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revision 1.1597 by mlosch, Tue Feb 14 14:53:17 2012 UTC revision 1.1719 by gforget, Tue Aug 21 14:28:07 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/seaice: remove (almost) all divisions by constants within loops  o pkg/autodiff/ctrl/grdchk :
8    in seaice_growth.F and seaice_solve4temp.F    - attempt to sort out what works and what does not,
9  o pkg/seaice :      with regard to I/O, and to warn/stop accordingly.
10    - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.  o pkg/grdchk :
11    1 or 2, using newly added run time parameter SEAICE_availHeatTaper.    - attempt to fix grdchk in the case of useSingleCpuIO.
12      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
13       statements were moved from grdchk_main.F and into
14       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
15      - a global sum is applied to record numbers icvrec/layer
16       out of grdchk_loc so that they be passed to I/O routines.
17    o pkg/smooth :
18      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
19        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
20    o verification/testreport:
21      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
22      - can also use compressed (gzip) reference output file;
23      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
24        to be easier to collect by testreport.
25      - update existing TLM output (half out-of-date by more than 3 yrs).
26      - report NETCDF & LAPACK settings (from genmake2) in output dir.
27      - report run-time in each individual summary (previously only for AD test);
28        for TLM test, add also TAF version.
29      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
30    
31    checkpoint63r (2012/08/15)
32    o tools/genmake2:
33      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
34    o pkg/ecco/ecco_cost_final.F :
35      - fix fc print statements (to stdout and costfunction0000) so
36        that the printed value is always after the global sum.
37    o pkg/seaice/seaice_dynsolver.F :
38      - fix ice strength assymptote at SEAICE_area_max<1
39        (no change for the standard case of SEAICE_area_max=1)
40    o some cleaning:
41      - pkg source files: ensure that all *.F files from each pkg included the
42        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
43        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
44        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
45        includes;
46      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
47      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
48        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
49        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
50      - update option-file CPP_OPTIONS.h of all AD experiments:
51        * no longer include PACKAGES_CONFIG.h ;
52        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
53        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
54          including ECCO_CPPOPTIONS.h).
55    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
56      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
57        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
58        not necessary accurate).
59      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
60        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
61        deliberately break compilation (a remainder that it needs to be customized)
62      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
63      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
64      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
65    o tools/genamke2:
66      - check for lapack.
67    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
68      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
69        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
70        from both packages.
71      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
72      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
73      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
74        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
75    o pkg/cost : add comments to explain special and/or untested setups.
76    o pkg/exf:
77      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
78        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
79    o verification/*/code_ad:
80      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
81      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
82      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
83        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
84    o pkg/seaice :
85      - added possibility to change ice strength/PRESS0 relationship to
86        HEFF, according to the following run time parameters
87        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
88        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
89        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
90    o pkg/ggl90 :
91      - added run time flag mxlSurfFlag to include the code that ensure
92        mixing between first and second level (previously included as a comment)
93    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
94      - add test of newly added dumpAdByRec=T option where
95        we write all records to one file per variable.
96    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
97      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
98        to check that this code is ok with taf and compiles in adjoint.
99    o pkg/autodiff :
100      - added run time param dumpAdByRec : ad dump format switch.
101        If true then write all records to one file per variable.
102        Else write one file per record (remains the default).
103      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
104    o pkg/seaice:
105     - Added SEAICEuseTILT run time switch : if set to
106       false then omit the tilt term in seaice dynamics.
107     - Fix free drift calculation.
108    o pkg/shelfice:
109      When initializing SHELFICEDragQuadratic, set default to be
110      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
111      but retain option to set it independently
112      (inconsistenty spotted by Veronique Dansereau)
113    o eesupp/inc:
114      - in EEPARAMS.h, add real-type constant for some frequently used simple number
115         (0,1,2,1/2), with name explicitly referring to RS/RL type.
116    o model/src:
117      - move balancing of relaxation terms to new S/R balance_relax.F.
118    o pkg/autodiff:
119      re-write active I/O high-level (control) S/R:
120      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
121      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
122      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
123        MDS_READ/WRITE_FIELD); change loops to multi-threads.
124      - update and merge active_file_control_slice.flow into active_file_control.flow
125      - update the calls in lower level S/R (active_file.F, active_file_g.F and
126        active_file_ad.F) keeping the argument list and function unchanged.
127      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
128        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
129      - new low-level active I/O routines, one for each type (RL/RS), for active var
130        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
131        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
132        right type.
133    o autodiff and RS=real*4:
134      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
135        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
136      - change argument type of 3-D mask argument to _RS to match type in the call
137        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
138    o pkg/thsice:
139      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
140      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
141        fresh-water flux: uniform correction or proportional to local precip.
