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revision 1.1571 by mlosch, Fri Jan 6 09:40:35 2012 UTC revision 1.1694 by jmc, Mon Jul 23 23:27:10 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 verification (adjoint exp):
8      - reduce length of simulation by half for experiment global_ocean.cs32x15
9        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
10    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
11      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
12        of KE that can occur with aggressive optimization
13      + put quadratic bottom drag calculation in separated loops (only done if
14        using bottomDragQuadratic)
15    o model/src: CG2D_NSA
16      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
17         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
18      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
19         change cg2d residual target to be expressed in Wunits (=> do not normalise
20         RHS ; this fix global_max Pb with TAF); update output.
21    o verification/tutorial_tracer_adjsens:
22       improve parameter consistency (and get rid of warnings):
23       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
24       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
25       - use staggerTimeStep (for stability) in som81; use default rotation period.
26    o pkg/exch2:
27      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
28        reset to 0 = 1 long line in X)
29    o pkg/mdsio:
30      - fix reading of dimensions from meta file for large-size domain
31    o model/src:
32      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
33      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
34        Cubed-Sphere Exch with CS-corners inside the domain;
35        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
36        globalArea and to set hasWetCSCorners.
37      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
38        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
39      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
40        useCDscheme and useCubedSphereExchange).
41    o pkg/seaice/seaice_growth.F :
42      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
43        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
44        when the previous code was not correct.
45      - in all cases diagnoze the boundary condition mismatch to SIaaflux
46      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
47        that term to QNET (essentially to set the melt/freeze water to 0degC).
48        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
49    o verification/global_ocean.cs32x15/input.seaice :
50      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
51      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
52      - update results (output.seaice.txt) accordingly.
53    o verification/lab_sea/input/data.seaice :
54      - remove SEAICEheatConsFix, which is now be tested
55        in global_ocean.cs32x15. The presently coded fix
56        is only consistent with real fresh water + nlfs.
57      - update results (output.txt) accordingly.
58    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
59    o AD_CONFIG.h file:
60      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
61      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
62        add it explicitly in each fortran src file where it is needed.
63        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
64        thus introducing potentially wrong dependency; therefore, better to include
65        it only where it's really needed, and after any other included OPTIONS file
66        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
67        or ALLOW_TANGENTLINEAR_RUN).
68    
69    checkpoint63p (2012/07/06)
70    o pkg/autodiff:
71      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
72      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
73        which are now read from new parameter file "data.autodiff" (inAdExact
74        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
75      - add file "data.autodiff" in all verification/*/input_ad/ directories.
76      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
77        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
78    o verification/tutorial_tracer_adjsens/
79      - add extra sub-verification which uses "SOM" advection scheme
80        (2nd Order-Moment Advection Scheme, Prather Limiter) with
81          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
82        and in data:
83          multiDimAdvection=.TRUE.,
84          tempAdvScheme=81,
85          saltAdvScheme=81,
86    o model/src:
87      - introduce ALLOW_BALANCE_RELAX which allow the removal
88       of the global mean of relaxation terms by setting
89       balanceThetaClimRelax and balanceSaltClimRelax
90      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
91       This case is now treated appropriately in seaice_growth.F
92    o pkg/seaice:
93      - do balanceEmPmR and balanceQnet based on the net fluxes
94        (SItflux) that enter the ocean+ice system rather than QNET
95        and EMPMR. Works best in real fresh water.
96      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
97        out of the diagnotics bloc, and stored in global arrays.
98    
99    checkpoint63o (2012/06/29)
100    o vertical mixing schemes:
101      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
102      - replace computation of density (in Function STATE1, opps_calc.F) by a call
103        to S/R FIND_RHO_SCALAR
104      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
105        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
106        affects output (vermix.ggl90) at truncation level.
107    o testreport:
108      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
109        (nSx,nSy) for the number of threads (from eedata.mth)
110    o model/src:
111      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
112        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
113    o verification/tutorial_tracer_adjsens/
114      - compile with ALLOW_CG2D_NSA
115      - run with nonlinFreeSurf=3
116      - update reference output_adm.txt
117    o tools/genmake2:
118      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
119        refine usePROFILES switching off (only when NetCDF is not available).
120    o verification (atmospheric set-up):
121      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
122    o pkg/profiles : refine profiles and files handling.
