg/exf, autodiff, ctrl, ecco and seaice:
135        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
136    o pkg/ctrl, ecco:
137        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
138        Depending on useAtmWind, one is inactive, and the other is active (see
139        exf_getffields.F/exf_getsurfacefluxes.F).
140    o tools/genmake2:
141      - improve error msg when failing in 2nd test of check_for_broken_Ff
142      - fix option '-makefile' short-name (-mf according to genmake2 -help)
143      - source local config file "genmake_local" just after processing the genmake2
144        command arguments (previously done before processing arg).
145    o pkg/grdchk:
146      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
147        to this routine from cost_final has been dropped in g_cost_final)
148      - improve printed information (more explicit msg, no longer using "print *,"
149         fix fcpertminus printed value).
150    o model/src:
151      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
152        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
153        this prevents getting cost-funct reset in adinitialise_varia recomputations.
154    o pkg/dic:
155      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
156        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
157    o pkg/grdchk:
158      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
159      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
160    o pkg/autodiff/ctrl/grdchk :
161      - attempt to sort out what works and what does not,
162        with regard to I/O, and to warn/stop accordingly.
163    o pkg/grdchk:
164      - attempt to fix grdchk in the case of useSingleCpuIO.
165      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
166       statements were moved from grdchk_main.F and into
167       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
168      - a global sum is applied to record numbers icvrec/layer
169       out of grdchk_loc so that they be passed to I/O routines.
170    o pkg/smooth:
171      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
172        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
173    o verification/testreport:
174      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
175      - can also use compressed (gzip) reference output file;
176      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
177        to be easier to collect by testreport.
178      - update existing TLM output (half out-of-date by more than 3 yrs).
179      - report NETCDF & LAPACK settings (from genmake2) in output dir.
180      - report run-time in each individual summary (previously only for AD test);
181        for TLM test, add also TAF version.
182      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
183    
184    checkpoint63r (2012/08/15)
185    o tools/genmake2:
186      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
187    o pkg/ecco/ecco_cost_final.F :
188      - fix fc print statements (to stdout and costfunction0000) so
189        that the printed value is always after the global sum.
190    o pkg/seaice/seaice_dynsolver.F :
191      - fix ice strength assymptote at SEAICE_area_max<1
192        (no change for the standard case of SEAICE_area_max=1)
193    o some cleaning:
194      - pkg source files: ensure that all *.F files from each pkg included the
195        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
196        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
197        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
198        includes;
199      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
200      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
201        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
202        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
203      - update option-file CPP_OPTIONS.h of all AD experiments:
204        * no longer include PACKAGES_CONFIG.h ;
205        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
206        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
207          including ECCO_CPPOPTIONS.h).
208    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
209      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
210        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
211        not necessary accurate).
212      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
213        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
214        deliberately break compilation (a remainder that it needs to be customized)
215      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
216      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
217      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
218    o tools/genamke2:
219      - check for lapack.
220    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
221      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
222        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
223        from both packages.
224      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
225      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
226      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
227        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
228    o pkg/cost : add comments to explain special and/or untested setups.
229    o pkg/exf:
230      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
231        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
232    o verification/*/code_ad:
233      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
234      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
235      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
236        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
237    o pkg/seaice :
238      - added possibility to change ice strength/PRESS0 relationship to
239        HEFF, according to the following run time parameters
240        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
241        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
242        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
243    o pkg/ggl90 :
244      - added run time flag mxlSurfFlag to include the code that ensure
245        mixing between first and second level (previously included as a comment)
246    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
247      - add test of newly added dumpAdByRec=T option where
248        we write all records to one file per variable.
249    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
250      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
251        to check that this code is ok with taf and compiles in adjoint.
252    o pkg/autodiff :
253      - added run time param dumpAdByRec : ad dump format switch.
254        If true then write all records to one file per variable.
255        Else write one file per record (remains the default).
256      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
257    o pkg/seaice:
258     - Added SEAICEuseTILT run time switch : if set to
259       false then omit the tilt term in seaice dynamics.
260     - Fix free drift calculation.
261    o pkg/shelfice:
262      When initializing SHELFICEDragQuadratic, set default to be
263      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
264      but retain option to set it independently
265      (inconsistenty spotted by Veronique Dansereau)
266    o eesupp/inc:
267      - in EEPARAMS.h, add real-type constant for some frequently used simple number
268         (0,1,2,1/2), with name explicitly referring to RS/RL type.
269    o model/src:
270      - move balancing of relaxation terms to new S/R balance_relax.F.
