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revision 1.1469 by ifenty, Wed Jun 29 21:44:26 2011 UTC revision 1.1689 by jmc, Fri Jul 13 23:25:59 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 model/src:
8      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
9      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
10        Cubed-Sphere Exch with CS-corners inside the domain;
11        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
12        globalArea and to set hasWetCSCorners.
13      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
14        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
15      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
16        useCDscheme and useCubedSphereExchange).
17    o pkg/seaice/seaice_growth.F :
18      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
19        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
20        when the previous code was not correct.
21      - in all cases diagnoze the boundary condition mismatch to SIaaflux
22      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
23        that term to QNET (essentially to set the melt/freeze water to 0degC).
24        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
25    o verification/global_ocean.cs32x15/input.seaice :
26      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
27      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
28      - update results (output.seaice.txt) accordingly.
29    o verification/lab_sea/input/data.seaice :
30      - remove SEAICEheatConsFix, which is now be tested
31        in global_ocean.cs32x15. The presently coded fix
32        is only consistent with real fresh water + nlfs.
33      - update results (output.txt) accordingly.
34    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
35    o AD_CONFIG.h file:
36      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
37      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
38        add it explicitly in each fortran src file where it is needed.
39        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
40        thus introducing potentially wrong dependency; therefore, better to include
41        it only where it's really needed, and after any other included OPTIONS file
42        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
43        or ALLOW_TANGENTLINEAR_RUN).
44    
45    checkpoint63p (2012/07/06)
46    o pkg/autodiff:
47      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
48      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
49        which are now read from new parameter file "data.autodiff" (inAdExact
50        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
51      - add file "data.autodiff" in all verification/*/input_ad/ directories.
52      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
53        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
54    o verification/tutorial_tracer_adjsens/
55      - add extra sub-verification which uses "SOM" advection scheme
56        (2nd Order-Moment Advection Scheme, Prather Limiter) with
57          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
58        and in data:
59          multiDimAdvection=.TRUE.,
60          tempAdvScheme=81,
61          saltAdvScheme=81,
62    o model/src:
63      - introduce ALLOW_BALANCE_RELAX which allow the removal
64       of the global mean of relaxation terms by setting
65       balanceThetaClimRelax and balanceSaltClimRelax
66      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
67       This case is now treated appropriately in seaice_growth.F
68    o pkg/seaice:
69      - do balanceEmPmR and balanceQnet based on the net fluxes
70        (SItflux) that enter the ocean+ice system rather than QNET
71        and EMPMR. Works best in real fresh water.
72      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
73        out of the diagnotics bloc, and stored in global arrays.
74    
75    checkpoint63o (2012/06/29)
76    o vertical mixing schemes:
77      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
78      - replace computation of density (in Function STATE1, opps_calc.F) by a call
79        to S/R FIND_RHO_SCALAR
80      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
81        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
82        affects output (vermix.ggl90) at truncation level.
83    o testreport:
84      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
85        (nSx,nSy) for the number of threads (from eedata.mth)
86    o model/src:
87      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
88        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
89    o verification/tutorial_tracer_adjsens/
90      - compile with ALLOW_CG2D_NSA
91      - run with nonlinFreeSurf=3
92      - update reference output_adm.txt
93    o tools/genmake2:
94      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
95        refine usePROFILES switching off (only when NetCDF is not available).
96    o verification (atmospheric set-up):
97      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
98    o pkg/profiles : refine profiles and files handling.
99    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
100    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
101      - changes to use model/src/the_main_loop.F rather than the ecco version
102        in ecco type adjoint runs.
103    o model/src:
104      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
105      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
106      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
107    o model/src:
108      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
109        update output of test experiment bottom_ctrl_5x5.
110    o pkg/generic_advdiff:
111      - implement vertical bi-harmonic diffusion (for now, only for T & S and
112        only explicitly).
113    o verification/bottom_ctrl_5x5/
114      update reference output (results changed quite some time ago,
115      not sure when; but new reference results look ok in terms of grdchk)
116    o verification/1D_ocean_ice_column/
117      For verification purposes, the exact adjoint rather than an approx.
118      should be used (e.g., to comare against F.D. or TLM).
119      removed autodiff_inadmode*_ad.F routines in code_ad/
120      Update results/ accordingly.
121    o pkg/cal:
122      - change cal_getdate.F so that output date is function of input time only
123        (less ambiguous, not mixed up with input iteration number).
124      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
125    o pkg/diagnostics:
126      - implement calendarDumps also for stats-diags
127      - implement calendarDumps also for snap-shot output (negative freq)
128      - for now, ignores calendarDumps if non-zero phase-lag.
129    
130    checkpoint63n (2012/06/04)
131    o model/src:
132      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
133        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
134      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
135        similar to calc_r_star.F); update results of experiment internal_wave and
136        tutorial_global_oce_in_p (affected @ truncation level).
137    o pkg/shelfice:
138      - add parameterisation of advective-diffusive flux into the ice shelf
139        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
140      - simply eps3/3a computation
141    o eesupp:
142     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
143       between tiles, just fill-in edges assuming locally periodic subdomain) and
144       add corresponding exchange subroutines (EXCH0);
145     - new CG-solver version (_EX0) for disconnected-tiles special case.
