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revision 1.1579 by jmc, Sat Jan 21 19:41:43 2012 UTC revision 1.1715 by gforget, Tue Aug 14 18:01:13 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/ecco/ecco_cost_final.F :
8      - fix fc print statements (to stdout and costfunction0000) so
9        that the printed value is always after the global sum.
10    o pkg/seaice/seaice_dynsolver.F :
11      - fix ice strength assymptote at SEAICE_area_max<1
12        (no change for the standard case of SEAICE_area_max=1)
13    o some cleaning:
14      - pkg source files: ensure that all *.F files from each pkg included the
15        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
16        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
17        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
18        includes;
19      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
20      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
21        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
22        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
23      - update option-file CPP_OPTIONS.h of all AD experiments:
24        * no longer include PACKAGES_CONFIG.h ;
25        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
26        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
27          including ECCO_CPPOPTIONS.h).
28    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
29      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
30        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
31        not necessary accurate).
32      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
33        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
34        deliberately break compilation (a remainder that it needs to be customized)
35      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
36      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
37      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
38    o tools/genamke2:
39      - check for lapack.
40    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
41      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
42        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
43        from both packages.
44      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
45      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
46      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
47        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
48    o pkg/cost : add comments to explain special and/or untested setups.
49    o pkg/exf:
50      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
51        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
52    o verification/*/code_ad:
53      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
54      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
55      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
56        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
57    o pkg/seaice :
58      - added possibility to change ice strength/PRESS0 relationship to
59        HEFF, according to the following run time parameters
60        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
61        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
62        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
63    o pkg/ggl90 :
64      - added run time flag mxlSurfFlag to include the code that ensure
65        mixing between first and second level (previously included as a comment)
66    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
67      - add test of newly added dumpAdByRec=T option where
68        we write all records to one file per variable.
69    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
70      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
71        to check that this code is ok with taf and compiles in adjoint.
72    o pkg/autodiff :
73      - added run time param dumpAdByRec : ad dump format switch.
74        If true then write all records to one file per variable.
75        Else write one file per record (remains the default).
76      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
77    o pkg/seaice:
78     - Added SEAICEuseTILT run time switch : if set to
79       false then omit the tilt term in seaice dynamics.
80     - Fix free drift calculation.
81    o pkg/shelfice:
82      When initializing SHELFICEDragQuadratic, set default to be
83      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
84      but retain option to set it independently
85      (inconsistenty spotted by Veronique Dansereau)
86    o eesupp/inc:
87      - in EEPARAMS.h, add real-type constant for some frequently used simple number
88         (0,1,2,1/2), with name explicitly referring to RS/RL type.
89    o model/src:
90      - move balancing of relaxation terms to new S/R balance_relax.F.
91    o pkg/autodiff:
92      re-write active I/O high-level (control) S/R:
93      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
94      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
95      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
96        MDS_READ/WRITE_FIELD); change loops to multi-threads.
97      - update and merge active_file_control_slice.flow into active_file_control.flow
98      - update the calls in lower level S/R (active_file.F, active_file_g.F and
99        active_file_ad.F) keeping the argument list and function unchanged.
100      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
101        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
102      - new low-level active I/O routines, one for each type (RL/RS), for active var
103        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
104        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
105        right type.
106    o autodiff and RS=real*4:
107      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
108        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
109      - change argument type of 3-D mask argument to _RS to match type in the call
110        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
111    o pkg/thsice:
112      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
113      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
114        fresh-water flux: uniform correction or proportional to local precip.
115    o pkg/ctrl:
116      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
117      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
118                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
119      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
120    
121    checkpoint63q (2012/07/30)
122    o pkg/autodiff:
123      note about monitor and snap-shot of ad-variables:
124      a) need to apply ADEXCH before monitor or output of ad-vars to include
125       overlap contributions (was done for adjDump but missing for monitor).
126      b) since ADEXCH implies adding overlap values to interior array, machine
127       truncation error is expected when adding an ADEXCH call in the middle of
128       the time-stepping (although mathematically identical).