271    o pkg/autodiff:
272      re-write active I/O high-level (control) S/R:
273      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
274      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
275      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
276        MDS_READ/WRITE_FIELD); change loops to multi-threads.
277      - update and merge active_file_control_slice.flow into active_file_control.flow
278      - update the calls in lower level S/R (active_file.F, active_file_g.F and
279        active_file_ad.F) keeping the argument list and function unchanged.
280      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
281        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
282      - new low-level active I/O routines, one for each type (RL/RS), for active var
283        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
284        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
285        right type.
286    o autodiff and RS=real*4:
287      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
288        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
289      - change argument type of 3-D mask argument to _RS to match type in the call
290        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
291    o pkg/thsice:
292      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
293      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
294        fresh-water flux: uniform correction or proportional to local precip.
295    o pkg/ctrl:
296      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
297      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
298                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
299      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
300    
301    checkpoint63q (2012/07/30)
302    o pkg/autodiff:
303      note about monitor and snap-shot of ad-variables:
304      a) need to apply ADEXCH before monitor or output of ad-vars to include
305       overlap contributions (was done for adjDump but missing for monitor).
306      b) since ADEXCH implies adding overlap values to interior array, machine
307       truncation error is expected when adding an ADEXCH call in the middle of
308       the time-stepping (although mathematically identical).
309      modifs:
310      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
311        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
312      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
313        apply ADEXCH before monitor or snap-shot of ad-variables:
314           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
315      - implement new method (copy+adexch) for snap-shot and monitor of main model
316        ad-vars (initially not used by default -> output unchanged).
317      - change default (set to 2) to use new method and update few output_adm.txt
318        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
319        and both tutorial_tracer_adjsens tests).
320      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
321        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
322    o pkg/ctrl:
323      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
324      generic control variables via
325      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
326      Only required customization should be S/R ctrl_map_ini_genarr.F
327      (routine in repository contains example)
328    o pkg/exf:
329      - fix and refine checking of surface-relaxation setting when using EXF
330    o verification (adjoint exp):
331      - reduce length of simulation by half for experiment global_ocean.cs32x15
332        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
333    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
334      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
335        of KE that can occur with aggressive optimization
336      + put quadratic bottom drag calculation in separated loops (only done if
337        using bottomDragQuadratic)
338    o model/src: CG2D_NSA
339      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
340         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
341      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
342         change cg2d residual target to be expressed in Wunits (=> do not normalise
343         RHS ; this fix global_max Pb with TAF); update output.
344    o verification/tutorial_tracer_adjsens:
345       improve parameter consistency (and get rid of warnings):
346       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
347       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
348       - use staggerTimeStep (for stability) in som81; use default rotation period.
349    o pkg/exch2:
350      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
351        reset to 0 = 1 long line in X)
352    o pkg/mdsio:
353      - fix reading of dimensions from meta file for large-size domain
354    o model/src:
355      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
356      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
357        Cubed-Sphere Exch with CS-corners inside the domain;
358        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
359        globalArea and to set hasWetCSCorners.
360      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
361        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
362      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
363        useCDscheme and useCubedSphereExchange).
364    o pkg/seaice/seaice_growth.F :
365      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
366        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
367        when the previous code was not correct.
368      - in all cases diagnoze the boundary condition mismatch to SIaaflux
369      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
370        that term to QNET (essentially to set the melt/freeze water to 0degC).
371        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
372    o verification/global_ocean.cs32x15/input.seaice :
373      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
374      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
375      - update results (output.seaice.txt) accordingly.
376    o verification/lab_sea/input/data.seaice :
377      - remove SEAICEheatConsFix, which is now be tested
378        in global_ocean.cs32x15. The presently coded fix
379        is only consistent with real fresh water + nlfs.
380      - update results (output.txt) accordingly.
381    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
382    o AD_CONFIG.h file:
383      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
384      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
385        add it explicitly in each fortran src file where it is needed.
386        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
387        thus introducing potentially wrong dependency; therefore, better to include
388        it only where it's really needed, and after any other included OPTIONS file
389        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
390        or ALLOW_TANGENTLINEAR_RUN).
391    
392    checkpoint63p (2012/07/06)
393    o pkg/autodiff:
394      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
395      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
396        which are now read from new parameter file "data.autodiff" (inAdExact
397        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
398      - add file "data.autodiff" in all verification/*/input_ad/ directories.