142    o pkg/ctrl:
143      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
144      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
145                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
146      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
147    
148    checkpoint63q (2012/07/30)
149    o pkg/autodiff:
150      note about monitor and snap-shot of ad-variables:
151      a) need to apply ADEXCH before monitor or output of ad-vars to include
152       overlap contributions (was done for adjDump but missing for monitor).
153      b) since ADEXCH implies adding overlap values to interior array, machine
154       truncation error is expected when adding an ADEXCH call in the middle of
155       the time-stepping (although mathematically identical).
156      modifs:
157      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
158        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
159      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
160        apply ADEXCH before monitor or snap-shot of ad-variables:
161           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
162      - implement new method (copy+adexch) for snap-shot and monitor of main model
163        ad-vars (initially not used by default -> output unchanged).
164      - change default (set to 2) to use new method and update few output_adm.txt
165        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
166        and both tutorial_tracer_adjsens tests).
167      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
168        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
169    o pkg/ctrl:
170      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
171      generic control variables via
172      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
173      Only required customization should be S/R ctrl_map_ini_genarr.F
174      (routine in repository contains example)
175    o pkg/exf:
176      - fix and refine checking of surface-relaxation setting when using EXF
177    o verification (adjoint exp):
178      - reduce length of simulation by half for experiment global_ocean.cs32x15
179        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
180    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
181      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
182        of KE that can occur with aggressive optimization
183      + put quadratic bottom drag calculation in separated loops (only done if
184        using bottomDragQuadratic)
185    o model/src: CG2D_NSA
186      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
187         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
188      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
189         change cg2d residual target to be expressed in Wunits (=> do not normalise
190         RHS ; this fix global_max Pb with TAF); update output.
191    o verification/tutorial_tracer_adjsens:
192       improve parameter consistency (and get rid of warnings):
193       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
194       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
195       - use staggerTimeStep (for stability) in som81; use default rotation period.
196    o pkg/exch2:
197      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
198        reset to 0 = 1 long line in X)
199    o pkg/mdsio:
200      - fix reading of dimensions from meta file for large-size domain
201    o model/src:
202      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
203      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
204        Cubed-Sphere Exch with CS-corners inside the domain;
205        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
206        globalArea and to set hasWetCSCorners.
207      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
208        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
209      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
210        useCDscheme and useCubedSphereExchange).
211    o pkg/seaice/seaice_growth.F :
212      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
213        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
214        when the previous code was not correct.
215      - in all cases diagnoze the boundary condition mismatch to SIaaflux
216      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
217        that term to QNET (essentially to set the melt/freeze water to 0degC).
218        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
219    o verification/global_ocean.cs32x15/input.seaice :
220      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
221      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
222      - update results (output.seaice.txt) accordingly.
223    o verification/lab_sea/input/data.seaice :
224      - remove SEAICEheatConsFix, which is now be tested
225        in global_ocean.cs32x15. The presently coded fix
226        is only consistent with real fresh water + nlfs.
227      - update results (output.txt) accordingly.
228    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
229    o AD_CONFIG.h file:
230      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
231      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
232        add it explicitly in each fortran src file where it is needed.
233        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
234        thus introducing potentially wrong dependency; therefore, better to include
235        it only where it's really needed, and after any other included OPTIONS file
236        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
237        or ALLOW_TANGENTLINEAR_RUN).
238    
239    checkpoint63p (2012/07/06)
240    o pkg/autodiff:
241      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
242      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
243        which are now read from new parameter file "data.autodiff" (inAdExact
244        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
245      - add file "data.autodiff" in all verification/*/input_ad/ directories.
246      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
247        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
248    o verification/tutorial_tracer_adjsens/
249      - add extra sub-verification which uses "SOM" advection scheme
250        (2nd Order-Moment Advection Scheme, Prather Limiter) with
251          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
252        and in data:
253          multiDimAdvection=.TRUE.,
254          tempAdvScheme=81,
255          saltAdvScheme=81,
256    o model/src:
257      - introduce ALLOW_BALANCE_RELAX which allow the removal
258       of the global mean of relaxation terms by setting
259       balanceThetaClimRelax and balanceSaltClimRelax
260      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
261       This case is now treated appropriately in seaice_growth.F
262    o pkg/seaice:
263      - do balanceEmPmR and balanceQnet based on the net fluxes
264        (SItflux) that enter the ocean+ice system rather than QNET
265        and EMPMR. Works best in real fresh water.
266      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
267        out of the diagnotics bloc, and stored in global arrays.
