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revision 1.1518 by mlosch, Mon Oct 24 16:12:39 2011 UTC revision 1.1699 by jmc, Mon Jul 30 16:13:19 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63q (2012/07/30)
8    o pkg/autodiff:
9      note about monitor and snap-shot of ad-variables:
10      a) need to apply ADEXCH before monitor or output of ad-vars to include
11       overlap contributions (was done for adjDump but missing for monitor).
12      b) since ADEXCH implies adding overlap values to interior array, machine
13       truncation error is expected when adding an ADEXCH call in the middle of
14       the time-stepping (although mathematically identical).
15      modifs:
16      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
17        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
18      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
19        apply ADEXCH before monitor or snap-shot of ad-variables:
20           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
21      - implement new method (copy+adexch) for snap-shot and monitor of main model
22        ad-vars (initially not used by default -> output unchanged).
23      - change default (set to 2) to use new method and update few output_adm.txt
24        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
25        and both tutorial_tracer_adjsens tests).
26      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
27        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
28    o pkg/ctrl:
29      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
30      generic control variables via
31      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
32      Only required customization should be S/R ctrl_map_ini_genarr.F
33      (routine in repository contains example)
34    o pkg/exf:
35      - fix and refine checking of surface-relaxation setting when using EXF
36    o verification (adjoint exp):
37      - reduce length of simulation by half for experiment global_ocean.cs32x15
38        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
39    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
40      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
41        of KE that can occur with aggressive optimization
42      + put quadratic bottom drag calculation in separated loops (only done if
43        using bottomDragQuadratic)
44    o model/src: CG2D_NSA
45      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
46         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
47      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
48         change cg2d residual target to be expressed in Wunits (=> do not normalise
49         RHS ; this fix global_max Pb with TAF); update output.
50    o verification/tutorial_tracer_adjsens:
51       improve parameter consistency (and get rid of warnings):
52       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
53       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
54       - use staggerTimeStep (for stability) in som81; use default rotation period.
55    o pkg/exch2:
56      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
57        reset to 0 = 1 long line in X)
58    o pkg/mdsio:
59      - fix reading of dimensions from meta file for large-size domain
60    o model/src:
61      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
62      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
63        Cubed-Sphere Exch with CS-corners inside the domain;
64        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
65        globalArea and to set hasWetCSCorners.
66      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
67        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
68      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
69        useCDscheme and useCubedSphereExchange).
70    o pkg/seaice/seaice_growth.F :
71      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
72        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
73        when the previous code was not correct.
74      - in all cases diagnoze the boundary condition mismatch to SIaaflux
75      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
76        that term to QNET (essentially to set the melt/freeze water to 0degC).
77        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
78    o verification/global_ocean.cs32x15/input.seaice :
79      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
80      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
81      - update results (output.seaice.txt) accordingly.
82    o verification/lab_sea/input/data.seaice :
83      - remove SEAICEheatConsFix, which is now be tested
84        in global_ocean.cs32x15. The presently coded fix
85        is only consistent with real fresh water + nlfs.
86      - update results (output.txt) accordingly.
87    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
88    o AD_CONFIG.h file:
89      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
90      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
91        add it explicitly in each fortran src file where it is needed.
92        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
93        thus introducing potentially wrong dependency; therefore, better to include
94        it only where it's really needed, and after any other included OPTIONS file
95        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
96        or ALLOW_TANGENTLINEAR_RUN).
97    
98    checkpoint63p (2012/07/06)
99    o pkg/autodiff:
100      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
101      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
102        which are now read from new parameter file "data.autodiff" (inAdExact
103        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
104      - add file "data.autodiff" in all verification/*/input_ad/ directories.
105      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
106        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
107    o verification/tutorial_tracer_adjsens/
108      - add extra sub-verification which uses "SOM" advection scheme
109        (2nd Order-Moment Advection Scheme, Prather Limiter) with
110          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
111        and in data:
112          multiDimAdvection=.TRUE.,
113          tempAdvScheme=81,
114          saltAdvScheme=81,
115    o model/src:
116      - introduce ALLOW_BALANCE_RELAX which allow the removal
117       of the global mean of relaxation terms by setting
118       balanceThetaClimRelax and balanceSaltClimRelax
119      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
120       This case is now treated appropriately in seaice_growth.F
121    o pkg/seaice:
122      - do balanceEmPmR and balanceQnet based on the net fluxes
123        (SItflux) that enter the ocean+ice system rather than QNET
124        and EMPMR. Works best in real fresh water.