146    o model/src (CG-solvers):
147     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
148       (similar final residual output and max-Iter number as with standard version);
149     - allows to store and use lowest-residual solution (standard & _SR versions);
150     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
151     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
152    o eesup/src:
153     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
154       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
155    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
156    
157    checkpoint63m (2012/04/27)
158    o pkg/shelfice:
159     - account for partical cells in surface level below ice-shelf for hydrostatic
160       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
161    o ad test experiments:
162     - update and rename to "ad_optfile.local" local AD-optfile specific to a
163       particular adjoint verification experiment (in verification/*/code_ad/)
164    o pkg/seaice & pkg/exf:
165     - Part two of ECCO-CLIVAR code merges.
166       Completes merge of seaice area relax. code.
167       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
168       to be set in EXF_OPTIONS.h since this pkg controls its I/O
169       (and avoids second CPP option in SEAICE_OPTIONS.h)
170     - change default value of costIceStart & costIceEnd to a valid date.
171     - add snowPrecip to HSNOW in seaice_growth
172    o pkg/ptracers:
173     - move ptracers summary and setup check into separated S/R ; add a check for
174       valid PTRACERS_Iter0 value (error+stop or just warning).
175    o pkg/cal (+ pkg/ecco):
176     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
177       as input; and for AD, unless both are not differentiable (e.g., k index)).
178    o model/src:
179     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
180       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
181       temporary set to usingZCoords value (to be changed to F when using shelfice).
182     - hydrostatic pressure: implement partial cell near the surface also for
183       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
184       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
185    o pkg/ctrl/ctrl_init.F:
186     - add a formal parameter to s/r ctrl_init_rec to print
187       xx_$(ctrl_valiable)_file for easier debugging
188     - move call of cal_* routines into the if-block where they are really
189       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
190       to specify a startdate
191    o pkg/seaice:
192     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
193       global_ocean.cs32x15/code versions).
194     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
195       verification experiment global_ocean.cs32x15.seaice and update results.
196    o pkg/exf:
197     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
198       (according to useExfYearlyFields).
199    o pkg/cal:
200     - move calendar setting & summary (previously in cal_readparams.F) into new
201       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
202       length of the simulation is set (after SET_PARMS call); This is an attempt
203       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
204     - For safety: keep a record of pkg/cal parameter settings status
205               to allow to STOP if one pkg/cal S/R is called too early.
206     - add a stop in all basic pkg/cal subroutines if called before setting is done.
207     - modify cal_getdate.F: stop when nothing was returned;
208       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
209       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
210    
211    checkpoint63l (2012/04/04)
212    o pkg/bbl:
213      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
214        update global_with_exf output.yearly.txt file.
215    o pkg/cal:
216      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
217      - remove 2 unsused and very short (1 line only) functions ;
218      - remove unsused subroutines from AD-Diff list.
219    o model/src:
220      - start to implement clean wait to stop in initialization S/R (config_check.F,
221         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
222    o folowing PRINT_MESSAGE changes:
223      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
224    o pkg/bbl:
225      - modification so it can work with z*
226      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
227      - global_with_exf/input.yearly verification; changes output.yearly.txt
228    o eesupp/src:
229      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
230        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
231      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
232        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
233      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
234      - when using MPI, always set usingMPI=T ; set default accordingly and stop
235        if not consistent.
236      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
237        argument is zero (in case called within single-thread section).
238    o pkg/fizhi:
239        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
240        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
241    o pkg/exch2:
242      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
243        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
244      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
245        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
246        with bad ones coming from a not-yet-updated halo.
247        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
248    o pkg/frazil:
249        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
250        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
251    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
252    o verification/lab_sea
253      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
254      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
255      * nTimeSteps 3 -> 4
256      * changed reference output accordingly
257    o pkg/ctrl:
258      * fix ctrl_get_gen for xx_sst, xx_sss
259    o pkg/fizhi:
260      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
261        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
262      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
263        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
264        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
265    o pkg/gmredi:
266      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
267    o pkg/fizhi:
268      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
269        (old)aces open64 tuv test.
270    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
271    o pkg/mom_vecinv:
272      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
273        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
274        with non-lin free-surf).
275    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
276      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
277      some compilers (gfortran 4.6.0 on MacOS)
278    o momentum:
279      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
280        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
281        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
282    
283    checkpoint63k (2012/03/17)
284    o model/src:
285       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
286         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
287       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
288         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
289    o model/src: solve_*diagonal.F
290       - replace division with multiplication by inverse (similar to original version)
291         update output of AD exp. global_ocean.90x40x15.
292       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
293         to enable the use of the vectorized & differentiable solve_tridiagonal.F
294       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
295         vertical advection (to get solve_tridiagonal tested in AD mode).