399      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
400        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
401    o verification/tutorial_tracer_adjsens/
402      - add extra sub-verification which uses "SOM" advection scheme
403        (2nd Order-Moment Advection Scheme, Prather Limiter) with
404          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
405        and in data:
406          multiDimAdvection=.TRUE.,
407          tempAdvScheme=81,
408          saltAdvScheme=81,
409    o model/src:
410      - introduce ALLOW_BALANCE_RELAX which allow the removal
411       of the global mean of relaxation terms by setting
412       balanceThetaClimRelax and balanceSaltClimRelax
413      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
414       This case is now treated appropriately in seaice_growth.F
415    o pkg/seaice:
416      - do balanceEmPmR and balanceQnet based on the net fluxes
417        (SItflux) that enter the ocean+ice system rather than QNET
418        and EMPMR. Works best in real fresh water.
419      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
420        out of the diagnotics bloc, and stored in global arrays.
421    
422    checkpoint63o (2012/06/29)
423    o vertical mixing schemes:
424      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
425      - replace computation of density (in Function STATE1, opps_calc.F) by a call
426        to S/R FIND_RHO_SCALAR
427      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
428        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
429        affects output (vermix.ggl90) at truncation level.
430    o testreport:
431      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
432        (nSx,nSy) for the number of threads (from eedata.mth)
433    o model/src:
434      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
435        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
436    o verification/tutorial_tracer_adjsens/
437      - compile with ALLOW_CG2D_NSA
438      - run with nonlinFreeSurf=3
439      - update reference output_adm.txt
440    o tools/genmake2:
441      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
442        refine usePROFILES switching off (only when NetCDF is not available).
443    o verification (atmospheric set-up):
444      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
445    o pkg/profiles : refine profiles and files handling.
446    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
447    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
448      - changes to use model/src/the_main_loop.F rather than the ecco version
449        in ecco type adjoint runs.
450    o model/src:
451      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
452      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
453      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
454    o model/src:
455      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
456        update output of test experiment bottom_ctrl_5x5.
457    o pkg/generic_advdiff:
458      - implement vertical bi-harmonic diffusion (for now, only for T & S and
459        only explicitly).
460    o verification/bottom_ctrl_5x5/
461      update reference output (results changed quite some time ago,
462      not sure when; but new reference results look ok in terms of grdchk)
463    o verification/1D_ocean_ice_column/
464      For verification purposes, the exact adjoint rather than an approx.
465      should be used (e.g., to comare against F.D. or TLM).
466      removed autodiff_inadmode*_ad.F routines in code_ad/
467      Update results/ accordingly.
468    o pkg/cal:
469      - change cal_getdate.F so that output date is function of input time only
470        (less ambiguous, not mixed up with input iteration number).
471      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
472    o pkg/diagnostics:
473      - implement calendarDumps also for stats-diags
474      - implement calendarDumps also for snap-shot output (negative freq)
475      - for now, ignores calendarDumps if non-zero phase-lag.
476    
477    checkpoint63n (2012/06/04)
478    o model/src:
479      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
480        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
481      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
482        similar to calc_r_star.F); update results of experiment internal_wave and
483        tutorial_global_oce_in_p (affected @ truncation level).
484    o pkg/shelfice:
485      - add parameterisation of advective-diffusive flux into the ice shelf
486        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
487      - simply eps3/3a computation
488    o eesupp:
489     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
490       between tiles, just fill-in edges assuming locally periodic subdomain) and
491       add corresponding exchange subroutines (EXCH0);
492     - new CG-solver version (_EX0) for disconnected-tiles special case.
493    o model/src (CG-solvers):
494     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
495       (similar final residual output and max-Iter number as with standard version);
496     - allows to store and use lowest-residual solution (standard & _SR versions);
497     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
498     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
499    o eesup/src:
500     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
501       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
502    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
503    
504    checkpoint63m (2012/04/27)
505    o pkg/shelfice:
506     - account for partical cells in surface level below ice-shelf for hydrostatic
507       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
508    o ad test experiments:
509     - update and rename to "ad_optfile.local" local AD-optfile specific to a
510       particular adjoint verification experiment (in verification/*/code_ad/)
511    o pkg/seaice & pkg/exf:
512     - Part two of ECCO-CLIVAR code merges.
513       Completes merge of seaice area relax. code.
514       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
515       to be set in EXF_OPTIONS.h since this pkg controls its I/O
516       (and avoids second CPP option in SEAICE_OPTIONS.h)
517     - change default value of costIceStart & costIceEnd to a valid date.
518     - add snowPrecip to HSNOW in seaice_growth
519    o pkg/ptracers:
520     - move ptracers summary and setup check into separated S/R ; add a check for
521       valid PTRACERS_Iter0 value (error+stop or just warning).
522    o pkg/cal (+ pkg/ecco):
523     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
524       as input; and for AD, unless both are not differentiable (e.g., k index)).
