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revision 1.1596 by gforget, Mon Feb 13 23:45:41 2012 UTC revision 1.1703 by jmc, Fri Aug 3 18:51:48 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 :  o pkg/autodiff:
8    - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.    re-write active I/O high-level (control) S/R:
9    1 or 2, using newly added run time parameter SEAICE_availHeatTaper.    - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
10      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
11      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
12        MDS_READ/WRITE_FIELD); change loops to multi-threads.
13      - update and merge active_file_control_slice.flow into active_file_control.flow
14      - update the calls in lower level S/R (active_file.F, active_file_g.F and
15        active_file_ad.F) keeping the argument list and function unchanged.
16      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
17        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
18    o autodiff and RS=real*4:
19      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
20        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
21      - change argument type of 3-D mask argument to _RS to match type in the call
22        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
23    o pkg/thsice:
24      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
25      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
26        fresh-water flux: uniform correction or proportional to local precip.
27    o pkg/ctrl:
28      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
29      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
30                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
31      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
32    
33    checkpoint63q (2012/07/30)
34    o pkg/autodiff:
35      note about monitor and snap-shot of ad-variables:
36      a) need to apply ADEXCH before monitor or output of ad-vars to include
37       overlap contributions (was done for adjDump but missing for monitor).
38      b) since ADEXCH implies adding overlap values to interior array, machine
39       truncation error is expected when adding an ADEXCH call in the middle of
40       the time-stepping (although mathematically identical).
41      modifs:
42      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
43        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
44      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
45        apply ADEXCH before monitor or snap-shot of ad-variables:
46           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
47      - implement new method (copy+adexch) for snap-shot and monitor of main model
48        ad-vars (initially not used by default -> output unchanged).
49      - change default (set to 2) to use new method and update few output_adm.txt
50        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
51        and both tutorial_tracer_adjsens tests).
52      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
53        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
54    o pkg/ctrl:
55      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
56      generic control variables via
57      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
58      Only required customization should be S/R ctrl_map_ini_genarr.F
59      (routine in repository contains example)
60    o pkg/exf:
61      - fix and refine checking of surface-relaxation setting when using EXF
62    o verification (adjoint exp):
63      - reduce length of simulation by half for experiment global_ocean.cs32x15
64        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
65    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
66      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
67        of KE that can occur with aggressive optimization
68      + put quadratic bottom drag calculation in separated loops (only done if
69        using bottomDragQuadratic)
70    o model/src: CG2D_NSA
71      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
72         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
73      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
74         change cg2d residual target to be expressed in Wunits (=> do not normalise
75         RHS ; this fix global_max Pb with TAF); update output.
76    o verification/tutorial_tracer_adjsens:
77       improve parameter consistency (and get rid of warnings):
78       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
79       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
80       - use staggerTimeStep (for stability) in som81; use default rotation period.
81    o pkg/exch2:
82      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
83        reset to 0 = 1 long line in X)
84    o pkg/mdsio:
85      - fix reading of dimensions from meta file for large-size domain
86    o model/src:
87      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
88      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
89        Cubed-Sphere Exch with CS-corners inside the domain;
90        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
91        globalArea and to set hasWetCSCorners.
92      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
93        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
94      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
95        useCDscheme and useCubedSphereExchange).
96    o pkg/seaice/seaice_growth.F :
97      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
98        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
99        when the previous code was not correct.
100      - in all cases diagnoze the boundary condition mismatch to SIaaflux
101      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
102        that term to QNET (essentially to set the melt/freeze water to 0degC).
103        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
104    o verification/global_ocean.cs32x15/input.seaice :
105      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
106      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
107      - update results (output.seaice.txt) accordingly.
108    o verification/lab_sea/input/data.seaice :
109      - remove SEAICEheatConsFix, which is now be tested
110        in global_ocean.cs32x15. The presently coded fix
111        is only consistent with real fresh water + nlfs.
112      - update results (output.txt) accordingly.
113    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
114    o AD_CONFIG.h file:
115      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
116      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
117        add it explicitly in each fortran src file where it is needed.
118        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
119        thus introducing potentially wrong dependency; therefore, better to include
120        it only where it's really needed, and after any other included OPTIONS file
121        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
122        or ALLOW_TANGENTLINEAR_RUN).
123    
124    checkpoint63p (2012/07/06)
125    o pkg/autodiff:
126      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
127      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
128        which are now read from new parameter file "data.autodiff" (inAdExact
129        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
130      - add file "data.autodiff" in all verification/*/input_ad/ directories.