296    o pkg/seaice: ECCO-CLIVAR merge:
297      1. seaice AREA relaxation
298         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
299         * runtime flag: SEAICE_tauAreaObsRelax
300      2. modified global mean cost imbalance code: CPP option
301          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
302    o another iteration on solve_*diagonal.F
303       Make choices independent of AUTODIFF
304       Default will be the adjoinable vectorized version.
305       Alternative choices are:
306       * non-adjoinable original version with low memory footprint:
307         #define SOLVE_DIAGONAL_LOWMEMORY
308       * still adjoinable but does not vectorize (k as inner-most loop):
309         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
310    o testreport
311     - add option to use a home made wrapper around "make"
312     - remove MITGCM_IEEE env. variable (no longer active)
313    o pkg/shelfice
314     - improve computation of friction velocity for velocity dependent
315       exchange coefficients: include velocities into SHELFICEBoundaryLayer
316       block to average velocities vertically
317     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
318    o Modify diagonal solvers, now three versions (upon request):
319      #ifndef SOLVE_DIAGONAL_AUTODIFF
320        1. default version (dating back a while ago)
321      #else /* def SOLVE_DIAGONAL_AUTODIFF */
322      # ifdef SOLVE_DIAGONAL_KINNER
323        2. adjoinable version with k-innermost loop (G. Forget)
324      # else
325        3. adjoinable vectorized version of 2.
326      # endif
327      #endif /* SOLVE_DIAGONAL_AUTODIFF */
328      All flags are currently set within routines, but could/should be moved to CPP-options.
329      Array bounds for 1. are as before, for 2.,3. cover the entire domain
330      (could be changed for 1. too).
331    o verification/lab_sea (fwd):
332      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
333        use 7 categories (except hb87), new solve4temp params (except salt_plume),
334        constant salinity (=4) or variable salinity (salt_plume) done through
335        SItracer.
336    o pkg/seaice:
337      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
338      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
339         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
340        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
341        SEAICE_freeze got retired) but already better than previously with
342        SEAICE_freeze=123456.7 deg.C;
343      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
344        (safer multi-threaded setting); always set SEAICEuseEVP;
345      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
346        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
347        stop if multiple specifications for the same coeff; make sure default
348        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
349    o pkg/obcs:
350      - allow to switch to upwind 1rst order advection scheme for the advective
351        flux computation at the open-boundary; disabled for adjoint built.
352    o pkg/ptracers:
353      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
354      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
355      - add parameter to decide when to start a tracer; use internal flag to
356        know which tracer to step-forward; switch this internal flag at the top
357        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
358        for adjoint built.
359    o pkg/seaice:
360      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
361      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
362      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
363    o pkg/ecco:
364      - fix writing of output file DiagnosCost_ClimSalt/Theta
365        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
366    o pkg/seaice:
367      - add missing initialisation of COR_ICE array in dynsolver.F
368      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
369        compiled either way, and is tested in all exps (multidim was only tested
370        in lab_sea ad before).
371      - cosmetic change to prepare for future addition of ITD. no change to results.
372        no defaults change.
373      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
374      - by lack of adequate verification experiments, I further used custom versions
375        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
376        should be correct.
377      - avoid recomputations in ad.
378    o array initialisation in adjoint mode:
379      1) pkg/mom_common/mom_calc_ke.F:
380        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
381        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
382        part this initialisation is gone, resulting in Floating Point Exception
383        (caught by open64 compiler with debug option).
384      2) model/src/convective_weights.F
385        set output convectCount over the full array range (instead of doing
386        an update): this fix a similar issue when called within recomputation (adjoint)
387        which could by-pass the initialisation (normally done in the caller S/R).
388    o pkg/seaice:
389      - final version of turbulent flux params, as agreed at MIT ice meet:
390           SEAICE_mcPheePiston (default is ~ 0.000875)
391           SEAICE_mcPheeTaper (default is 0.)
392           SEAICE_frazilFrac (defualt is 1.)
393           SEAICE_mcPheeStepFunc (default is false)
394      - changes results at trunction error level
395      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
396    o added pkg/frazil:
397      - see frazil_description.tex for details
398      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
399    o pkg/shelfice/shelfice_thermodynamics.F
400      - fix exponents for velocity dependent exchange coefficients: change
401        from 2/3(=0) to 0.66666666666666667
402      - move computation of velocity dependent exchange coefficients into
403        separate loop, so that it applies to both thermodynamics
404      - move some divisions by constants out of loops
405    
406    checkpoint63j (2012/02/16)
407    o pkg/seaice:
408      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
409      - SItracer:  added run time params, and allow coupling to ocn salinity.
410    o pkg/seaice: remove (almost) all divisions by constants within loops
411      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
412      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
413      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
414      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
415    o pkg/seaice :
416      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
417        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
418      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
419      - add permanent SItflux diag that corresponds to TFLUX but includes
420        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
421      - allow activation/testing of a fix for suspected missing term in
422        ocn-ice heat budget (to be confirmed). To test this, you want to
423        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
424        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
425      - no change in results, fwd or ad.
426    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
427      - switch to variable freezing point.
428           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
429      - bug fix : the sublimation term that was missing is now activated.
430           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
431      - bug fix : flooding sign term for SIsal0.NE.0.
432           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
433    o pkg/seaice:
434      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
435        is now the default, and the old default constant freezing point is recovered
436        with SEAICE_tempFrz0    = -1.96,
437             SEAICE_dTempFrz_dS = 0.,
438      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
439      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
440      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
441        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
442      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
443        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
444      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
445        seaice_growth r149 for legacy branch (no results change).
446      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
447        from I. Fenty).
448      - results did not change except for global_ocean.cs32x15, mostly due to the
449        switch to variable freezing point (see above item for detail).
450    o pkg/thsice:
451      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
452        seawater freezing in thsice_calc_thickn (not used).