125      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
126        out of the diagnotics bloc, and stored in global arrays.
127    
128    checkpoint63o (2012/06/29)
129    o vertical mixing schemes:
130      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
131      - replace computation of density (in Function STATE1, opps_calc.F) by a call
132        to S/R FIND_RHO_SCALAR
133      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
134        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
135        affects output (vermix.ggl90) at truncation level.
136    o testreport:
137      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
138        (nSx,nSy) for the number of threads (from eedata.mth)
139    o model/src:
140      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
141        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
142    o verification/tutorial_tracer_adjsens/
143      - compile with ALLOW_CG2D_NSA
144      - run with nonlinFreeSurf=3
145      - update reference output_adm.txt
146    o tools/genmake2:
147      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
148        refine usePROFILES switching off (only when NetCDF is not available).
149    o verification (atmospheric set-up):
150      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
151    o pkg/profiles : refine profiles and files handling.
152    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
153    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
154      - changes to use model/src/the_main_loop.F rather than the ecco version
155        in ecco type adjoint runs.
156    o model/src:
157      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
158      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
159      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
160    o model/src:
161      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
162        update output of test experiment bottom_ctrl_5x5.
163    o pkg/generic_advdiff:
164      - implement vertical bi-harmonic diffusion (for now, only for T & S and
165        only explicitly).
166    o verification/bottom_ctrl_5x5/
167      update reference output (results changed quite some time ago,
168      not sure when; but new reference results look ok in terms of grdchk)
169    o verification/1D_ocean_ice_column/
170      For verification purposes, the exact adjoint rather than an approx.
171      should be used (e.g., to comare against F.D. or TLM).
172      removed autodiff_inadmode*_ad.F routines in code_ad/
173      Update results/ accordingly.
174    o pkg/cal:
175      - change cal_getdate.F so that output date is function of input time only
176        (less ambiguous, not mixed up with input iteration number).
177      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
178    o pkg/diagnostics:
179      - implement calendarDumps also for stats-diags
180      - implement calendarDumps also for snap-shot output (negative freq)
181      - for now, ignores calendarDumps if non-zero phase-lag.
182    
183    checkpoint63n (2012/06/04)
184    o model/src:
185      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
186        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
187      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
188        similar to calc_r_star.F); update results of experiment internal_wave and
189        tutorial_global_oce_in_p (affected @ truncation level).
190    o pkg/shelfice:
191      - add parameterisation of advective-diffusive flux into the ice shelf
192        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
193      - simply eps3/3a computation
194    o eesupp:
195     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
196       between tiles, just fill-in edges assuming locally periodic subdomain) and
197       add corresponding exchange subroutines (EXCH0);
198     - new CG-solver version (_EX0) for disconnected-tiles special case.
199    o model/src (CG-solvers):
200     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
201       (similar final residual output and max-Iter number as with standard version);
202     - allows to store and use lowest-residual solution (standard & _SR versions);
203     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
204     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
205    o eesup/src:
206     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
207       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
208    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
209    
210    checkpoint63m (2012/04/27)
211    o pkg/shelfice:
212     - account for partical cells in surface level below ice-shelf for hydrostatic
213       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
214    o ad test experiments:
215     - update and rename to "ad_optfile.local" local AD-optfile specific to a
216       particular adjoint verification experiment (in verification/*/code_ad/)
217    o pkg/seaice & pkg/exf:
218     - Part two of ECCO-CLIVAR code merges.
219       Completes merge of seaice area relax. code.
220       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
221       to be set in EXF_OPTIONS.h since this pkg controls its I/O
222       (and avoids second CPP option in SEAICE_OPTIONS.h)
223     - change default value of costIceStart & costIceEnd to a valid date.