525    o model/src:
526     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
527       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
528       temporary set to usingZCoords value (to be changed to F when using shelfice).
529     - hydrostatic pressure: implement partial cell near the surface also for
530       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
531       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
532    o pkg/ctrl/ctrl_init.F:
533     - add a formal parameter to s/r ctrl_init_rec to print
534       xx_$(ctrl_valiable)_file for easier debugging
535     - move call of cal_* routines into the if-block where they are really
536       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
537       to specify a startdate
538    o pkg/seaice:
539     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
540       global_ocean.cs32x15/code versions).
541     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
542       verification experiment global_ocean.cs32x15.seaice and update results.
543    o pkg/exf:
544     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
545       (according to useExfYearlyFields).
546    o pkg/cal:
547     - move calendar setting & summary (previously in cal_readparams.F) into new
548       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
549       length of the simulation is set (after SET_PARMS call); This is an attempt
550       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
551     - For safety: keep a record of pkg/cal parameter settings status
552               to allow to STOP if one pkg/cal S/R is called too early.
553     - add a stop in all basic pkg/cal subroutines if called before setting is done.
554     - modify cal_getdate.F: stop when nothing was returned;
555       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
556       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
557    
558    checkpoint63l (2012/04/04)
559    o pkg/bbl:
560      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
561        update global_with_exf output.yearly.txt file.
562    o pkg/cal:
563      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
564      - remove 2 unsused and very short (1 line only) functions ;
565      - remove unsused subroutines from AD-Diff list.
566    o model/src:
567      - start to implement clean wait to stop in initialization S/R (config_check.F,
568         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
569    o folowing PRINT_MESSAGE changes:
570      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
571    o pkg/bbl:
572      - modification so it can work with z*
573      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
574      - global_with_exf/input.yearly verification; changes output.yearly.txt
575    o eesupp/src:
576      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
577        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
578      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
579        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
580      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
581      - when using MPI, always set usingMPI=T ; set default accordingly and stop
582        if not consistent.
583      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
584        argument is zero (in case called within single-thread section).
585    o pkg/fizhi:
586        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
587        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
588    o pkg/exch2:
589      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
590        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
591      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
592        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
593        with bad ones coming from a not-yet-updated halo.
594        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
595    o pkg/frazil:
596        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
597        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
598    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
599    o verification/lab_sea
600      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
601      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
602      * nTimeSteps 3 -> 4
603      * changed reference output accordingly
604    o pkg/ctrl:
605      * fix ctrl_get_gen for xx_sst, xx_sss
606    o pkg/fizhi:
607      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
608        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
609      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
610        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
611        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
612    o pkg/gmredi:
613      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
614    o pkg/fizhi:
615      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
616        (old)aces open64 tuv test.
617    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
618    o pkg/mom_vecinv:
619      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
620        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
621        with non-lin free-surf).
622    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
623      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
624      some compilers (gfortran 4.6.0 on MacOS)
625    o momentum:
626      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
627        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
628        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
629    
630    checkpoint63k (2012/03/17)
631    o model/src:
632       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
633         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
634       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
635         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
636    o model/src: solve_*diagonal.F
637       - replace division with multiplication by inverse (similar to original version)
638         update output of AD exp. global_ocean.90x40x15.
639       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
640         to enable the use of the vectorized & differentiable solve_tridiagonal.F
641       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
642         vertical advection (to get solve_tridiagonal tested in AD mode).
643    o pkg/seaice: ECCO-CLIVAR merge:
644      1. seaice AREA relaxation
645         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
646         * runtime flag: SEAICE_tauAreaObsRelax
647      2. modified global mean cost imbalance code: CPP option
648          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
649    o another iteration on solve_*diagonal.F
650       Make choices independent of AUTODIFF
651       Default will be the adjoinable vectorized version.
652       Alternative choices are:
653       * non-adjoinable original version with low memory footprint:
654         #define SOLVE_DIAGONAL_LOWMEMORY
655       * still adjoinable but does not vectorize (k as inner-most loop):
656         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
657    o testreport
658     - add option to use a home made wrapper around "make"
659     - remove MITGCM_IEEE env. variable (no longer active)
660    o pkg/shelfice
661     - improve computation of friction velocity for velocity dependent
662       exchange coefficients: include velocities into SHELFICEBoundaryLayer
663       block to average velocities vertically
664     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
665    o Modify diagonal solvers, now three versions (upon request):
666      #ifndef SOLVE_DIAGONAL_AUTODIFF
667        1. default version (dating back a while ago)
668      #else /* def SOLVE_DIAGONAL_AUTODIFF */
669      # ifdef SOLVE_DIAGONAL_KINNER
670        2. adjoinable version with k-innermost loop (G. Forget)
671      # else
672        3. adjoinable vectorized version of 2.