453    o pkg/seaice: turbulent flux term specification via run time params.
454      - replace CPP switches with run time switches to facilitate testing
455      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
456                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
457      - added runtime parameter : SEAICEturbFluxFormula
458      - move Mcphee constants to SEAICE_PARAMS.h
459      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
460                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
461                 remove seaice_summary call (moved to seaice_init_fixed)
462      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
463        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
464      - seaice_summary.F : add missing report of read turbulent flux term set up
465                           and SITRACER.
466      - seaice_check.F : check range; inform and stop if retired CPPs are used
467                         (incl. SEAICE_AGE).
468      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
469             CPP switch, same computation as before for the different options.
470      - change results at the truncation level.
471    o pkg/seaice:
472      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
473        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
474        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
475      - update verification/*/input*/data.seaice:
476        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
477        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
478        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
479        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
480    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
481      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
482        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
483        difference in results only due to machine truncation.
484      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
485        MaykutPolySatVap; keep MIN_LWDOWN.
486      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
487      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
488        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
489    o pkg/salt_plume:
490      - isolate saltPlumeFlux array exch into a specific S/R called from
491        do_oceanic_phys.F
492      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
493    o verification:
494      - move untested set-up to MITgcm_contrib/verification_other.
495    o pkg/seaice:
496      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
497    o pkg/seaice:
498      - seaice_solve4temp.F (keeping results unchanged):
499        * add 2 future run-time params to select which saturation vapor pressure
500          formula is used and how post-iteration fluxes are set.
501          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
502        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
503          the linearized expression to stay consistent with tsurf finding.
504      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
505        can be < 0.
506    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
507      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
508        conductive heat flux F_c , and add it explicitly when updating tsurf as
509        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
510        so that now F_ia has a consistent meaning through the entire routine.
511        This causes differences at truncation level: update output of fwd exp.
512        global_ocean.cs32x15.seaice.
513    o pkg/seaice:
514      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
515        of arrays, sign/direction of fluxes; no effect on results.
516      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
517        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
518        note: this should have been done before changing celsius2K default.
519      - to keep results unchanged, add back old value of celsius2K in verification
520        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
521      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
522        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
523        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
524        freezing temp is consistent with value in seaice_growth.F ; this causes
525        differences at machine truncation level: update lab_sea AD output (3/4).
526    o pkg/seaice:
527      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
528        and climsst/sss even when using seaice (to prevent calculation that might
529        use SST on land); does not affect any verification exp.
530      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
531        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
532    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
533      over land (non-legacy code)
534    o vectorize salt_plume package:
535      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
536      - this code computes plumebk everywhere (also over land), thus requires
537        code to avoid divisions by zero and catch the case of kLev=Nr.
538      - efficiency of salt_plume_frac is still sub-optimal
539    o tools (genmake2):
540      - fix makefile NAME specification (option: -makefile NAME) by adding
541        "-f $MAKEFILE" in few places where it was missing including makedepend
542        command (contribution from Paul).
543    
544    checkpoint63i (2012/01/24)
545    o model/src:
546      - add factorized versions of some EOS code to find_rho.F,
547        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
548    o model/src:
549      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
550      - change default celsius2K from 273.16 to 273.15
551      - to keep results unchanged, add back old value of celsius2K in verification
552        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
553         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
554    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
555      to make TAF generate vectorizable code
556    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
557       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
558       have flags that do this more efficiently.
559    o pkg/diagnostics/diagstats_calc.F
560      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
561    o pkg/obcs (with exch2):
562      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
563        and remove code (in obcs_readparms.F) which was based on EXCH of indices
564        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
565    o pkg/exf and seaice exp:
566      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
567        so that switching off area & heff advection flags does not affect results.
568      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
569      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
570        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
571        results of verification experiments: 1D_ocean_ice_column(fwd),
572        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
573        and offline_exf_seaice (all 4).
574    o pkg/seaice:
575      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
576        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
577      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
578        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
579        not multi-dim advection;
580      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
581        SHORTWAVE_HEATING #undef.
582    o optim: make Makefile more robust (?)
583    o pkg/obcs:
584      * fix treatment of obcs_read_pickup for TAF
585    o pkg/shelfice:
586      * add missing initialisation of num_shifwflx
587      * new adjoint verification exp. for isomip
588      * change Prandtl and Schmidt numbers from generic formulations
589        (in terms of model diffus. and visc.) to separate runtime
590        parameters, with Holland and Jenkins (1999) default values.
591    o pkg/exf (interpolation):
592      - extended input field (2 rows) near the N & S poles:
593        * fill in with the symetric value (when even Nb of data in longitude)
594        * add average value at the poles only for scalar quantities ; for vector
595          component interpolation, skip the averaging and keep duplicated values,
596          unless the 2 components have same location (uvInterp=T) in which case
597          interpolate the 2 components together using S/R EXF_INTERP_UV.
598      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
599        together: this allows to account properly for local orientation when
600        averaging at N & S pole.
601      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
602        exf-interpolation near N & S poles. Undef by default.
603      - add debug check/print on 1rst iter if debugLevel >=2.
604    o pkg/exf:
605      - change masking flags definition (no longer "parameter"), put them in
606        common block and set them in S/R EXF_INIT_FIXED.