224     - add snowPrecip to HSNOW in seaice_growth
225    o pkg/ptracers:
226     - move ptracers summary and setup check into separated S/R ; add a check for
227       valid PTRACERS_Iter0 value (error+stop or just warning).
228    o pkg/cal (+ pkg/ecco):
229     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
230       as input; and for AD, unless both are not differentiable (e.g., k index)).
231    o model/src:
232     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
233       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
234       temporary set to usingZCoords value (to be changed to F when using shelfice).
235     - hydrostatic pressure: implement partial cell near the surface also for
236       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
237       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
238    o pkg/ctrl/ctrl_init.F:
239     - add a formal parameter to s/r ctrl_init_rec to print
240       xx_$(ctrl_valiable)_file for easier debugging
241     - move call of cal_* routines into the if-block where they are really
242       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
243       to specify a startdate
244    o pkg/seaice:
245     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
246       global_ocean.cs32x15/code versions).
247     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
248       verification experiment global_ocean.cs32x15.seaice and update results.
249    o pkg/exf:
250     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
251       (according to useExfYearlyFields).
252    o pkg/cal:
253     - move calendar setting & summary (previously in cal_readparams.F) into new
254       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
255       length of the simulation is set (after SET_PARMS call); This is an attempt
256       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
257     - For safety: keep a record of pkg/cal parameter settings status
258               to allow to STOP if one pkg/cal S/R is called too early.
259     - add a stop in all basic pkg/cal subroutines if called before setting is done.
260     - modify cal_getdate.F: stop when nothing was returned;
261       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
262       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
263    
264    checkpoint63l (2012/04/04)
265    o pkg/bbl:
266      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
267        update global_with_exf output.yearly.txt file.
268    o pkg/cal:
269      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
270      - remove 2 unsused and very short (1 line only) functions ;
271      - remove unsused subroutines from AD-Diff list.
272    o model/src:
273      - start to implement clean wait to stop in initialization S/R (config_check.F,
274         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
275    o folowing PRINT_MESSAGE changes:
276      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
277    o pkg/bbl:
278      - modification so it can work with z*
279      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
280      - global_with_exf/input.yearly verification; changes output.yearly.txt
281    o eesupp/src:
282      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
283        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
284      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
285        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
286      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
287      - when using MPI, always set usingMPI=T ; set default accordingly and stop
288        if not consistent.
289      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
290        argument is zero (in case called within single-thread section).
291    o pkg/fizhi:
292        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
293        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
294    o pkg/exch2:
295      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
296        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
297      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
298        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
299        with bad ones coming from a not-yet-updated halo.
300        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
301    o pkg/frazil:
302        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
303        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
304    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
305    o verification/lab_sea
306      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
307      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
308      * nTimeSteps 3 -> 4
309      * changed reference output accordingly
310    o pkg/ctrl:
311      * fix ctrl_get_gen for xx_sst, xx_sss
312    o pkg/fizhi:
313      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
314        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
315      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
316        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
317        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
318    o pkg/gmredi:
319      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
320    o pkg/fizhi:
321      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
322        (old)aces open64 tuv test.
323    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
324    o pkg/mom_vecinv:
325      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
326        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
327        with non-lin free-surf).
328    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
329      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
330      some compilers (gfortran 4.6.0 on MacOS)
331    o momentum:
332      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
333        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
334        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
335    
336    checkpoint63k (2012/03/17)
337    o model/src:
338       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
339         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
340       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
341         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
342    o model/src: solve_*diagonal.F
343       - replace division with multiplication by inverse (similar to original version)
344         update output of AD exp. global_ocean.90x40x15.
345       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
346         to enable the use of the vectorized & differentiable solve_tridiagonal.F
347       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
348         vertical advection (to get solve_tridiagonal tested in AD mode).