129      modifs:
130      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
131        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
132      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
133        apply ADEXCH before monitor or snap-shot of ad-variables:
134           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
135      - implement new method (copy+adexch) for snap-shot and monitor of main model
136        ad-vars (initially not used by default -> output unchanged).
137      - change default (set to 2) to use new method and update few output_adm.txt
138        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
139        and both tutorial_tracer_adjsens tests).
140      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
141        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
142    o pkg/ctrl:
143      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
144      generic control variables via
145      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
146      Only required customization should be S/R ctrl_map_ini_genarr.F
147      (routine in repository contains example)
148    o pkg/exf:
149      - fix and refine checking of surface-relaxation setting when using EXF
150    o verification (adjoint exp):
151      - reduce length of simulation by half for experiment global_ocean.cs32x15
152        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
153    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
154      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
155        of KE that can occur with aggressive optimization
156      + put quadratic bottom drag calculation in separated loops (only done if
157        using bottomDragQuadratic)
158    o model/src: CG2D_NSA
159      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
160         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
161      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
162         change cg2d residual target to be expressed in Wunits (=> do not normalise
163         RHS ; this fix global_max Pb with TAF); update output.
164    o verification/tutorial_tracer_adjsens:
165       improve parameter consistency (and get rid of warnings):
166       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
167       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
168       - use staggerTimeStep (for stability) in som81; use default rotation period.
169    o pkg/exch2:
170      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
171        reset to 0 = 1 long line in X)
172    o pkg/mdsio:
173      - fix reading of dimensions from meta file for large-size domain
174    o model/src:
175      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
176      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
177        Cubed-Sphere Exch with CS-corners inside the domain;
178        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
179        globalArea and to set hasWetCSCorners.
180      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
181        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
182      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
183        useCDscheme and useCubedSphereExchange).
184    o pkg/seaice/seaice_growth.F :
185      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
186        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
187        when the previous code was not correct.
188      - in all cases diagnoze the boundary condition mismatch to SIaaflux
189      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
190        that term to QNET (essentially to set the melt/freeze water to 0degC).
191        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
192    o verification/global_ocean.cs32x15/input.seaice :
193      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
194      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
195      - update results (output.seaice.txt) accordingly.
196    o verification/lab_sea/input/data.seaice :
197      - remove SEAICEheatConsFix, which is now be tested
198        in global_ocean.cs32x15. The presently coded fix
199        is only consistent with real fresh water + nlfs.
200      - update results (output.txt) accordingly.
201    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
202    o AD_CONFIG.h file:
203      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
204      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
205        add it explicitly in each fortran src file where it is needed.
206        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
207        thus introducing potentially wrong dependency; therefore, better to include
208        it only where it's really needed, and after any other included OPTIONS file
209        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
210        or ALLOW_TANGENTLINEAR_RUN).
211    
212    checkpoint63p (2012/07/06)
213    o pkg/autodiff:
214      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
215      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
216        which are now read from new parameter file "data.autodiff" (inAdExact
217        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
218      - add file "data.autodiff" in all verification/*/input_ad/ directories.
219      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
220        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
221    o verification/tutorial_tracer_adjsens/
222      - add extra sub-verification which uses "SOM" advection scheme
223        (2nd Order-Moment Advection Scheme, Prather Limiter) with
224          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
225        and in data:
226          multiDimAdvection=.TRUE.,
227          tempAdvScheme=81,
228          saltAdvScheme=81,
229    o model/src:
230      - introduce ALLOW_BALANCE_RELAX which allow the removal
231       of the global mean of relaxation terms by setting
232       balanceThetaClimRelax and balanceSaltClimRelax
233      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
234       This case is now treated appropriately in seaice_growth.F
235    o pkg/seaice:
236      - do balanceEmPmR and balanceQnet based on the net fluxes
237        (SItflux) that enter the ocean+ice system rather than QNET
238        and EMPMR. Works best in real fresh water.
239      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
240        out of the diagnotics bloc, and stored in global arrays.
241    
242    checkpoint63o (2012/06/29)
243    o vertical mixing schemes:
244      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
245      - replace computation of density (in Function STATE1, opps_calc.F) by a call
246        to S/R FIND_RHO_SCALAR
247      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
248        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
249        affects output (vermix.ggl90) at truncation level.