607      - change recognized masking flag from s,u,v to c,w,s since the mask
608        to use (maskC,W,S) depends on position on model grid and has little to
609        do with scalar/vector difference; fix masking if using P-coordinates.
610      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
611        and update results of exp. global_with_exf (x2).
612      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
613    o pkg/obcs
614      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
615    o pkg/exf (interpolation):
616      - assume periodicity in X only if input field cover full longitude range.
617      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
618        and should vectorise).
619      - fix input lat of the 2 added row (in case we provide N.pole data).
620    
621    checkpoint63h (2011/12/30)
622    o pkg/seaice:
623      - change declaration of UVM from _RL to _RS in order to get B-grid
624        uIce,vIce monitor when _RS = real*4
625    o pkg/offline:
626      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
627      - compute vertical velocity if not read from file (switch on exactConserv
628        & staggerTimeStep);
629      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
630    o verification:
631      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
632        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
633        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
634      - update output of exp. global_ocean.cs32x15.viscA4 after changing
635        grid-file angles (used here for coriolis-3d);
636      - remove (or gzip) few files not needed to run fizhi-cs experiments.
637    o pkg/exf (vector interpolation):
638      - rotate vector component toward local grid-axis orientation using grid-angles
639        (stored in GRID.h) instead of locally computed rotation angle; keep old code
640        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
641    o pkg/seaice:
642      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
643        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
644    o pkg/PKG_OPTIONS.h files:
645      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
646        outside of the #ifdef ALLOW_THISPKG / #endif block.
647      - update verification/*/code/PKG_OPTIONS.h files.
648    o add a verification experiment (offline_exf_seaice/input.seaice) that test
649      the B-grid LSOR solver
650    o pkg/seaice: sort out emissivity and long wave radiation step 2:
651      - add emissivity for snow and ice as new run-time parameters
652        (unfortunately) that default to the corresponding exf values; this
653        changes results in most verification experiments so that for backward
654        compatibility these parameter have to be set explicitly to inconsistent
655        values (ugly);
656      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
657        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
658        until we agree how to handle this bug properly
659    o pkg/exf (interpolation):
660      - add a set of run-time param ({inputfield}_interpMethod), one for
661        each interpolated input field, to select the interpolation method
662        with a value of zero switching off the interpolation;
663      - print interpolation parameters to standard output;
664      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
665        (to use instead runoff_interpMethod=0 in data.exf).
666      - simplify default setting of interpolation parameters (for all fields,
667        set position to match model grid cell-center position, leading to trivial
668        interpolation in case of regular Lat-Lon grid) and fix for the case of
669        non-uniform delY.
670    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
671       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
672       this factor is absolutely required, because the lw exitance (= out-going
673       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
674       where the reflectivity rho = 1-emissivity for conservation reasons. Once
675       this is established, we can remove the CPP-Flag (if we want to).
676    o pkg/seaice:
677      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
678        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
679      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
680        what the name implies (and not emissivity*BoltzmannConstant), this means
681        the old default value of 5.5e-8 now means
682        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
683        S/R exf_readparms
684      - FV-discretization of the B-grid LSOR solver, turn on with
685        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
686        of the calling routine dynsolver, so that B and C-grid code look a
687        little more alike.
688      - fix index bugs in ostres.F (B-grid code)
689    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
690    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
691      default for SEAICE_emissivity, if useEXF; requires setting a wrong
692      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
693      backward compatiblity
694    o model/src: use sigmaR in calc_ivdc
695    
696    checkpoint63g (2011/12/16)
697    o pkg/seaice/seaice_growth.F:
698      fix heat conservation of the coupled ocean-seaice system.
699      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
700      solid vs liquid water treatment is resolved via QNET.
701    o pkg/seaice/seaice_growth.F:
702      add missing term for sublimation in saltFlux, which was breaking conservation.
703    o pkg/seaice/seaice_model.F:
704      Remove this patholigical case treatment in evolution branch,
705      where it is un-necessary and breaks conservation.
706      Update global_ocean.cs32x15/results accordingly for
707      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
708    o model/src:
709      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
710      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
711    o pkg/obcs:
712      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
713      tendency for temperature and salinity that is then applied to update
714      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
715      horizontal advection and diffusion contributions on the boundary (in
716      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
717      removing the mask in S/R timestep_tracer. The advantage of this approach is
718      that the updated tracer values include contributions from the surface
719      forcing and vertical diffusion.
720      This modification changes exp4.stevens because of vertical diffusion.
721    o model/src:
722      change non-curvilinear grid setting to also work with exch2 + blank tiles:
723      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
724        face dimensions.
725      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
726        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
727        and INI_SPHERICAL_POLAR_GRID.
728      change test-experiment global_ocean.90x40x15:
729      - split the domain in many more tiles (9x4 tiles of 10x10 each);
730      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
731      - update results of both test (std & dwnslp).
732    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
733       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
734    o model/src:
735      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
736        and fix initialisation when using sigma-coords.
737    o model/src:
738     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
739       to their current value at the beginning of forward_step.F": add a new run-time
740       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
741     - set doResetHFactors=T in the following test exp:
742        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
743        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
744        and tutorial_global_oce_in_p (nonLinFS in p)
745    o pkg/ecco
746      - added IES cost term
747    o verification/advect_xz
748      - scale down the depth by 1/100 (from 200 km to just 2.km)
749      - add secondary test using divergent flow, r-star and implicit vertical advection.