673      # endif
674      #endif /* SOLVE_DIAGONAL_AUTODIFF */
675      All flags are currently set within routines, but could/should be moved to CPP-options.
676      Array bounds for 1. are as before, for 2.,3. cover the entire domain
677      (could be changed for 1. too).
678    o verification/lab_sea (fwd):
679      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
680        use 7 categories (except hb87), new solve4temp params (except salt_plume),
681        constant salinity (=4) or variable salinity (salt_plume) done through
682        SItracer.
683    o pkg/seaice:
684      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
685      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
686         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
687        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
688        SEAICE_freeze got retired) but already better than previously with
689        SEAICE_freeze=123456.7 deg.C;
690      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
691        (safer multi-threaded setting); always set SEAICEuseEVP;
692      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
693        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
694        stop if multiple specifications for the same coeff; make sure default
695        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
696    o pkg/obcs:
697      - allow to switch to upwind 1rst order advection scheme for the advective
698        flux computation at the open-boundary; disabled for adjoint built.
699    o pkg/ptracers:
700      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
701      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
702      - add parameter to decide when to start a tracer; use internal flag to
703        know which tracer to step-forward; switch this internal flag at the top
704        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
705        for adjoint built.
706    o pkg/seaice:
707      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
708      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
709      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
710    o pkg/ecco:
711      - fix writing of output file DiagnosCost_ClimSalt/Theta
712        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
713    o pkg/seaice:
714      - add missing initialisation of COR_ICE array in dynsolver.F
715      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
716        compiled either way, and is tested in all exps (multidim was only tested
717        in lab_sea ad before).
718      - cosmetic change to prepare for future addition of ITD. no change to results.
719        no defaults change.
720      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
721      - by lack of adequate verification experiments, I further used custom versions
722        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
723        should be correct.
724      - avoid recomputations in ad.
725    o array initialisation in adjoint mode:
726      1) pkg/mom_common/mom_calc_ke.F:
727        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
728        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
729        part this initialisation is gone, resulting in Floating Point Exception
730        (caught by open64 compiler with debug option).
731      2) model/src/convective_weights.F
732        set output convectCount over the full array range (instead of doing
733        an update): this fix a similar issue when called within recomputation (adjoint)
734        which could by-pass the initialisation (normally done in the caller S/R).
735    o pkg/seaice:
736      - final version of turbulent flux params, as agreed at MIT ice meet:
737           SEAICE_mcPheePiston (default is ~ 0.000875)
738           SEAICE_mcPheeTaper (default is 0.)
739           SEAICE_frazilFrac (defualt is 1.)
740           SEAICE_mcPheeStepFunc (default is false)
741      - changes results at trunction error level
742      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
743    o added pkg/frazil:
744      - see frazil_description.tex for details
745      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
746    o pkg/shelfice/shelfice_thermodynamics.F
747      - fix exponents for velocity dependent exchange coefficients: change
748        from 2/3(=0) to 0.66666666666666667
749      - move computation of velocity dependent exchange coefficients into
750        separate loop, so that it applies to both thermodynamics
751      - move some divisions by constants out of loops
752    
753    checkpoint63j (2012/02/16)
754    o pkg/seaice:
755      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
756      - SItracer:  added run time params, and allow coupling to ocn salinity.
757    o pkg/seaice: remove (almost) all divisions by constants within loops
758      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
759      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
760      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
761      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
762    o pkg/seaice :
763      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
764        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
765      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
766      - add permanent SItflux diag that corresponds to TFLUX but includes
767        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
768      - allow activation/testing of a fix for suspected missing term in
769        ocn-ice heat budget (to be confirmed). To test this, you want to
770        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
771        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
772      - no change in results, fwd or ad.
773    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
774      - switch to variable freezing point.
775           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
776      - bug fix : the sublimation term that was missing is now activated.
777           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
778      - bug fix : flooding sign term for SIsal0.NE.0.
779           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
780    o pkg/seaice:
781      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
782        is now the default, and the old default constant freezing point is recovered
783        with SEAICE_tempFrz0    = -1.96,
784             SEAICE_dTempFrz_dS = 0.,
785      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
786      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
787      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
788        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
789      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
790        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
791      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
792        seaice_growth r149 for legacy branch (no results change).
793      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
794        from I. Fenty).
795      - results did not change except for global_ocean.cs32x15, mostly due to the
796        switch to variable freezing point (see above item for detail).