250    o testreport:
251      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
252        (nSx,nSy) for the number of threads (from eedata.mth)
253    o model/src:
254      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
255        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
256    o verification/tutorial_tracer_adjsens/
257      - compile with ALLOW_CG2D_NSA
258      - run with nonlinFreeSurf=3
259      - update reference output_adm.txt
260    o tools/genmake2:
261      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
262        refine usePROFILES switching off (only when NetCDF is not available).
263    o verification (atmospheric set-up):
264      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
265    o pkg/profiles : refine profiles and files handling.
266    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
267    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
268      - changes to use model/src/the_main_loop.F rather than the ecco version
269        in ecco type adjoint runs.
270    o model/src:
271      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
272      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
273      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
274    o model/src:
275      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
276        update output of test experiment bottom_ctrl_5x5.
277    o pkg/generic_advdiff:
278      - implement vertical bi-harmonic diffusion (for now, only for T & S and
279        only explicitly).
280    o verification/bottom_ctrl_5x5/
281      update reference output (results changed quite some time ago,
282      not sure when; but new reference results look ok in terms of grdchk)
283    o verification/1D_ocean_ice_column/
284      For verification purposes, the exact adjoint rather than an approx.
285      should be used (e.g., to comare against F.D. or TLM).
286      removed autodiff_inadmode*_ad.F routines in code_ad/
287      Update results/ accordingly.
288    o pkg/cal:
289      - change cal_getdate.F so that output date is function of input time only
290        (less ambiguous, not mixed up with input iteration number).
291      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
292    o pkg/diagnostics:
293      - implement calendarDumps also for stats-diags
294      - implement calendarDumps also for snap-shot output (negative freq)
295      - for now, ignores calendarDumps if non-zero phase-lag.
296    
297    checkpoint63n (2012/06/04)
298    o model/src:
299      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
300        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
301      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
302        similar to calc_r_star.F); update results of experiment internal_wave and
303        tutorial_global_oce_in_p (affected @ truncation level).
304    o pkg/shelfice:
305      - add parameterisation of advective-diffusive flux into the ice shelf
306        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
307      - simply eps3/3a computation
308    o eesupp:
309     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
310       between tiles, just fill-in edges assuming locally periodic subdomain) and
311       add corresponding exchange subroutines (EXCH0);
312     - new CG-solver version (_EX0) for disconnected-tiles special case.
313    o model/src (CG-solvers):
314     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
315       (similar final residual output and max-Iter number as with standard version);
316     - allows to store and use lowest-residual solution (standard & _SR versions);
317     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
318     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
319    o eesup/src:
320     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
321       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
322    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
323    
324    checkpoint63m (2012/04/27)
325    o pkg/shelfice:
326     - account for partical cells in surface level below ice-shelf for hydrostatic
327       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
328    o ad test experiments:
329     - update and rename to "ad_optfile.local" local AD-optfile specific to a
330       particular adjoint verification experiment (in verification/*/code_ad/)
331    o pkg/seaice & pkg/exf:
332     - Part two of ECCO-CLIVAR code merges.
333       Completes merge of seaice area relax. code.
334       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
335       to be set in EXF_OPTIONS.h since this pkg controls its I/O
336       (and avoids second CPP option in SEAICE_OPTIONS.h)
337     - change default value of costIceStart & costIceEnd to a valid date.
338     - add snowPrecip to HSNOW in seaice_growth
339    o pkg/ptracers:
340     - move ptracers summary and setup check into separated S/R ; add a check for
341       valid PTRACERS_Iter0 value (error+stop or just warning).
342    o pkg/cal (+ pkg/ecco):
343     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
344       as input; and for AD, unless both are not differentiable (e.g., k index)).
345    o model/src:
346     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
347       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
348       temporary set to usingZCoords value (to be changed to F when using shelfice).
349     - hydrostatic pressure: implement partial cell near the surface also for
350       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
351       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
352    o pkg/ctrl/ctrl_init.F:
353     - add a formal parameter to s/r ctrl_init_rec to print
354       xx_$(ctrl_valiable)_file for easier debugging
355     - move call of cal_* routines into the if-block where they are really
356       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
357       to specify a startdate
358    o pkg/seaice:
359     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
360       global_ocean.cs32x15/code versions).