750      - add note (check_conserve_TS.txt) and matlab script to check global
751        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
752    o pkg/rbcs:
753      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
754    o pkg/obcs (Stevens BCs):
755      - fix various problems in the phase speed computations of the Stevens
756        boundary conditions:
757        - sign error for western and southern boundaries,
758        - time tendencies were underestimated by factor of dTracerLev and some just
759          zero (for multidim advection schemes) -> now estimate time tendencies
760          from difference between previous (n) time level and the one before (n-1);
761          this requires storing a field per tracer per boundary, also in the pickup
762          files.
763        - replace deltaTmom in cflMer/Zon computation with dTracerLev
764        - set default phase velocity to cflMer/Zon
765      - update verification experiment exp4.stevens
766    o pkg/generic_advdiff (implicit_r):
767      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
768        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
769      - fix implicit vertical diffusion or advection with NonLin FreeSurf
770        (was using current recip_hFacC instead of future recip_hFacC): set future
771        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
772        solver S/R ;
773      - fill diagnostics of vertical advective fluxes (computed from tendency)
774        when using implicit vert. advection;
775      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
776         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
777         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
778         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
779    o pkg/diagnostics:
780      - add diags for T & S tendency which goes through Adams-Bashforth.
781    
782    checkpoint63f (2011/11/30)
783    o pkg/obcs/obcs_calc_stevens.F:
784      - join some loops to reduce number of if-statements
785      - fix a bug in code for northern and southern boundaries.
786    o pkg/seaice/seaice_init_varia.F
787      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
788        caused zero ice-velocities for the B-grid code
789    o pkg/seaice/seaice_init_fixed.F
790      - fix a bug in the initialisation of the second metric terms
791        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
792      - this affects all seaice configurations with useCurviLinearGrid = .true.
793        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
794        = .true. (default)
795      - the only verification experiment affected is global_ocean.cs32x15:
796        icedyn, seaice, and seaice_dynmix (AD)
797    o pkg/thsice/thsice_diagnostics_state.F
798      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
799        not contain garbage that can lead to surprises in diagstats_calc.F
800    o model/src:
801      - move bi,bj loops inside INTEGR_CONTINUITY ;
802      - call INTEGR_CONTINUITY directly from forward_step.F
803        (previously called from momentum_correction_step.F)
804      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
805        forward_step.F and pkg/ecco/the_main_loop.F
806    o model/src/do_oceanic_phys.F:
807      - reset addMass to zero only if useICEFRONT ;
808      - separated k-loop for rhoInSitu calculation ;
809      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
810        and at constant T,S (= WdRHOdP);
811      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
812        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
813        transport of locally-referenced potential density);
814        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
815    o gluemnc:
816      - replace ncrcat with ncks when adding variables to *.glob.nc
817      - change the way variables without record dimensions are handled so that
818        files that have variables with and without record variables can be glued:
819        add a record dimension with a new unique name to be able to differentiate
820        between variable with and without a-prior record dimensions. Remove
821        this record dimension before adding the variable to the *.glob.nc file.
822        This procedure automatically works also for grid.*.nc files that do not
823        have any record dimension.
824    o verification/cpl_aim+ocn:
825      - generate new reference output on baudelaire (gfortran, mpich2) (previously
826        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
827    o pkg/obcs/obcs_calc_stevens.F:
828      - add code for northern and southern boundaries.
829      - reorder some loops to save some operations and so that drFBar can be scalar
830    o model/src:
831      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
832        truncation) and add diagnostics for Adams-Bashforth tendency increment.
833      - update test-exp. AD output:
834        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
835      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
836        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
837        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
838        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
839        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
840        tutorial_plume_on_slope.
841    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
842      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
843      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
844      does not even come with an F77 compiler anymore, this should not be
845      a limitation
846    
847    checkpoint63e (2011/11/06)
848    o pkg/seaice adjoint of LSR:
849      - substantially rework STORE dirs.
850      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
851        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
852        and only perform SOLV_MAX_FIXED adjoint iters.
853        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
854        always goes to same record, meaning that the last forward field will be
855        the one used in the adjoint - an approximation.
856      - now produces non-zero LSR-related gradients, and acceptable gradients for
857        An's zonal (x-z) test case (to be checked in)
858      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
859        (but these are screwed up by the thermodynamics in the first place);
860        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
861        output_adm.txt also reflects changes to seaice_lsr
862      - global_ocean.cs32x15:
863        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
864          (output_adm.seaice.txt was updated)
865        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
866          (output_adm.seaice_dynmix.txt)
867    o test-exp. exp4+stevens:
868      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
869    o pkg/seaice (lsr solver):
870      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
871        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
872      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
873      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
874        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
875      - compute (with new S/R) and print initial (+ free-driff sol. if available)
876        and final residual of linearised system.