131      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
132        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
133    o verification/tutorial_tracer_adjsens/
134      - add extra sub-verification which uses "SOM" advection scheme
135        (2nd Order-Moment Advection Scheme, Prather Limiter) with
136          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
137        and in data:
138          multiDimAdvection=.TRUE.,
139          tempAdvScheme=81,
140          saltAdvScheme=81,
141    o model/src:
142      - introduce ALLOW_BALANCE_RELAX which allow the removal
143       of the global mean of relaxation terms by setting
144       balanceThetaClimRelax and balanceSaltClimRelax
145      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
146       This case is now treated appropriately in seaice_growth.F
147    o pkg/seaice:
148      - do balanceEmPmR and balanceQnet based on the net fluxes
149        (SItflux) that enter the ocean+ice system rather than QNET
150        and EMPMR. Works best in real fresh water.
151      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
152        out of the diagnotics bloc, and stored in global arrays.
153    
154    checkpoint63o (2012/06/29)
155    o vertical mixing schemes:
156      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
157      - replace computation of density (in Function STATE1, opps_calc.F) by a call
158        to S/R FIND_RHO_SCALAR
159      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
160        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
161        affects output (vermix.ggl90) at truncation level.
162    o testreport:
163      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
164        (nSx,nSy) for the number of threads (from eedata.mth)
165    o model/src:
166      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
167        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
168    o verification/tutorial_tracer_adjsens/
169      - compile with ALLOW_CG2D_NSA
170      - run with nonlinFreeSurf=3
171      - update reference output_adm.txt
172    o tools/genmake2:
173      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
174        refine usePROFILES switching off (only when NetCDF is not available).
175    o verification (atmospheric set-up):
176      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
177    o pkg/profiles : refine profiles and files handling.
178    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
179    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
180      - changes to use model/src/the_main_loop.F rather than the ecco version
181        in ecco type adjoint runs.
182    o model/src:
183      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
184      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
185      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
186    o model/src:
187      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
188        update output of test experiment bottom_ctrl_5x5.
189    o pkg/generic_advdiff:
190      - implement vertical bi-harmonic diffusion (for now, only for T & S and
191        only explicitly).
192    o verification/bottom_ctrl_5x5/
193      update reference output (results changed quite some time ago,
194      not sure when; but new reference results look ok in terms of grdchk)
195    o verification/1D_ocean_ice_column/
196      For verification purposes, the exact adjoint rather than an approx.
197      should be used (e.g., to comare against F.D. or TLM).
198      removed autodiff_inadmode*_ad.F routines in code_ad/
199      Update results/ accordingly.
200    o pkg/cal:
201      - change cal_getdate.F so that output date is function of input time only
202        (less ambiguous, not mixed up with input iteration number).
203      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
204    o pkg/diagnostics:
205      - implement calendarDumps also for stats-diags
206      - implement calendarDumps also for snap-shot output (negative freq)
207      - for now, ignores calendarDumps if non-zero phase-lag.
208    
209    checkpoint63n (2012/06/04)
210    o model/src:
211      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
212        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
213      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
214        similar to calc_r_star.F); update results of experiment internal_wave and
215        tutorial_global_oce_in_p (affected @ truncation level).
216    o pkg/shelfice:
217      - add parameterisation of advective-diffusive flux into the ice shelf
218        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
219      - simply eps3/3a computation
220    o eesupp:
221     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
222       between tiles, just fill-in edges assuming locally periodic subdomain) and
223       add corresponding exchange subroutines (EXCH0);
224     - new CG-solver version (_EX0) for disconnected-tiles special case.
225    o model/src (CG-solvers):
226     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
227       (similar final residual output and max-Iter number as with standard version);
228     - allows to store and use lowest-residual solution (standard & _SR versions);
229     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
230     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
231    o eesup/src:
232     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
233       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
234    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
235    
236    checkpoint63m (2012/04/27)
237    o pkg/shelfice:
238     - account for partical cells in surface level below ice-shelf for hydrostatic
239       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
240    o ad test experiments:
241     - update and rename to "ad_optfile.local" local AD-optfile specific to a
242       particular adjoint verification experiment (in verification/*/code_ad/)
243    o pkg/seaice & pkg/exf:
244     - Part two of ECCO-CLIVAR code merges.
245       Completes merge of seaice area relax. code.
246       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
247       to be set in EXF_OPTIONS.h since this pkg controls its I/O
248       (and avoids second CPP option in SEAICE_OPTIONS.h)
249     - change default value of costIceStart & costIceEnd to a valid date.
250     - add snowPrecip to HSNOW in seaice_growth
251    o pkg/ptracers:
252     - move ptracers summary and setup check into separated S/R ; add a check for
253       valid PTRACERS_Iter0 value (error+stop or just warning).
254    o pkg/cal (+ pkg/ecco):
255     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
256       as input; and for AD, unless both are not differentiable (e.g., k index)).
257    o model/src:
258     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
259       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
260       temporary set to usingZCoords value (to be changed to F when using shelfice).