123    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
124    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
125      - changes to use model/src/the_main_loop.F rather than the ecco version
126        in ecco type adjoint runs.
127    o model/src:
128      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
129      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
130      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
131    o model/src:
132      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
133        update output of test experiment bottom_ctrl_5x5.
134    o pkg/generic_advdiff:
135      - implement vertical bi-harmonic diffusion (for now, only for T & S and
136        only explicitly).
137    o verification/bottom_ctrl_5x5/
138      update reference output (results changed quite some time ago,
139      not sure when; but new reference results look ok in terms of grdchk)
140    o verification/1D_ocean_ice_column/
141      For verification purposes, the exact adjoint rather than an approx.
142      should be used (e.g., to comare against F.D. or TLM).
143      removed autodiff_inadmode*_ad.F routines in code_ad/
144      Update results/ accordingly.
145    o pkg/cal:
146      - change cal_getdate.F so that output date is function of input time only
147        (less ambiguous, not mixed up with input iteration number).
148      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
149    o pkg/diagnostics:
150      - implement calendarDumps also for stats-diags
151      - implement calendarDumps also for snap-shot output (negative freq)
152      - for now, ignores calendarDumps if non-zero phase-lag.
153    
154    checkpoint63n (2012/06/04)
155    o model/src:
156      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
157        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
158      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
159        similar to calc_r_star.F); update results of experiment internal_wave and
160        tutorial_global_oce_in_p (affected @ truncation level).
161    o pkg/shelfice:
162      - add parameterisation of advective-diffusive flux into the ice shelf
163        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
164      - simply eps3/3a computation
165    o eesupp:
166     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
167       between tiles, just fill-in edges assuming locally periodic subdomain) and
168       add corresponding exchange subroutines (EXCH0);
169     - new CG-solver version (_EX0) for disconnected-tiles special case.
170    o model/src (CG-solvers):
171     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
172       (similar final residual output and max-Iter number as with standard version);
173     - allows to store and use lowest-residual solution (standard & _SR versions);
174     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
175     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
176    o eesup/src:
177     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
178       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
179    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
180    
181    checkpoint63m (2012/04/27)
182    o pkg/shelfice:
183     - account for partical cells in surface level below ice-shelf for hydrostatic
184       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
185    o ad test experiments:
186     - update and rename to "ad_optfile.local" local AD-optfile specific to a
187       particular adjoint verification experiment (in verification/*/code_ad/)
188    o pkg/seaice & pkg/exf:
189     - Part two of ECCO-CLIVAR code merges.
190       Completes merge of seaice area relax. code.
191       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
192       to be set in EXF_OPTIONS.h since this pkg controls its I/O
193       (and avoids second CPP option in SEAICE_OPTIONS.h)
194     - change default value of costIceStart & costIceEnd to a valid date.
195     - add snowPrecip to HSNOW in seaice_growth
196    o pkg/ptracers:
197     - move ptracers summary and setup check into separated S/R ; add a check for
198       valid PTRACERS_Iter0 value (error+stop or just warning).
199    o pkg/cal (+ pkg/ecco):
200     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
201       as input; and for AD, unless both are not differentiable (e.g., k index)).
202    o model/src:
203     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
204       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
205       temporary set to usingZCoords value (to be changed to F when using shelfice).
206     - hydrostatic pressure: implement partial cell near the surface also for
207       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
208       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
209    o pkg/ctrl/ctrl_init.F:
210     - add a formal parameter to s/r ctrl_init_rec to print
211       xx_$(ctrl_valiable)_file for easier debugging
212     - move call of cal_* routines into the if-block where they are really
213       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
214       to specify a startdate
215    o pkg/seaice:
216     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
217       global_ocean.cs32x15/code versions).
218     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
219       verification experiment global_ocean.cs32x15.seaice and update results.
220    o pkg/exf:
221     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
222       (according to useExfYearlyFields).
223    o pkg/cal:
224     - move calendar setting & summary (previously in cal_readparams.F) into new
225       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
226       length of the simulation is set (after SET_PARMS call); This is an attempt
227       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
228     - For safety: keep a record of pkg/cal parameter settings status
229               to allow to STOP if one pkg/cal S/R is called too early.
230     - add a stop in all basic pkg/cal subroutines if called before setting is done.