361     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
362       verification experiment global_ocean.cs32x15.seaice and update results.
363    o pkg/exf:
364     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
365       (according to useExfYearlyFields).
366    o pkg/cal:
367     - move calendar setting & summary (previously in cal_readparams.F) into new
368       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
369       length of the simulation is set (after SET_PARMS call); This is an attempt
370       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
371     - For safety: keep a record of pkg/cal parameter settings status
372               to allow to STOP if one pkg/cal S/R is called too early.
373     - add a stop in all basic pkg/cal subroutines if called before setting is done.
374     - modify cal_getdate.F: stop when nothing was returned;
375       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
376       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
377    
378    checkpoint63l (2012/04/04)
379    o pkg/bbl:
380      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
381        update global_with_exf output.yearly.txt file.
382    o pkg/cal:
383      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
384      - remove 2 unsused and very short (1 line only) functions ;
385      - remove unsused subroutines from AD-Diff list.
386    o model/src:
387      - start to implement clean wait to stop in initialization S/R (config_check.F,
388         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
389    o folowing PRINT_MESSAGE changes:
390      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
391    o pkg/bbl:
392      - modification so it can work with z*
393      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
394      - global_with_exf/input.yearly verification; changes output.yearly.txt
395    o eesupp/src:
396      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
397        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
398      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
399        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
400      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
401      - when using MPI, always set usingMPI=T ; set default accordingly and stop
402        if not consistent.
403      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
404        argument is zero (in case called within single-thread section).
405    o pkg/fizhi:
406        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
407        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
408    o pkg/exch2:
409      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
410        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
411      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
412        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
413        with bad ones coming from a not-yet-updated halo.
414        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
415    o pkg/frazil:
416        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
417        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
418    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
419    o verification/lab_sea
420      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
421      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
422      * nTimeSteps 3 -> 4
423      * changed reference output accordingly
424    o pkg/ctrl:
425      * fix ctrl_get_gen for xx_sst, xx_sss
426    o pkg/fizhi:
427      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
428        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
429      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
430        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
431        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
432    o pkg/gmredi:
433      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
434    o pkg/fizhi:
435      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
436        (old)aces open64 tuv test.
437    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
438    o pkg/mom_vecinv:
439      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
440        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
441        with non-lin free-surf).
442    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
443      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
444      some compilers (gfortran 4.6.0 on MacOS)
445    o momentum:
446      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
447        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
448        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
449    
450    checkpoint63k (2012/03/17)
451    o model/src:
452       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
453         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
454       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
455         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
456    o model/src: solve_*diagonal.F
457       - replace division with multiplication by inverse (similar to original version)
458         update output of AD exp. global_ocean.90x40x15.
459       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
460         to enable the use of the vectorized & differentiable solve_tridiagonal.F
461       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
462         vertical advection (to get solve_tridiagonal tested in AD mode).
463    o pkg/seaice: ECCO-CLIVAR merge:
464      1. seaice AREA relaxation
465         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
466         * runtime flag: SEAICE_tauAreaObsRelax
467      2. modified global mean cost imbalance code: CPP option
468          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
469    o another iteration on solve_*diagonal.F
470       Make choices independent of AUTODIFF
471       Default will be the adjoinable vectorized version.
472       Alternative choices are:
473       * non-adjoinable original version with low memory footprint:
474         #define SOLVE_DIAGONAL_LOWMEMORY
475       * still adjoinable but does not vectorize (k as inner-most loop):
476         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
477    o testreport
478     - add option to use a home made wrapper around "make"
479     - remove MITGCM_IEEE env. variable (no longer active)
480    o pkg/shelfice
481     - improve computation of friction velocity for velocity dependent
482       exchange coefficients: include velocities into SHELFICEBoundaryLayer
483       block to average velocities vertically
484     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
485    o Modify diagonal solvers, now three versions (upon request):
486      #ifndef SOLVE_DIAGONAL_AUTODIFF
487        1. default version (dating back a while ago)
488      #else /* def SOLVE_DIAGONAL_AUTODIFF */
489      # ifdef SOLVE_DIAGONAL_KINNER
490        2. adjoinable version with k-innermost loop (G. Forget)
491      # else
492        3. adjoinable vectorized version of 2.