261     - hydrostatic pressure: implement partial cell near the surface also for
262       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
263       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
264    o pkg/ctrl/ctrl_init.F:
265     - add a formal parameter to s/r ctrl_init_rec to print
266       xx_$(ctrl_valiable)_file for easier debugging
267     - move call of cal_* routines into the if-block where they are really
268       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
269       to specify a startdate
270    o pkg/seaice:
271     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
272       global_ocean.cs32x15/code versions).
273     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
274       verification experiment global_ocean.cs32x15.seaice and update results.
275    o pkg/exf:
276     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
277       (according to useExfYearlyFields).
278    o pkg/cal:
279     - move calendar setting & summary (previously in cal_readparams.F) into new
280       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
281       length of the simulation is set (after SET_PARMS call); This is an attempt
282       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
283     - For safety: keep a record of pkg/cal parameter settings status
284               to allow to STOP if one pkg/cal S/R is called too early.
285     - add a stop in all basic pkg/cal subroutines if called before setting is done.
286     - modify cal_getdate.F: stop when nothing was returned;
287       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
288       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
289    
290    checkpoint63l (2012/04/04)
291    o pkg/bbl:
292      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
293        update global_with_exf output.yearly.txt file.
294    o pkg/cal:
295      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
296      - remove 2 unsused and very short (1 line only) functions ;
297      - remove unsused subroutines from AD-Diff list.
298    o model/src:
299      - start to implement clean wait to stop in initialization S/R (config_check.F,
300         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
301    o folowing PRINT_MESSAGE changes:
302      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
303    o pkg/bbl:
304      - modification so it can work with z*
305      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
306      - global_with_exf/input.yearly verification; changes output.yearly.txt
307    o eesupp/src:
308      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
309        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
310      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
311        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
312      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
313      - when using MPI, always set usingMPI=T ; set default accordingly and stop
314        if not consistent.
315      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
316        argument is zero (in case called within single-thread section).
317    o pkg/fizhi:
318        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
319        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
320    o pkg/exch2:
321      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
322        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
323      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
324        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
325        with bad ones coming from a not-yet-updated halo.
326        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
327    o pkg/frazil:
328        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
329        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
330    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
331    o verification/lab_sea
332      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
333      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
334      * nTimeSteps 3 -> 4
335      * changed reference output accordingly
336    o pkg/ctrl:
337      * fix ctrl_get_gen for xx_sst, xx_sss
338    o pkg/fizhi:
339      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
340        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
341      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
342        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
343        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
344    o pkg/gmredi:
345      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
346    o pkg/fizhi:
347      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
348        (old)aces open64 tuv test.
349    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
350    o pkg/mom_vecinv:
351      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
352        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
353        with non-lin free-surf).
354    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
355      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
356      some compilers (gfortran 4.6.0 on MacOS)
357    o momentum:
358      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
359        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
360        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
361    
362    checkpoint63k (2012/03/17)
363    o model/src:
364       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
365         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
366       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
367         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
368    o model/src: solve_*diagonal.F
369       - replace division with multiplication by inverse (similar to original version)
370         update output of AD exp. global_ocean.90x40x15.
371       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
372         to enable the use of the vectorized & differentiable solve_tridiagonal.F
373       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
374         vertical advection (to get solve_tridiagonal tested in AD mode).
375    o pkg/seaice: ECCO-CLIVAR merge:
376      1. seaice AREA relaxation
377         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
378         * runtime flag: SEAICE_tauAreaObsRelax
379      2. modified global mean cost imbalance code: CPP option
380          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
381    o another iteration on solve_*diagonal.F
382       Make choices independent of AUTODIFF
383       Default will be the adjoinable vectorized version.
384       Alternative choices are:
385       * non-adjoinable original version with low memory footprint:
386         #define SOLVE_DIAGONAL_LOWMEMORY
387       * still adjoinable but does not vectorize (k as inner-most loop):
388         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
389    o testreport
390     - add option to use a home made wrapper around "make"
391     - remove MITGCM_IEEE env. variable (no longer active)
392    o pkg/shelfice
393     - improve computation of friction velocity for velocity dependent
394       exchange coefficients: include velocities into SHELFICEBoundaryLayer
395       block to average velocities vertically
396     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
397    o Modify diagonal solvers, now three versions (upon request):
398      #ifndef SOLVE_DIAGONAL_AUTODIFF
399        1. default version (dating back a while ago)
400      #else /* def SOLVE_DIAGONAL_AUTODIFF */
401      # ifdef SOLVE_DIAGONAL_KINNER
402        2. adjoinable version with k-innermost loop (G. Forget)
403      # else
404        3. adjoinable vectorized version of 2.