797    o pkg/thsice:
798      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
799        seawater freezing in thsice_calc_thickn (not used).
800    o pkg/seaice: turbulent flux term specification via run time params.
801      - replace CPP switches with run time switches to facilitate testing
802      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
803                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
804      - added runtime parameter : SEAICEturbFluxFormula
805      - move Mcphee constants to SEAICE_PARAMS.h
806      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
807                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
808                 remove seaice_summary call (moved to seaice_init_fixed)
809      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
810        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
811      - seaice_summary.F : add missing report of read turbulent flux term set up
812                           and SITRACER.
813      - seaice_check.F : check range; inform and stop if retired CPPs are used
814                         (incl. SEAICE_AGE).
815      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
816             CPP switch, same computation as before for the different options.
817      - change results at the truncation level.
818    o pkg/seaice:
819      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
820        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
821        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
822      - update verification/*/input*/data.seaice:
823        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
824        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
825        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
826        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
827    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
828      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
829        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
830        difference in results only due to machine truncation.
831      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
832        MaykutPolySatVap; keep MIN_LWDOWN.
833      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
834      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
835        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
836    o pkg/salt_plume:
837      - isolate saltPlumeFlux array exch into a specific S/R called from
838        do_oceanic_phys.F
839      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
840    o verification:
841      - move untested set-up to MITgcm_contrib/verification_other.
842    o pkg/seaice:
843      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
844    o pkg/seaice:
845      - seaice_solve4temp.F (keeping results unchanged):
846        * add 2 future run-time params to select which saturation vapor pressure
847          formula is used and how post-iteration fluxes are set.
848          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
849        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
850          the linearized expression to stay consistent with tsurf finding.
851      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
852        can be < 0.
853    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
854      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
855        conductive heat flux F_c , and add it explicitly when updating tsurf as
856        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
857        so that now F_ia has a consistent meaning through the entire routine.
858        This causes differences at truncation level: update output of fwd exp.
859        global_ocean.cs32x15.seaice.
860    o pkg/seaice:
861      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
862        of arrays, sign/direction of fluxes; no effect on results.
863      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
864        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
865        note: this should have been done before changing celsius2K default.
866      - to keep results unchanged, add back old value of celsius2K in verification
867        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
868      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
869        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
870        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
871        freezing temp is consistent with value in seaice_growth.F ; this causes
872        differences at machine truncation level: update lab_sea AD output (3/4).
873    o pkg/seaice:
874      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
875        and climsst/sss even when using seaice (to prevent calculation that might
876        use SST on land); does not affect any verification exp.
877      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
878        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
879    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
880      over land (non-legacy code)
881    o vectorize salt_plume package:
882      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
883      - this code computes plumebk everywhere (also over land), thus requires
884        code to avoid divisions by zero and catch the case of kLev=Nr.
885      - efficiency of salt_plume_frac is still sub-optimal
886    o tools (genmake2):
887      - fix makefile NAME specification (option: -makefile NAME) by adding
888        "-f $MAKEFILE" in few places where it was missing including makedepend
889        command (contribution from Paul).
890    
891    checkpoint63i (2012/01/24)
892    o model/src:
893      - add factorized versions of some EOS code to find_rho.F,
894        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
895    o model/src:
896      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
897      - change default celsius2K from 273.16 to 273.15
898      - to keep results unchanged, add back old value of celsius2K in verification
899        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
900         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
901    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
902      to make TAF generate vectorizable code
903    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
904       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
905       have flags that do this more efficiently.
906    o pkg/diagnostics/diagstats_calc.F
907      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
908    o pkg/obcs (with exch2):
909      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
910        and remove code (in obcs_readparms.F) which was based on EXCH of indices
911        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
912    o pkg/exf and seaice exp:
913      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
914        so that switching off area & heff advection flags does not affect results.
915      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
916      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
917        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
918        results of verification experiments: 1D_ocean_ice_column(fwd),
919        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
920        and offline_exf_seaice (all 4).
921    o pkg/seaice:
922      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
923        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
924      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
925        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
926        not multi-dim advection;
927      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
928        SHORTWAVE_HEATING #undef.
929    o optim: make Makefile more robust (?)
930    o pkg/obcs:
931      * fix treatment of obcs_read_pickup for TAF
932    o pkg/shelfice:
933      * add missing initialisation of num_shifwflx
934      * new adjoint verification exp. for isomip
935      * change Prandtl and Schmidt numbers from generic formulations
936        (in terms of model diffus. and visc.) to separate runtime
937        parameters, with Holland and Jenkins (1999) default values.