349    o pkg/seaice: ECCO-CLIVAR merge:
350      1. seaice AREA relaxation
351         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
352         * runtime flag: SEAICE_tauAreaObsRelax
353      2. modified global mean cost imbalance code: CPP option
354          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
355    o another iteration on solve_*diagonal.F
356       Make choices independent of AUTODIFF
357       Default will be the adjoinable vectorized version.
358       Alternative choices are:
359       * non-adjoinable original version with low memory footprint:
360         #define SOLVE_DIAGONAL_LOWMEMORY
361       * still adjoinable but does not vectorize (k as inner-most loop):
362         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
363    o testreport
364     - add option to use a home made wrapper around "make"
365     - remove MITGCM_IEEE env. variable (no longer active)
366    o pkg/shelfice
367     - improve computation of friction velocity for velocity dependent
368       exchange coefficients: include velocities into SHELFICEBoundaryLayer
369       block to average velocities vertically
370     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
371    o Modify diagonal solvers, now three versions (upon request):
372      #ifndef SOLVE_DIAGONAL_AUTODIFF
373        1. default version (dating back a while ago)
374      #else /* def SOLVE_DIAGONAL_AUTODIFF */
375      # ifdef SOLVE_DIAGONAL_KINNER
376        2. adjoinable version with k-innermost loop (G. Forget)
377      # else
378        3. adjoinable vectorized version of 2.
379      # endif
380      #endif /* SOLVE_DIAGONAL_AUTODIFF */
381      All flags are currently set within routines, but could/should be moved to CPP-options.
382      Array bounds for 1. are as before, for 2.,3. cover the entire domain
383      (could be changed for 1. too).
384    o verification/lab_sea (fwd):
385      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
386        use 7 categories (except hb87), new solve4temp params (except salt_plume),
387        constant salinity (=4) or variable salinity (salt_plume) done through
388        SItracer.
389    o pkg/seaice:
390      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
391      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
392         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
393        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
394        SEAICE_freeze got retired) but already better than previously with
395        SEAICE_freeze=123456.7 deg.C;
396      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
397        (safer multi-threaded setting); always set SEAICEuseEVP;
398      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
399        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
400        stop if multiple specifications for the same coeff; make sure default
401        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
402    o pkg/obcs:
403      - allow to switch to upwind 1rst order advection scheme for the advective
404        flux computation at the open-boundary; disabled for adjoint built.
405    o pkg/ptracers:
406      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
407      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
408      - add parameter to decide when to start a tracer; use internal flag to
409        know which tracer to step-forward; switch this internal flag at the top
410        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
411        for adjoint built.
412    o pkg/seaice:
413      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
414      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
415      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
416    o pkg/ecco:
417      - fix writing of output file DiagnosCost_ClimSalt/Theta
418        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
419    o pkg/seaice:
420      - add missing initialisation of COR_ICE array in dynsolver.F
421      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
422        compiled either way, and is tested in all exps (multidim was only tested
423        in lab_sea ad before).
424      - cosmetic change to prepare for future addition of ITD. no change to results.
425        no defaults change.
426      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
427      - by lack of adequate verification experiments, I further used custom versions
428        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
429        should be correct.
430      - avoid recomputations in ad.
431    o array initialisation in adjoint mode:
432      1) pkg/mom_common/mom_calc_ke.F:
433        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
434        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
435        part this initialisation is gone, resulting in Floating Point Exception
436        (caught by open64 compiler with debug option).
437      2) model/src/convective_weights.F
438        set output convectCount over the full array range (instead of doing
439        an update): this fix a similar issue when called within recomputation (adjoint)
440        which could by-pass the initialisation (normally done in the caller S/R).
441    o pkg/seaice:
442      - final version of turbulent flux params, as agreed at MIT ice meet:
443           SEAICE_mcPheePiston (default is ~ 0.000875)
444           SEAICE_mcPheeTaper (default is 0.)
445           SEAICE_frazilFrac (defualt is 1.)
446           SEAICE_mcPheeStepFunc (default is false)
447      - changes results at trunction error level
448      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
449    o added pkg/frazil:
450      - see frazil_description.tex for details
451      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
452    o pkg/shelfice/shelfice_thermodynamics.F
453      - fix exponents for velocity dependent exchange coefficients: change
454        from 2/3(=0) to 0.66666666666666667
455      - move computation of velocity dependent exchange coefficients into
456        separate loop, so that it applies to both thermodynamics
457      - move some divisions by constants out of loops
458    
459    checkpoint63j (2012/02/16)
460    o pkg/seaice:
461      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
462      - SItracer:  added run time params, and allow coupling to ocn salinity.