231     - modify cal_getdate.F: stop when nothing was returned;
232       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
233       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
234    
235    checkpoint63l (2012/04/04)
236    o pkg/bbl:
237      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
238        update global_with_exf output.yearly.txt file.
239    o pkg/cal:
240      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
241      - remove 2 unsused and very short (1 line only) functions ;
242      - remove unsused subroutines from AD-Diff list.
243    o model/src:
244      - start to implement clean wait to stop in initialization S/R (config_check.F,
245         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
246    o folowing PRINT_MESSAGE changes:
247      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
248    o pkg/bbl:
249      - modification so it can work with z*
250      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
251      - global_with_exf/input.yearly verification; changes output.yearly.txt
252    o eesupp/src:
253      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
254        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
255      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
256        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
257      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
258      - when using MPI, always set usingMPI=T ; set default accordingly and stop
259        if not consistent.
260      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
261        argument is zero (in case called within single-thread section).
262    o pkg/fizhi:
263        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
264        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
265    o pkg/exch2:
266      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
267        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
268      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
269        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
270        with bad ones coming from a not-yet-updated halo.
271        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
272    o pkg/frazil:
273        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
274        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
275    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
276    o verification/lab_sea
277      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
278      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
279      * nTimeSteps 3 -> 4
280      * changed reference output accordingly
281    o pkg/ctrl:
282      * fix ctrl_get_gen for xx_sst, xx_sss
283    o pkg/fizhi:
284      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
285        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
286      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
287        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
288        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
289    o pkg/gmredi:
290      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
291    o pkg/fizhi:
292      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
293        (old)aces open64 tuv test.
294    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
295    o pkg/mom_vecinv:
296      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
297        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
298        with non-lin free-surf).
299    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
300      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
301      some compilers (gfortran 4.6.0 on MacOS)
302    o momentum:
303      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
304        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
305        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
306    
307    checkpoint63k (2012/03/17)
308    o model/src:
309       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
310         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
311       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
312         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
313    o model/src: solve_*diagonal.F
314       - replace division with multiplication by inverse (similar to original version)
315         update output of AD exp. global_ocean.90x40x15.
316       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
317         to enable the use of the vectorized & differentiable solve_tridiagonal.F
318       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
319         vertical advection (to get solve_tridiagonal tested in AD mode).
320    o pkg/seaice: ECCO-CLIVAR merge:
321      1. seaice AREA relaxation
322         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
323         * runtime flag: SEAICE_tauAreaObsRelax
324      2. modified global mean cost imbalance code: CPP option
325          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
326    o another iteration on solve_*diagonal.F
327       Make choices independent of AUTODIFF
328       Default will be the adjoinable vectorized version.
329       Alternative choices are:
330       * non-adjoinable original version with low memory footprint:
331         #define SOLVE_DIAGONAL_LOWMEMORY
332       * still adjoinable but does not vectorize (k as inner-most loop):
333         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
334    o testreport
335     - add option to use a home made wrapper around "make"
336     - remove MITGCM_IEEE env. variable (no longer active)
337    o pkg/shelfice
338     - improve computation of friction velocity for velocity dependent
339       exchange coefficients: include velocities into SHELFICEBoundaryLayer
340       block to average velocities vertically
341     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
342    o Modify diagonal solvers, now three versions (upon request):
343      #ifndef SOLVE_DIAGONAL_AUTODIFF
344        1. default version (dating back a while ago)
345      #else /* def SOLVE_DIAGONAL_AUTODIFF */
346      # ifdef SOLVE_DIAGONAL_KINNER
347        2. adjoinable version with k-innermost loop (G. Forget)
348      # else
349        3. adjoinable vectorized version of 2.
350      # endif
351      #endif /* SOLVE_DIAGONAL_AUTODIFF */
352      All flags are currently set within routines, but could/should be moved to CPP-options.
353      Array bounds for 1. are as before, for 2.,3. cover the entire domain
354      (could be changed for 1. too).
355    o verification/lab_sea (fwd):
356      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
357        use 7 categories (except hb87), new solve4temp params (except salt_plume),
358        constant salinity (=4) or variable salinity (salt_plume) done through
359        SItracer.
360    o pkg/seaice:
361      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
362      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
363         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
364        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
365        SEAICE_freeze got retired) but already better than previously with
366        SEAICE_freeze=123456.7 deg.C;
367      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
368        (safer multi-threaded setting); always set SEAICEuseEVP;
369      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
370        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
371        stop if multiple specifications for the same coeff; make sure default
372        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
373    o pkg/obcs:
374      - allow to switch to upwind 1rst order advection scheme for the advective
375        flux computation at the open-boundary; disabled for adjoint built.