493      # endif
494      #endif /* SOLVE_DIAGONAL_AUTODIFF */
495      All flags are currently set within routines, but could/should be moved to CPP-options.
496      Array bounds for 1. are as before, for 2.,3. cover the entire domain
497      (could be changed for 1. too).
498    o verification/lab_sea (fwd):
499      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
500        use 7 categories (except hb87), new solve4temp params (except salt_plume),
501        constant salinity (=4) or variable salinity (salt_plume) done through
502        SItracer.
503    o pkg/seaice:
504      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
505      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
506         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
507        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
508        SEAICE_freeze got retired) but already better than previously with
509        SEAICE_freeze=123456.7 deg.C;
510      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
511        (safer multi-threaded setting); always set SEAICEuseEVP;
512      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
513        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
514        stop if multiple specifications for the same coeff; make sure default
515        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
516    o pkg/obcs:
517      - allow to switch to upwind 1rst order advection scheme for the advective
518        flux computation at the open-boundary; disabled for adjoint built.
519    o pkg/ptracers:
520      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
521      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
522      - add parameter to decide when to start a tracer; use internal flag to
523        know which tracer to step-forward; switch this internal flag at the top
524        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
525        for adjoint built.
526    o pkg/seaice:
527      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
528      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
529      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
530    o pkg/ecco:
531      - fix writing of output file DiagnosCost_ClimSalt/Theta
532        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
533    o pkg/seaice:
534      - add missing initialisation of COR_ICE array in dynsolver.F
535      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
536        compiled either way, and is tested in all exps (multidim was only tested
537        in lab_sea ad before).
538      - cosmetic change to prepare for future addition of ITD. no change to results.
539        no defaults change.
540      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
541      - by lack of adequate verification experiments, I further used custom versions
542        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
543        should be correct.
544      - avoid recomputations in ad.
545    o array initialisation in adjoint mode:
546      1) pkg/mom_common/mom_calc_ke.F:
547        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
548        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
549        part this initialisation is gone, resulting in Floating Point Exception
550        (caught by open64 compiler with debug option).
551      2) model/src/convective_weights.F
552        set output convectCount over the full array range (instead of doing
553        an update): this fix a similar issue when called within recomputation (adjoint)
554        which could by-pass the initialisation (normally done in the caller S/R).
555    o pkg/seaice:
556      - final version of turbulent flux params, as agreed at MIT ice meet:
557           SEAICE_mcPheePiston (default is ~ 0.000875)
558           SEAICE_mcPheeTaper (default is 0.)
559           SEAICE_frazilFrac (defualt is 1.)
560           SEAICE_mcPheeStepFunc (default is false)
561      - changes results at trunction error level
562      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
563    o added pkg/frazil:
564      - see frazil_description.tex for details
565      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
566    o pkg/shelfice/shelfice_thermodynamics.F
567      - fix exponents for velocity dependent exchange coefficients: change
568        from 2/3(=0) to 0.66666666666666667
569      - move computation of velocity dependent exchange coefficients into
570        separate loop, so that it applies to both thermodynamics
571      - move some divisions by constants out of loops
572    
573    checkpoint63j (2012/02/16)
574    o pkg/seaice:
575      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
576      - SItracer:  added run time params, and allow coupling to ocn salinity.
577    o pkg/seaice: remove (almost) all divisions by constants within loops
578      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
579      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
580      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
581      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
582    o pkg/seaice :
583      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
584        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
585      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
586      - add permanent SItflux diag that corresponds to TFLUX but includes
587        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
588      - allow activation/testing of a fix for suspected missing term in
589        ocn-ice heat budget (to be confirmed). To test this, you want to
590        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
591        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
592      - no change in results, fwd or ad.
593    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
594      - switch to variable freezing point.
595           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
596      - bug fix : the sublimation term that was missing is now activated.
597           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
598      - bug fix : flooding sign term for SIsal0.NE.0.