877    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
878      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
879    o pkg/obcs: Stevens BCs (still only for east and west)
880      - fix Stevens BCs by using intermediate velocities of previous
881        time step as "baroclinic" contribution rather velocity of one grid cell
882        inside the boundaries; more consistent but makes the entire treatment
883        more complicated, requires new pickup files and two new S/Rs:
884        obcs_copy_uv_n and obcs_save_uv_n
885        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
886        (undefined by default)
887      - silently move computation of some grid factors into separate loops to
888        save some recomputations
889      - add a hack for non-linear free surface
890      - add a verification experiment to exp4 that tests this code
891    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
892    
893    checkpoint63d (2011/10/25)
894    o pkg/obcs + seaice-dynamics:
895      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
896        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
897        values (consistent with an implicit method).
898      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
899        return to older implementation (same results as before); note that none of
900        the "experimental" OBCS_SEAICE options are implemented in the new version.
901      - switch test exp. seaice_obcs to use new version (update output).
902    o pkg/seaice:
903      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
904      - add parenthesis in Water-Ice drag calculations (evp & lsr);
905      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
906        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
907      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
908        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
909    o pkg/layers:
910      - Include potential density as new coordinate (Thanks to David Munday)
911    o pkg/dic:
912      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
913        carbonate computation/output to CALC_PCO2_APPROX
914    o pkg/generic_advdiff
915      - make TAF generate code that vectorizes:
916        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
917    o model/src:
918      - improve vectorization also for adjoint code of
919        solve_tridiagonal and solve_pentadiagonal. As this requires up to
920        5 new 3D-fields, this code is only turned on for the combination of
921        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
922        for singular matrix check (only for TARGET_NEC_SX).
923      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
924        ALLOW_AUTODIFF. This flag now needs to be set outside of
925        solve_tri/pentadiagonal.F
926    o pkg/exf:
927      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
928        optional namelist EXF_NML_OBCS).
929      - add many debug-print (to trace down where pkg/cal error msg comes from)
930    o pkg/mom_vecinv/mom_vi_hdissip.F
931      - rearrange loops so that vectorization is improved and in particular
932        the adjoint routine vectorizes. The code is a little longer now, but I
933        think easier to read.
934        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
935    o pkg/seaice:
936      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
937    o pkg/exch2:
938      - alternative code (without tile x tile matrix) for cumulated (global) sum;
939        used as default; keep using matrix version in adjustment.cs-32x32x1.
940    o tools/build_options:
941      - after merging some MPI and/or multi-threads specific optfiles so that
942        the modified default optfile support both built (using genmake2 -mpi
943        for the MPI built, using genmake2 -omp for OpenMP built),
944        move now obsolete optfiles to tools/build_options/unsupported/
945       (add copy of email sent to support list in doc/optfiles_changes.txt)
946    
947    checkpoint63c (2011/09/28)
948    o pkg/ebm:
949      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
950        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
951    o pkg/seaice (SItracer pickup)
952    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
953      To be done:
954      - thorough testing of missing fields in S/R seaice_read_pickup
955      - thorough matching between generic tracers and specific fields used
956        (e.g. volume-weighted age, area-weighted age, salinity, ...)
957    o pkg/grdchk:
958      - all procs calculate and print finite-difference gradient (for testreport)
959      - change description output used by testreport;
960      - AD testing: also compare and report Finite-difference gradient;
961        => update all output_adm*.txt
962    o test exp. global_ocean_ebm:
963      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
964        and turn on exactConserve; update (fwd) output.
965    o pkg/seaice (LSR):
966      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
967      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
968        * identical results with non-CS topology (but save up to half of EXCH calls)
969        * no much changes in cs-32 verification tests since no ice at face edges
970         (differences due to convergence criteria, since nb of iterations changed)
971        * expect some differences on lat-lon-cap grid.
972        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
973    o pkg/exch2:
974      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
975        many tiles); until alternative coding is added, just add a stop.
976    o pkg/kpp:
977      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
978        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
979    o optfiles:
980      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
981        into corresponding standard one, which now support different build:
982        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
983      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
984    o pkg/obcs (seaice):
985      - add missing EXCH for uIce,vIce after applying OBCS;
986      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
987        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
988        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
989      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
990      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
991        and eedata.mth for MPI and mutlti-threaded testing.
992    o pkg/flt:
993      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
994      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
995      - fix pickup and trajectories + profiles output with multi-threads;
996      - add parameter to select group of fields to write along trajectory and
997        profile (default unchanged);
998      - only call PORT_RAND* function when flt_noise <> 0;
999      - add multi-threaded test for verification exp. flt_example.
1000    o eesupp/src:
1001      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1002      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1003        actual number (from env.var. setting).
1004    o pkg/ebm:
1005      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1006      - add multi-threaded test for verification exp. global_ocean_ebm
1007    
1008    checkpoint63b (2011/08/29)
1009    o pkg/ebm:
1010      - fix sign of runoff;
1011      - update directly forcing fields (Qnet,EmPmR) to use standard
1012        external_forcing_surf.F (remove ebm_forcing_surf.F);
1013      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1014      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1015        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1016      - update global_ocean_ebm parameters file data and update output (fwd+ad).
1017    o verification/matrix_example:
1018      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1019        MPI and mutlti-threaded testing.
1020    o pkg/matrix:
1021      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1022      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1023      - fix for multi-threaded (remove DATA statement);
1024      - use standard DIFFERENT_MULTIPLE function;
1025      - add MATRIX_OPTIONS.h
1026    o verification/matrix_example:
1027       To allow to split the domain in several tiles, change the domain size
1028        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1029        Western side) of land points.