268    
269    checkpoint63o (2012/06/29)
270    o vertical mixing schemes:
271      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
272      - replace computation of density (in Function STATE1, opps_calc.F) by a call
273        to S/R FIND_RHO_SCALAR
274      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
275        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
276        affects output (vermix.ggl90) at truncation level.
277    o testreport:
278      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
279        (nSx,nSy) for the number of threads (from eedata.mth)
280    o model/src:
281      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
282        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
283    o verification/tutorial_tracer_adjsens/
284      - compile with ALLOW_CG2D_NSA
285      - run with nonlinFreeSurf=3
286      - update reference output_adm.txt
287    o tools/genmake2:
288      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
289        refine usePROFILES switching off (only when NetCDF is not available).
290    o verification (atmospheric set-up):
291      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
292    o pkg/profiles : refine profiles and files handling.
293    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
294    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
295      - changes to use model/src/the_main_loop.F rather than the ecco version
296        in ecco type adjoint runs.
297    o model/src:
298      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
299      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
300      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
301    o model/src:
302      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
303        update output of test experiment bottom_ctrl_5x5.
304    o pkg/generic_advdiff:
305      - implement vertical bi-harmonic diffusion (for now, only for T & S and
306        only explicitly).
307    o verification/bottom_ctrl_5x5/
308      update reference output (results changed quite some time ago,
309      not sure when; but new reference results look ok in terms of grdchk)
310    o verification/1D_ocean_ice_column/
311      For verification purposes, the exact adjoint rather than an approx.
312      should be used (e.g., to comare against F.D. or TLM).
313      removed autodiff_inadmode*_ad.F routines in code_ad/
314      Update results/ accordingly.
315    o pkg/cal:
316      - change cal_getdate.F so that output date is function of input time only
317        (less ambiguous, not mixed up with input iteration number).
318      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
319    o pkg/diagnostics:
320      - implement calendarDumps also for stats-diags
321      - implement calendarDumps also for snap-shot output (negative freq)
322      - for now, ignores calendarDumps if non-zero phase-lag.
323    
324    checkpoint63n (2012/06/04)
325    o model/src:
326      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
327        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
328      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
329        similar to calc_r_star.F); update results of experiment internal_wave and
330        tutorial_global_oce_in_p (affected @ truncation level).
331    o pkg/shelfice:
332      - add parameterisation of advective-diffusive flux into the ice shelf
333        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
334      - simply eps3/3a computation
335    o eesupp:
336     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
337       between tiles, just fill-in edges assuming locally periodic subdomain) and
338       add corresponding exchange subroutines (EXCH0);
339     - new CG-solver version (_EX0) for disconnected-tiles special case.
340    o model/src (CG-solvers):
341     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
342       (similar final residual output and max-Iter number as with standard version);
343     - allows to store and use lowest-residual solution (standard & _SR versions);
344     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
345     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
346    o eesup/src:
347     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
348       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
349    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
350    
351    checkpoint63m (2012/04/27)
352    o pkg/shelfice:
353     - account for partical cells in surface level below ice-shelf for hydrostatic
354       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
355    o ad test experiments:
356     - update and rename to "ad_optfile.local" local AD-optfile specific to a
357       particular adjoint verification experiment (in verification/*/code_ad/)
358    o pkg/seaice & pkg/exf:
359     - Part two of ECCO-CLIVAR code merges.
360       Completes merge of seaice area relax. code.
361       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
362       to be set in EXF_OPTIONS.h since this pkg controls its I/O
363       (and avoids second CPP option in SEAICE_OPTIONS.h)
364     - change default value of costIceStart & costIceEnd to a valid date.
365     - add snowPrecip to HSNOW in seaice_growth
366    o pkg/ptracers:
367     - move ptracers summary and setup check into separated S/R ; add a check for
368       valid PTRACERS_Iter0 value (error+stop or just warning).
369    o pkg/cal (+ pkg/ecco):
370     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
371       as input; and for AD, unless both are not differentiable (e.g., k index)).
372    o model/src:
373     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
374       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
375       temporary set to usingZCoords value (to be changed to F when using shelfice).
376     - hydrostatic pressure: implement partial cell near the surface also for
377       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
378       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
379    o pkg/ctrl/ctrl_init.F:
380     - add a formal parameter to s/r ctrl_init_rec to print
381       xx_$(ctrl_valiable)_file for easier debugging
382     - move call of cal_* routines into the if-block where they are really
383       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
384       to specify a startdate
385    o pkg/seaice:
386     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
387       global_ocean.cs32x15/code versions).
388     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
389       verification experiment global_ocean.cs32x15.seaice and update results.