376    o pkg/ptracers:
377      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
378      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
379      - add parameter to decide when to start a tracer; use internal flag to
380        know which tracer to step-forward; switch this internal flag at the top
381        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
382        for adjoint built.
383    o pkg/seaice:
384      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
385      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
386      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
387    o pkg/ecco:
388      - fix writing of output file DiagnosCost_ClimSalt/Theta
389        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
390    o pkg/seaice:
391      - add missing initialisation of COR_ICE array in dynsolver.F
392      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
393        compiled either way, and is tested in all exps (multidim was only tested
394        in lab_sea ad before).
395      - cosmetic change to prepare for future addition of ITD. no change to results.
396        no defaults change.
397      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
398      - by lack of adequate verification experiments, I further used custom versions
399        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
400        should be correct.
401      - avoid recomputations in ad.
402    o array initialisation in adjoint mode:
403      1) pkg/mom_common/mom_calc_ke.F:
404        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
405        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
406        part this initialisation is gone, resulting in Floating Point Exception
407        (caught by open64 compiler with debug option).
408      2) model/src/convective_weights.F
409        set output convectCount over the full array range (instead of doing
410        an update): this fix a similar issue when called within recomputation (adjoint)
411        which could by-pass the initialisation (normally done in the caller S/R).
412    o pkg/seaice:
413      - final version of turbulent flux params, as agreed at MIT ice meet:
414           SEAICE_mcPheePiston (default is ~ 0.000875)
415           SEAICE_mcPheeTaper (default is 0.)
416           SEAICE_frazilFrac (defualt is 1.)
417           SEAICE_mcPheeStepFunc (default is false)
418      - changes results at trunction error level
419      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
420    o added pkg/frazil:
421      - see frazil_description.tex for details
422      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
423    o pkg/shelfice/shelfice_thermodynamics.F
424      - fix exponents for velocity dependent exchange coefficients: change
425        from 2/3(=0) to 0.66666666666666667
426      - move computation of velocity dependent exchange coefficients into
427        separate loop, so that it applies to both thermodynamics
428      - move some divisions by constants out of loops
429    
430    checkpoint63j (2012/02/16)
431    o pkg/seaice:
432      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
433      - SItracer:  added run time params, and allow coupling to ocn salinity.
434    o pkg/seaice: remove (almost) all divisions by constants within loops
435      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
436      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
437      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
438      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
439    o pkg/seaice :
440      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
441        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
442      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
443      - add permanent SItflux diag that corresponds to TFLUX but includes
444        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
445      - allow activation/testing of a fix for suspected missing term in
446        ocn-ice heat budget (to be confirmed). To test this, you want to
447        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
448        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
449      - no change in results, fwd or ad.
450    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
451      - switch to variable freezing point.
452           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
453      - bug fix : the sublimation term that was missing is now activated.
454           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
455      - bug fix : flooding sign term for SIsal0.NE.0.
456           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
457    o pkg/seaice:
458      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
459        is now the default, and the old default constant freezing point is recovered
460        with SEAICE_tempFrz0    = -1.96,
461             SEAICE_dTempFrz_dS = 0.,
462      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
463      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
464      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
465        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
466      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
467        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
468      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
469        seaice_growth r149 for legacy branch (no results change).
470      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
471        from I. Fenty).
472      - results did not change except for global_ocean.cs32x15, mostly due to the
473        switch to variable freezing point (see above item for detail).
474    o pkg/thsice:
475      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
476        seawater freezing in thsice_calc_thickn (not used).
477    o pkg/seaice: turbulent flux term specification via run time params.
478      - replace CPP switches with run time switches to facilitate testing
479      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
480                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
481      - added runtime parameter : SEAICEturbFluxFormula
482      - move Mcphee constants to SEAICE_PARAMS.h
483      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
484                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
485                 remove seaice_summary call (moved to seaice_init_fixed)
486      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
487        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
488      - seaice_summary.F : add missing report of read turbulent flux term set up
489                           and SITRACER.
490      - seaice_check.F : check range; inform and stop if retired CPPs are used
491                         (incl. SEAICE_AGE).