405      # endif
406      #endif /* SOLVE_DIAGONAL_AUTODIFF */
407      All flags are currently set within routines, but could/should be moved to CPP-options.
408      Array bounds for 1. are as before, for 2.,3. cover the entire domain
409      (could be changed for 1. too).
410    o verification/lab_sea (fwd):
411      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
412        use 7 categories (except hb87), new solve4temp params (except salt_plume),
413        constant salinity (=4) or variable salinity (salt_plume) done through
414        SItracer.
415    o pkg/seaice:
416      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
417      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
418         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
419        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
420        SEAICE_freeze got retired) but already better than previously with
421        SEAICE_freeze=123456.7 deg.C;
422      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
423        (safer multi-threaded setting); always set SEAICEuseEVP;
424      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
425        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
426        stop if multiple specifications for the same coeff; make sure default
427        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
428    o pkg/obcs:
429      - allow to switch to upwind 1rst order advection scheme for the advective
430        flux computation at the open-boundary; disabled for adjoint built.
431    o pkg/ptracers:
432      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
433      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
434      - add parameter to decide when to start a tracer; use internal flag to
435        know which tracer to step-forward; switch this internal flag at the top
436        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
437        for adjoint built.
438    o pkg/seaice:
439      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
440      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
441      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
442    o pkg/ecco:
443      - fix writing of output file DiagnosCost_ClimSalt/Theta
444        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
445    o pkg/seaice:
446      - add missing initialisation of COR_ICE array in dynsolver.F
447      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
448        compiled either way, and is tested in all exps (multidim was only tested
449        in lab_sea ad before).
450      - cosmetic change to prepare for future addition of ITD. no change to results.
451        no defaults change.
452      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
453      - by lack of adequate verification experiments, I further used custom versions
454        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
455        should be correct.
456      - avoid recomputations in ad.
457    o array initialisation in adjoint mode:
458      1) pkg/mom_common/mom_calc_ke.F:
459        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
460        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
461        part this initialisation is gone, resulting in Floating Point Exception
462        (caught by open64 compiler with debug option).
463      2) model/src/convective_weights.F
464        set output convectCount over the full array range (instead of doing
465        an update): this fix a similar issue when called within recomputation (adjoint)
466        which could by-pass the initialisation (normally done in the caller S/R).
467    o pkg/seaice:
468      - final version of turbulent flux params, as agreed at MIT ice meet:
469           SEAICE_mcPheePiston (default is ~ 0.000875)
470           SEAICE_mcPheeTaper (default is 0.)
471           SEAICE_frazilFrac (defualt is 1.)
472           SEAICE_mcPheeStepFunc (default is false)
473      - changes results at trunction error level
474      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
475    o added pkg/frazil:
476      - see frazil_description.tex for details
477      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
478    o pkg/shelfice/shelfice_thermodynamics.F
479      - fix exponents for velocity dependent exchange coefficients: change
480        from 2/3(=0) to 0.66666666666666667
481      - move computation of velocity dependent exchange coefficients into
482        separate loop, so that it applies to both thermodynamics
483      - move some divisions by constants out of loops
484    
485    checkpoint63j (2012/02/16)
486    o pkg/seaice:
487      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
488      - SItracer:  added run time params, and allow coupling to ocn salinity.
489    o pkg/seaice: remove (almost) all divisions by constants within loops
490      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
491      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
492      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
493      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
494    o pkg/seaice :
495      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
496        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
497    - 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.
498    - add permanent SItflux diag that corresponds to TFLUX but includes    - add permanent SItflux diag that corresponds to TFLUX but includes
499    ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
500    - allow activation/testing of a fix for suspected missing term in    - allow activation/testing of a fix for suspected missing term in
501    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
502    undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
503    SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
504    - no change in results, fwd or ad.    - no change in results, fwd or ad.
505  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:
506    - switch to variable freezing point.    - switch to variable freezing point.
507         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
508    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
509         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
510    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
511         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
512  o pkg/seaice:  o pkg/seaice:
513    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
514   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
515   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
516   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
517    - 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)
518    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
519    - 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
520   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.
521    - 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)
522   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).
523    - 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
524   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
525    - 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
526    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
527    to variable freezing point (see above item for detail).    - results did not change except for global_ocean.cs32x15, mostly due to the
528        switch to variable freezing point (see above item for detail).
529  o pkg/thsice:  o pkg/thsice:
530    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
531      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
532  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
533    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
534    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
535                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
536    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
537    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
538    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
539      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
540      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
541    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
542      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
543    - 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
544    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
545      - seaice_check.F : check range; inform and stop if retired CPPs are used
546                         (incl. SEAICE_AGE).
547    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
548          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
549    - change results at the truncation level.    - change results at the truncation level.
550  o pkg/seaice:  o pkg/seaice:
551    - 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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