390    o pkg/exf:
391     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
392       (according to useExfYearlyFields).
393    o pkg/cal:
394     - move calendar setting & summary (previously in cal_readparams.F) into new
395       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
396       length of the simulation is set (after SET_PARMS call); This is an attempt
397       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
398     - For safety: keep a record of pkg/cal parameter settings status
399               to allow to STOP if one pkg/cal S/R is called too early.
400     - add a stop in all basic pkg/cal subroutines if called before setting is done.
401     - modify cal_getdate.F: stop when nothing was returned;
402       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
403       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
404    
405    checkpoint63l (2012/04/04)
406    o pkg/bbl:
407      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
408        update global_with_exf output.yearly.txt file.
409    o pkg/cal:
410      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
411      - remove 2 unsused and very short (1 line only) functions ;
412      - remove unsused subroutines from AD-Diff list.
413    o model/src:
414      - start to implement clean wait to stop in initialization S/R (config_check.F,
415         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
416    o folowing PRINT_MESSAGE changes:
417      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
418    o pkg/bbl:
419      - modification so it can work with z*
420      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
421      - global_with_exf/input.yearly verification; changes output.yearly.txt
422    o eesupp/src:
423      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
424        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
425      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
426        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
427      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
428      - when using MPI, always set usingMPI=T ; set default accordingly and stop
429        if not consistent.
430      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
431        argument is zero (in case called within single-thread section).
432    o pkg/fizhi:
433        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
434        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
435    o pkg/exch2:
436      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
437        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
438      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
439        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
440        with bad ones coming from a not-yet-updated halo.
441        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
442    o pkg/frazil:
443        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
444        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
445    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
446    o verification/lab_sea
447      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
448      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
449      * nTimeSteps 3 -> 4
450      * changed reference output accordingly
451    o pkg/ctrl:
452      * fix ctrl_get_gen for xx_sst, xx_sss
453    o pkg/fizhi:
454      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
455        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
456      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
457        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
458        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
459    o pkg/gmredi:
460      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
461    o pkg/fizhi:
462      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
463        (old)aces open64 tuv test.
464    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
465    o pkg/mom_vecinv:
466      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
467        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
468        with non-lin free-surf).
469    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
470      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
471      some compilers (gfortran 4.6.0 on MacOS)
472    o momentum:
473      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
474        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
475        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
476    
477    checkpoint63k (2012/03/17)
478    o model/src:
479       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
480         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
481       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
482         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
483    o model/src: solve_*diagonal.F
484       - replace division with multiplication by inverse (similar to original version)
485         update output of AD exp. global_ocean.90x40x15.
486       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
487         to enable the use of the vectorized & differentiable solve_tridiagonal.F
488       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
489         vertical advection (to get solve_tridiagonal tested in AD mode).
490    o pkg/seaice: ECCO-CLIVAR merge:
491      1. seaice AREA relaxation
492         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
493         * runtime flag: SEAICE_tauAreaObsRelax
494      2. modified global mean cost imbalance code: CPP option
495          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
496    o another iteration on solve_*diagonal.F
497       Make choices independent of AUTODIFF
498       Default will be the adjoinable vectorized version.
499       Alternative choices are:
500       * non-adjoinable original version with low memory footprint:
501         #define SOLVE_DIAGONAL_LOWMEMORY
502       * still adjoinable but does not vectorize (k as inner-most loop):
503         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
504    o testreport
505     - add option to use a home made wrapper around "make"
506     - remove MITGCM_IEEE env. variable (no longer active)
507    o pkg/shelfice
508     - improve computation of friction velocity for velocity dependent
509       exchange coefficients: include velocities into SHELFICEBoundaryLayer
510       block to average velocities vertically
511     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
512    o Modify diagonal solvers, now three versions (upon request):
513      #ifndef SOLVE_DIAGONAL_AUTODIFF
514        1. default version (dating back a while ago)
515      #else /* def SOLVE_DIAGONAL_AUTODIFF */
516      # ifdef SOLVE_DIAGONAL_KINNER
517        2. adjoinable version with k-innermost loop (G. Forget)
518      # else
519        3. adjoinable vectorized version of 2.
520      # endif
521      #endif /* SOLVE_DIAGONAL_AUTODIFF */
522      All flags are currently set within routines, but could/should be moved to CPP-options.
523      Array bounds for 1. are as before, for 2.,3. cover the entire domain
524      (could be changed for 1. too).