938    o pkg/exf (interpolation):
939      - extended input field (2 rows) near the N & S poles:
940        * fill in with the symetric value (when even Nb of data in longitude)
941        * add average value at the poles only for scalar quantities ; for vector
942          component interpolation, skip the averaging and keep duplicated values,
943          unless the 2 components have same location (uvInterp=T) in which case
944          interpolate the 2 components together using S/R EXF_INTERP_UV.
945      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
946        together: this allows to account properly for local orientation when
947        averaging at N & S pole.
948      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
949        exf-interpolation near N & S poles. Undef by default.
950      - add debug check/print on 1rst iter if debugLevel >=2.
951    o pkg/exf:
952      - change masking flags definition (no longer "parameter"), put them in
953        common block and set them in S/R EXF_INIT_FIXED.
954      - change recognized masking flag from s,u,v to c,w,s since the mask
955        to use (maskC,W,S) depends on position on model grid and has little to
956        do with scalar/vector difference; fix masking if using P-coordinates.
957      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
958        and update results of exp. global_with_exf (x2).
959      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
960    o pkg/obcs
961      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
962    o pkg/exf (interpolation):
963      - assume periodicity in X only if input field cover full longitude range.
964      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
965        and should vectorise).
966      - fix input lat of the 2 added row (in case we provide N.pole data).
967    
968    checkpoint63h (2011/12/30)
969    o pkg/seaice:
970      - change declaration of UVM from _RL to _RS in order to get B-grid
971        uIce,vIce monitor when _RS = real*4
972    o pkg/offline:
973      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
974      - compute vertical velocity if not read from file (switch on exactConserv
975        & staggerTimeStep);
976      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
977    o verification:
978      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
979        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
980        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
981      - update output of exp. global_ocean.cs32x15.viscA4 after changing
982        grid-file angles (used here for coriolis-3d);
983      - remove (or gzip) few files not needed to run fizhi-cs experiments.
984    o pkg/exf (vector interpolation):
985      - rotate vector component toward local grid-axis orientation using grid-angles
986        (stored in GRID.h) instead of locally computed rotation angle; keep old code
987        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
988    o pkg/seaice:
989      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
990        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
991    o pkg/PKG_OPTIONS.h files:
992      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
993        outside of the #ifdef ALLOW_THISPKG / #endif block.
994      - update verification/*/code/PKG_OPTIONS.h files.
995    o add a verification experiment (offline_exf_seaice/input.seaice) that test
996      the B-grid LSOR solver
997    o pkg/seaice: sort out emissivity and long wave radiation step 2:
998      - add emissivity for snow and ice as new run-time parameters
999        (unfortunately) that default to the corresponding exf values; this
1000        changes results in most verification experiments so that for backward
1001        compatibility these parameter have to be set explicitly to inconsistent
1002        values (ugly);
1003      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
1004        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
1005        until we agree how to handle this bug properly
1006    o pkg/exf (interpolation):
1007      - add a set of run-time param ({inputfield}_interpMethod), one for
1008        each interpolated input field, to select the interpolation method
1009        with a value of zero switching off the interpolation;
1010      - print interpolation parameters to standard output;
1011      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1012        (to use instead runoff_interpMethod=0 in data.exf).
1013      - simplify default setting of interpolation parameters (for all fields,
1014        set position to match model grid cell-center position, leading to trivial
1015        interpolation in case of regular Lat-Lon grid) and fix for the case of
1016        non-uniform delY.
1017    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1018       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1019       this factor is absolutely required, because the lw exitance (= out-going
1020       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1021       where the reflectivity rho = 1-emissivity for conservation reasons. Once
1022       this is established, we can remove the CPP-Flag (if we want to).
1023    o pkg/seaice:
1024      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1025        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1026      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1027        what the name implies (and not emissivity*BoltzmannConstant), this means
1028        the old default value of 5.5e-8 now means
1029        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1030        S/R exf_readparms
1031      - FV-discretization of the B-grid LSOR solver, turn on with
1032        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1033        of the calling routine dynsolver, so that B and C-grid code look a
1034        little more alike.
1035      - fix index bugs in ostres.F (B-grid code)
1036    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1037    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1038      default for SEAICE_emissivity, if useEXF; requires setting a wrong
1039      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1040      backward compatiblity
1041    o model/src: use sigmaR in calc_ivdc
1042    
1043    checkpoint63g (2011/12/16)
1044    o pkg/seaice/seaice_growth.F:
1045      fix heat conservation of the coupled ocean-seaice system.
1046      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1047      solid vs liquid water treatment is resolved via QNET.