463    o pkg/seaice: remove (almost) all divisions by constants within loops
464      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
465      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
466      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
467      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
468    o pkg/seaice :
469      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
470        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
471      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
472      - add permanent SItflux diag that corresponds to TFLUX but includes
473        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
474      - allow activation/testing of a fix for suspected missing term in
475        ocn-ice heat budget (to be confirmed). To test this, you want to
476        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
477        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
478      - no change in results, fwd or ad.
479    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
480      - switch to variable freezing point.
481           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
482      - bug fix : the sublimation term that was missing is now activated.
483           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
484      - bug fix : flooding sign term for SIsal0.NE.0.
485           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
486    o pkg/seaice:
487      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
488        is now the default, and the old default constant freezing point is recovered
489        with SEAICE_tempFrz0    = -1.96,
490             SEAICE_dTempFrz_dS = 0.,
491      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
492      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
493      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
494        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
495      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
496        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
497      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
498        seaice_growth r149 for legacy branch (no results change).
499      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
500        from I. Fenty).
501      - results did not change except for global_ocean.cs32x15, mostly due to the
502        switch to variable freezing point (see above item for detail).
503    o pkg/thsice:
504      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
505        seawater freezing in thsice_calc_thickn (not used).
506    o pkg/seaice: turbulent flux term specification via run time params.
507      - replace CPP switches with run time switches to facilitate testing
508      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
509                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
510      - added runtime parameter : SEAICEturbFluxFormula
511      - move Mcphee constants to SEAICE_PARAMS.h
512      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
513                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
514                 remove seaice_summary call (moved to seaice_init_fixed)
515      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
516        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
517      - seaice_summary.F : add missing report of read turbulent flux term set up
518                           and SITRACER.
519      - seaice_check.F : check range; inform and stop if retired CPPs are used
520                         (incl. SEAICE_AGE).
521      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
522             CPP switch, same computation as before for the different options.
523      - change results at the truncation level.
524    o pkg/seaice:
525      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
526        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
527        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
528      - update verification/*/input*/data.seaice:
529        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
530        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
531        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
532        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
533    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
534      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
535        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
536        difference in results only due to machine truncation.
537      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
538        MaykutPolySatVap; keep MIN_LWDOWN.
539      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
540      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
541        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
542    o pkg/salt_plume:
543      - isolate saltPlumeFlux array exch into a specific S/R called from
544        do_oceanic_phys.F
545      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
546    o verification:
547      - move untested set-up to MITgcm_contrib/verification_other.
548    o pkg/seaice:
549      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
550    o pkg/seaice:
551      - seaice_solve4temp.F (keeping results unchanged):
552        * add 2 future run-time params to select which saturation vapor pressure
553          formula is used and how post-iteration fluxes are set.
554          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
555        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
556          the linearized expression to stay consistent with tsurf finding.
557      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
558        can be < 0.
559    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
560      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
561        conductive heat flux F_c , and add it explicitly when updating tsurf as
562        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
563        so that now F_ia has a consistent meaning through the entire routine.
564        This causes differences at truncation level: update output of fwd exp.
565        global_ocean.cs32x15.seaice.
566    o pkg/seaice:
567      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
568        of arrays, sign/direction of fluxes; no effect on results.
569      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
570        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
571        note: this should have been done before changing celsius2K default.
572      - to keep results unchanged, add back old value of celsius2K in verification
573        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
574      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
575        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
576        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
577        freezing temp is consistent with value in seaice_growth.F ; this causes
578        differences at machine truncation level: update lab_sea AD output (3/4).
579    o pkg/seaice:
580      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
581        and climsst/sss even when using seaice (to prevent calculation that might
582        use SST on land); does not affect any verification exp.
583      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
584        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
585    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
586      over land (non-legacy code)
587    o vectorize salt_plume package:
588      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
589      - this code computes plumebk everywhere (also over land), thus requires
590        code to avoid divisions by zero and catch the case of kLev=Nr.