525    o verification/lab_sea (fwd):
526      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
527        use 7 categories (except hb87), new solve4temp params (except salt_plume),
528        constant salinity (=4) or variable salinity (salt_plume) done through
529        SItracer.
530    o pkg/seaice:
531      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
532      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
533         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
534        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
535        SEAICE_freeze got retired) but already better than previously with
536        SEAICE_freeze=123456.7 deg.C;
537      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
538        (safer multi-threaded setting); always set SEAICEuseEVP;
539      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
540        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
541        stop if multiple specifications for the same coeff; make sure default
542        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
543    o pkg/obcs:
544      - allow to switch to upwind 1rst order advection scheme for the advective
545        flux computation at the open-boundary; disabled for adjoint built.
546    o pkg/ptracers:
547      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
548      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
549      - add parameter to decide when to start a tracer; use internal flag to
550        know which tracer to step-forward; switch this internal flag at the top
551        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
552        for adjoint built.
553    o pkg/seaice:
554      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
555      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
556      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
557    o pkg/ecco:
558      - fix writing of output file DiagnosCost_ClimSalt/Theta
559        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
560    o pkg/seaice:
561      - add missing initialisation of COR_ICE array in dynsolver.F
562      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
563        compiled either way, and is tested in all exps (multidim was only tested
564        in lab_sea ad before).
565      - cosmetic change to prepare for future addition of ITD. no change to results.
566        no defaults change.
567      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
568      - by lack of adequate verification experiments, I further used custom versions
569        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
570        should be correct.
571      - avoid recomputations in ad.
572    o array initialisation in adjoint mode:
573      1) pkg/mom_common/mom_calc_ke.F:
574        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
575        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
576        part this initialisation is gone, resulting in Floating Point Exception
577        (caught by open64 compiler with debug option).
578      2) model/src/convective_weights.F
579        set output convectCount over the full array range (instead of doing
580        an update): this fix a similar issue when called within recomputation (adjoint)
581        which could by-pass the initialisation (normally done in the caller S/R).
582    o pkg/seaice:
583      - final version of turbulent flux params, as agreed at MIT ice meet:
584           SEAICE_mcPheePiston (default is ~ 0.000875)
585           SEAICE_mcPheeTaper (default is 0.)
586           SEAICE_frazilFrac (defualt is 1.)
587           SEAICE_mcPheeStepFunc (default is false)
588      - changes results at trunction error level
589      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
590    o added pkg/frazil:
591      - see frazil_description.tex for details
592      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
593    o pkg/shelfice/shelfice_thermodynamics.F
594      - fix exponents for velocity dependent exchange coefficients: change
595        from 2/3(=0) to 0.66666666666666667
596      - move computation of velocity dependent exchange coefficients into
597        separate loop, so that it applies to both thermodynamics
598      - move some divisions by constants out of loops
599    
600    checkpoint63j (2012/02/16)
601    o pkg/seaice:
602      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
603      - SItracer:  added run time params, and allow coupling to ocn salinity.
604    o pkg/seaice: remove (almost) all divisions by constants within loops
605      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
606      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
607      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
608      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
609    o pkg/seaice :
610      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
611        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
612    - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.    - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
613    - add permanent SItflux diag that corresponds to TFLUX but includes    - add permanent SItflux diag that corresponds to TFLUX but includes
614    ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
615    - allow activation/testing of a fix for suspected missing term in    - allow activation/testing of a fix for suspected missing term in
616    ocn-ice heat budget (to be confirmed). To test this, you want to      ocn-ice heat budget (to be confirmed). To test this, you want to
617    undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
618    SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
619    - no change in results, fwd or ad.    - no change in results, fwd or ad.
620  o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.  o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
621    - switch to variable freezing point.    - switch to variable freezing point.
622         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
623    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
624         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
625    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
626         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
627  o pkg/seaice:  o pkg/seaice:
628    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
629   is now the default, and the old default constant freezing point is recovered with      is now the default, and the old default constant freezing point is recovered
630   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
631   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
632    - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.    - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
633    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
634    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
635   activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.      activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
636    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
637   was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).      was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
638    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
639   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
640    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
641    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
642    to variable freezing point (see above item for detail).    - results did not change except for global_ocean.cs32x15, mostly due to the
643        switch to variable freezing point (see above item for detail).
644  o pkg/thsice:  o pkg/thsice:
645    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
646      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
647  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
648    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
649    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
650                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
651    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
652    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
653    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
654      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
655      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
656    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
657      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
658    - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).    - seaice_summary.F : add missing report of read turbulent flux term set up
659    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
660      - seaice_check.F : check range; inform and stop if retired CPPs are used
661                         (incl. SEAICE_AGE).
662    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
663          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
664    - change results at the truncation level.    - change results at the truncation level.
665  o pkg/seaice:  o pkg/seaice:
666    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
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