599           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
600    o pkg/seaice:
601      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
602        is now the default, and the old default constant freezing point is recovered
603        with SEAICE_tempFrz0    = -1.96,
604             SEAICE_dTempFrz_dS = 0.,
605      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
606      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
607      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
608        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
609      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
610        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
611      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
612        seaice_growth r149 for legacy branch (no results change).
613      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
614        from I. Fenty).
615      - results did not change except for global_ocean.cs32x15, mostly due to the
616        switch to variable freezing point (see above item for detail).
617    o pkg/thsice:
618      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
619        seawater freezing in thsice_calc_thickn (not used).
620    o pkg/seaice: turbulent flux term specification via run time params.
621      - replace CPP switches with run time switches to facilitate testing
622      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
623                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
624      - added runtime parameter : SEAICEturbFluxFormula
625      - move Mcphee constants to SEAICE_PARAMS.h
626      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
627                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
628                 remove seaice_summary call (moved to seaice_init_fixed)
629      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
630        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
631      - seaice_summary.F : add missing report of read turbulent flux term set up
632                           and SITRACER.
633      - seaice_check.F : check range; inform and stop if retired CPPs are used
634                         (incl. SEAICE_AGE).
635      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
636             CPP switch, same computation as before for the different options.
637      - change results at the truncation level.
638    o pkg/seaice:
639      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
640        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
641        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
642      - update verification/*/input*/data.seaice:
643        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
644        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
645        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
646        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
647    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
648      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
649        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
650        difference in results only due to machine truncation.
651      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
652        MaykutPolySatVap; keep MIN_LWDOWN.
653      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
654      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
655        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
656    o pkg/salt_plume:
657      - isolate saltPlumeFlux array exch into a specific S/R called from
658        do_oceanic_phys.F
659      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
660    o verification:
661      - move untested set-up to MITgcm_contrib/verification_other.
662    o pkg/seaice:
663      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
664    o pkg/seaice:
665      - seaice_solve4temp.F (keeping results unchanged):
666        * add 2 future run-time params to select which saturation vapor pressure
667          formula is used and how post-iteration fluxes are set.
668          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
669        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
670          the linearized expression to stay consistent with tsurf finding.
671      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
672        can be < 0.
673    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
674      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
675        conductive heat flux F_c , and add it explicitly when updating tsurf as
676        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
677        so that now F_ia has a consistent meaning through the entire routine.
678        This causes differences at truncation level: update output of fwd exp.
679        global_ocean.cs32x15.seaice.
680    o pkg/seaice:
681      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
682        of arrays, sign/direction of fluxes; no effect on results.
683      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
684        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
685        note: this should have been done before changing celsius2K default.
686      - to keep results unchanged, add back old value of celsius2K in verification
687        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
688      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
689        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
690        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
691        freezing temp is consistent with value in seaice_growth.F ; this causes
692        differences at machine truncation level: update lab_sea AD output (3/4).
693    o pkg/seaice:
694      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
695        and climsst/sss even when using seaice (to prevent calculation that might
696        use SST on land); does not affect any verification exp.
697      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
698        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
699    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
700      over land (non-legacy code)
701    o vectorize salt_plume package:
702      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
703      - this code computes plumebk everywhere (also over land), thus requires
704        code to avoid divisions by zero and catch the case of kLev=Nr.
705      - efficiency of salt_plume_frac is still sub-optimal
706    o tools (genmake2):
707      - fix makefile NAME specification (option: -makefile NAME) by adding
708        "-f $MAKEFILE" in few places where it was missing including makedepend
709        command (contribution from Paul).
710    
711    checkpoint63i (2012/01/24)
712    o model/src:
713      - add factorized versions of some EOS code to find_rho.F,
714        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
715  o model/src:  o model/src:
716    - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;    - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
717    - change default celsius2K from 273.16 to 273.15    - change default celsius2K from 273.16 to 273.15
718    - to keep results unchanged, add back old value of celsius2K in verification    - to keep results unchanged, add back old value of celsius2K in verification
719      exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd) &      exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
720       global_ocean.cs32x15(seaice).       global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
721  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
722    to make TAF generate vectorizable code    to make TAF generate vectorizable code
723  o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.  o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
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