1030    o (*_)write_pickup:
1031      - fix few bugs in mypackage_read/write_pickup.F
1032      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1033        array of length 1 (was caught by compiler syntax-check).
1034    o pkg/diagnostics (velocity potential solver):
1035      - fix initialisation of main diagonal matrix (for overlap values)
1036    o tools/build_options:
1037      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1038        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1039      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1040        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1041        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1042        and use "-devel" testreport option for standard testing on baudelaire.
1043    o pkg/grdchk:
1044      - Assume that all gradient-check position are within the same tile
1045        corresponding to global indices (iGloTile,jGloTile) and that
1046        positions (i,j indices or nbeg) are local to this tile;
1047      - set tile local-indices and proc. number according to tile global-indices;
1048      - remove grdchkwhichproc from namelist (retired param);
1049      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1050      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1051    o adding package bbl (Bottom Boundary Layer)
1052      description in MITgcm/pkg/bbl/bbl_description.tex
1053      example/test experiment in MITgcm_contrib/bbl
1054    o adjoint verifications
1055      - changed 5 experiments to multi-tiles
1056        * global_ocean.90x40x15
1057        * obcs_ctrl
1058        * offline_exf_seaice
1059        * tutorial_dic_adjoffline
1060        * tutorial_tracer_adjsens
1061        changed reference output for those that crossed tile boundaries
1062        (changed choices of gradient check positions)
1063      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1064      - temporary bug fix in grdchk_loc.F for obcs
1065    o genmake2 & testreport
1066      - add target "obj" (just for OBJFILES files) to Makefile;
1067      - add option to specify FEXTRAFLAGS on command line.
1068    o pkg/mypackage:
1069      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1070    
1071    checkpoint63a (2011/08/02)
1072    o pkg/diagnostics (velocity potential):
1073      - fix velocity-potential calculation when using OBCS: balance net inflow
1074        at each level (new S/R OBCS_DIAG_BALANCE).
1075      - fix some of the problems with OBCS in stream-function calculation.
1076    o pkg/exf/exf_readparms.F
1077      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1078        EXF_NML_OBCS) more consistent, so that you need not have these lists
1079        in data.exf when they are not used.
1080    o optim/optim_readdata.F:
1081      - add some output about obcs variables that might help debugging
1082      - add a check about nvarlength
1083    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1084    o pkg/diagnostics (velocity potential):
1085      - fix mask for OBCS (still problems in stream-function with OBCS);
1086      - add specific parameter (default = main code CG2D params) for solver;
1087      - in case of poor convergence, use solution corresponding to lowest residual.
1088    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1089      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1090      and should be avoided where possible.
1091    o model/src (rStar):
1092      - include r* effect on reference-state (PhiRef) in totPhiHyd
1093        (so that it's really the potential anomaly at the cell center);
1094        affect solution only if z* with full pressure in EOS.
1095      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1096        update output (because of z* in totPhiHyd and viscA4 changes);
1097      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1098        @ constant r) until interpolation at constant r is implemented.
1099    o pkg/diagnostics
1100      - fix RCENTER diagnostics in case cell center is not at interface middle
1101    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1102      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1103      that THETA and SALT are "conservative temperature" and "absolute
1104      salinity"
1105    o pkg/ctrl
1106      - fix computation of endrec in s/r ctrl_init_rec
1107      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1108    o pkg/seaice/seaice_growth.F
1109      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1110        remove then obsolete STORE directives
1111      - fix STORE directives for tice and tices, so that only the
1112        appropriate part of the fields are stored (and not the entire
1113        field); update global_ocean.cs32x15.seaice AD output.
1114      - cosmetic changes: adjust CPP flags and indentation for better
1115        legibilty
1116    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1117      Chris Wilson)
1118    o pkg/gmredi:
1119       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1120       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1121    
1122    checkpoint63  (2011/07/11)
1123    o pkg/exch2:
1124     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1125     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1126       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1127       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1128    o pkg/diagnostics:
1129     - deal with pairs of post-processed diags which are computed together; in
1130       particular, re-order list of diags within 1 file to save 2nd computation.
1131     - add S/R to compute velocity stream-function (called after velocity-potential
1132       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1133     - add parameter to select grid-point location where PsiVEL == 0.
1134    o eesupp/src:
1135       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1136       (specific S/R needed with exch2 topology - for now, just print an error msg)
1137  o pkg/shelfice  o pkg/shelfice
1138   - Implement friction velocity-dependent transfer coefficients following   - Implement friction velocity-dependent transfer coefficients following
1139     Holland and Jenkins, JPO, 1999     Holland and Jenkins, JPO, 1999
# Line 27  o pkg/seaice/seaice_growth.F: Line 1157  o pkg/seaice/seaice_growth.F:
1157      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1158      non-legacy seaice_solve4temp.      non-legacy seaice_solve4temp.
1159    - add diagnostic of the residual sublimation freshwater flux (the freshwater    - add diagnostic of the residual sublimation freshwater flux (the freshwater
1160      flux taken from the ocean if the total actual latent heat fluxes exceed      flux taken from the ocean if the total actual latent heat fluxes exceed
1161      the maximum)      the maximum)
1162    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1163     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.

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