492      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
493             CPP switch, same computation as before for the different options.
494      - change results at the truncation level.
495    o pkg/seaice:
496      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
497        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
498        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
499      - update verification/*/input*/data.seaice:
500        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
501        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
502        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
503        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
504    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
505      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
506        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
507        difference in results only due to machine truncation.
508      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
509        MaykutPolySatVap; keep MIN_LWDOWN.
510      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
511      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
512        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
513    o pkg/salt_plume:
514      - isolate saltPlumeFlux array exch into a specific S/R called from
515        do_oceanic_phys.F
516      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
517    o verification:
518      - move untested set-up to MITgcm_contrib/verification_other.
519    o pkg/seaice:
520      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
521    o pkg/seaice:
522      - seaice_solve4temp.F (keeping results unchanged):
523        * add 2 future run-time params to select which saturation vapor pressure
524          formula is used and how post-iteration fluxes are set.
525          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
526        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
527          the linearized expression to stay consistent with tsurf finding.
528      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
529        can be < 0.
530    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
531      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
532        conductive heat flux F_c , and add it explicitly when updating tsurf as
533        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
534        so that now F_ia has a consistent meaning through the entire routine.
535        This causes differences at truncation level: update output of fwd exp.
536        global_ocean.cs32x15.seaice.
537    o pkg/seaice:
538      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
539        of arrays, sign/direction of fluxes; no effect on results.
540      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
541        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
542        note: this should have been done before changing celsius2K default.
543      - to keep results unchanged, add back old value of celsius2K in verification
544        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
545      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
546        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
547        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
548        freezing temp is consistent with value in seaice_growth.F ; this causes
549        differences at machine truncation level: update lab_sea AD output (3/4).
550    o pkg/seaice:
551      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
552        and climsst/sss even when using seaice (to prevent calculation that might
553        use SST on land); does not affect any verification exp.
554      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
555        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
556    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
557      over land (non-legacy code)
558    o vectorize salt_plume package:
559      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
560      - this code computes plumebk everywhere (also over land), thus requires
561        code to avoid divisions by zero and catch the case of kLev=Nr.
562      - efficiency of salt_plume_frac is still sub-optimal
563    o tools (genmake2):
564      - fix makefile NAME specification (option: -makefile NAME) by adding
565        "-f $MAKEFILE" in few places where it was missing including makedepend
566        command (contribution from Paul).
567    
568    checkpoint63i (2012/01/24)
569    o model/src:
570      - add factorized versions of some EOS code to find_rho.F,
571        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
572    o model/src:
573      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
574      - change default celsius2K from 273.16 to 273.15
575      - to keep results unchanged, add back old value of celsius2K in verification
576        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
577         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
578    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
579      to make TAF generate vectorizable code
580    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
581       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
582       have flags that do this more efficiently.
583    o pkg/diagnostics/diagstats_calc.F
584      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
585    o pkg/obcs (with exch2):
586      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
587        and remove code (in obcs_readparms.F) which was based on EXCH of indices
588        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
589    o pkg/exf and seaice exp:
590      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
591        so that switching off area & heff advection flags does not affect results.
592      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
593      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
594        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
595        results of verification experiments: 1D_ocean_ice_column(fwd),
596        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
597        and offline_exf_seaice (all 4).
598    o pkg/seaice:
599      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
600        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
601      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
602        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
603        not multi-dim advection;
604      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
605        SHORTWAVE_HEATING #undef.
606  o optim: make Makefile more robust (?)  o optim: make Makefile more robust (?)
607  o pkg/shelfice: add missing initialisation of num_shifwflx  o pkg/obcs:
608      * fix treatment of obcs_read_pickup for TAF
609    o pkg/shelfice:
610      * add missing initialisation of num_shifwflx
611      * new adjoint verification exp. for isomip
612      * change Prandtl and Schmidt numbers from generic formulations
613        (in terms of model diffus. and visc.) to separate runtime
614        parameters, with Holland and Jenkins (1999) default values.
615  o pkg/exf (interpolation):  o pkg/exf (interpolation):
616    - extended input field (2 rows) near the N & S poles:    - extended input field (2 rows) near the N & S poles:
617      * fill in with the symetric value (when even Nb of data in longitude)      * fill in with the symetric value (when even Nb of data in longitude)

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