1048    o pkg/seaice/seaice_growth.F:
1049      add missing term for sublimation in saltFlux, which was breaking conservation.
1050    o pkg/seaice/seaice_model.F:
1051      Remove this patholigical case treatment in evolution branch,
1052      where it is un-necessary and breaks conservation.
1053      Update global_ocean.cs32x15/results accordingly for
1054      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1055    o model/src:
1056      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1057      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1058    o pkg/obcs:
1059      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1060      tendency for temperature and salinity that is then applied to update
1061      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1062      horizontal advection and diffusion contributions on the boundary (in
1063      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1064      removing the mask in S/R timestep_tracer. The advantage of this approach is
1065      that the updated tracer values include contributions from the surface
1066      forcing and vertical diffusion.
1067      This modification changes exp4.stevens because of vertical diffusion.
1068    o model/src:
1069      change non-curvilinear grid setting to also work with exch2 + blank tiles:
1070      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1071        face dimensions.
1072      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1073        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1074        and INI_SPHERICAL_POLAR_GRID.
1075      change test-experiment global_ocean.90x40x15:
1076      - split the domain in many more tiles (9x4 tiles of 10x10 each);
1077      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1078      - update results of both test (std & dwnslp).
1079    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1080       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1081    o model/src:
1082      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1083        and fix initialisation when using sigma-coords.
1084    o model/src:
1085     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1086       to their current value at the beginning of forward_step.F": add a new run-time
1087       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1088     - set doResetHFactors=T in the following test exp:
1089        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1090        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1091        and tutorial_global_oce_in_p (nonLinFS in p)
1092    o pkg/ecco
1093      - added IES cost term
1094    o verification/advect_xz
1095      - scale down the depth by 1/100 (from 200 km to just 2.km)
1096      - add secondary test using divergent flow, r-star and implicit vertical advection.
1097      - add note (check_conserve_TS.txt) and matlab script to check global
1098        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1099    o pkg/rbcs:
1100      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1101    o pkg/obcs (Stevens BCs):
1102      - fix various problems in the phase speed computations of the Stevens
1103        boundary conditions:
1104        - sign error for western and southern boundaries,
1105        - time tendencies were underestimated by factor of dTracerLev and some just
1106          zero (for multidim advection schemes) -> now estimate time tendencies
1107          from difference between previous (n) time level and the one before (n-1);
1108          this requires storing a field per tracer per boundary, also in the pickup
1109          files.
1110        - replace deltaTmom in cflMer/Zon computation with dTracerLev
1111        - set default phase velocity to cflMer/Zon
1112      - update verification experiment exp4.stevens
1113    o pkg/generic_advdiff (implicit_r):
1114      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1115        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1116      - fix implicit vertical diffusion or advection with NonLin FreeSurf
1117        (was using current recip_hFacC instead of future recip_hFacC): set future
1118        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1119        solver S/R ;
1120      - fill diagnostics of vertical advective fluxes (computed from tendency)
1121        when using implicit vert. advection;
1122      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1123         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1124         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1125         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1126    o pkg/diagnostics:
1127      - add diags for T & S tendency which goes through Adams-Bashforth.
1128    
1129    checkpoint63f (2011/11/30)
1130    o pkg/obcs/obcs_calc_stevens.F:
1131      - join some loops to reduce number of if-statements
1132      - fix a bug in code for northern and southern boundaries.
1133    o pkg/seaice/seaice_init_varia.F
1134      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1135        caused zero ice-velocities for the B-grid code
1136    o pkg/seaice/seaice_init_fixed.F
1137      - fix a bug in the initialisation of the second metric terms
1138        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1139      - this affects all seaice configurations with useCurviLinearGrid = .true.
1140        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1141        = .true. (default)
1142      - the only verification experiment affected is global_ocean.cs32x15:
1143        icedyn, seaice, and seaice_dynmix (AD)
1144    o pkg/thsice/thsice_diagnostics_state.F
1145      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1146        not contain garbage that can lead to surprises in diagstats_calc.F
1147    o model/src:
1148      - move bi,bj loops inside INTEGR_CONTINUITY ;
1149      - call INTEGR_CONTINUITY directly from forward_step.F
1150        (previously called from momentum_correction_step.F)
1151      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1152        forward_step.F and pkg/ecco/the_main_loop.F
1153  o model/src/do_oceanic_phys.F:  o model/src/do_oceanic_phys.F:
1154    - reset addMass to zero only if useICEFRONT ;    - reset addMass to zero only if useICEFRONT ;
1155    - separated k-loop for rhoInSitu calculation ;    - separated k-loop for rhoInSitu calculation ;
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