591      - efficiency of salt_plume_frac is still sub-optimal
592    o tools (genmake2):
593      - fix makefile NAME specification (option: -makefile NAME) by adding
594        "-f $MAKEFILE" in few places where it was missing including makedepend
595        command (contribution from Paul).
596    
597    checkpoint63i (2012/01/24)
598    o model/src:
599      - add factorized versions of some EOS code to find_rho.F,
600        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
601    o model/src:
602      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
603      - change default celsius2K from 273.16 to 273.15
604      - to keep results unchanged, add back old value of celsius2K in verification
605        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
606         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
607    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
608      to make TAF generate vectorizable code
609    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
610       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
611       have flags that do this more efficiently.
612    o pkg/diagnostics/diagstats_calc.F
613      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
614    o pkg/obcs (with exch2):
615      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
616        and remove code (in obcs_readparms.F) which was based on EXCH of indices
617        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
618    o pkg/exf and seaice exp:
619      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
620        so that switching off area & heff advection flags does not affect results.
621      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
622      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
623        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
624        results of verification experiments: 1D_ocean_ice_column(fwd),
625        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
626        and offline_exf_seaice (all 4).
627    o pkg/seaice:
628      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
629        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
630      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
631        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
632        not multi-dim advection;
633      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
634        SHORTWAVE_HEATING #undef.
635    o optim: make Makefile more robust (?)
636    o pkg/obcs:
637      * fix treatment of obcs_read_pickup for TAF
638    o pkg/shelfice:
639      * add missing initialisation of num_shifwflx
640      * new adjoint verification exp. for isomip
641      * change Prandtl and Schmidt numbers from generic formulations
642        (in terms of model diffus. and visc.) to separate runtime
643        parameters, with Holland and Jenkins (1999) default values.
644    o pkg/exf (interpolation):
645      - extended input field (2 rows) near the N & S poles:
646        * fill in with the symetric value (when even Nb of data in longitude)
647        * add average value at the poles only for scalar quantities ; for vector
648          component interpolation, skip the averaging and keep duplicated values,
649          unless the 2 components have same location (uvInterp=T) in which case
650          interpolate the 2 components together using S/R EXF_INTERP_UV.
651      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
652        together: this allows to account properly for local orientation when
653        averaging at N & S pole.
654      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
655        exf-interpolation near N & S poles. Undef by default.
656      - add debug check/print on 1rst iter if debugLevel >=2.
657    o pkg/exf:
658      - change masking flags definition (no longer "parameter"), put them in
659        common block and set them in S/R EXF_INIT_FIXED.
660      - change recognized masking flag from s,u,v to c,w,s since the mask
661        to use (maskC,W,S) depends on position on model grid and has little to
662        do with scalar/vector difference; fix masking if using P-coordinates.
663      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
664        and update results of exp. global_with_exf (x2).
665      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
666    o pkg/obcs
667      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
668    o pkg/exf (interpolation):
669      - assume periodicity in X only if input field cover full longitude range.
670      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
671        and should vectorise).
672      - fix input lat of the 2 added row (in case we provide N.pole data).
673    
674    checkpoint63h (2011/12/30)
675    o pkg/seaice:
676      - change declaration of UVM from _RL to _RS in order to get B-grid
677        uIce,vIce monitor when _RS = real*4
678    o pkg/offline:
679      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
680      - compute vertical velocity if not read from file (switch on exactConserv
681        & staggerTimeStep);
682      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
683    o verification:
684      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
685        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
686        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
687      - update output of exp. global_ocean.cs32x15.viscA4 after changing
688        grid-file angles (used here for coriolis-3d);
689      - remove (or gzip) few files not needed to run fizhi-cs experiments.
690    o pkg/exf (vector interpolation):
691      - rotate vector component toward local grid-axis orientation using grid-angles
692        (stored in GRID.h) instead of locally computed rotation angle; keep old code
693        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
694    o pkg/seaice:
695      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
696        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
697    o pkg/PKG_OPTIONS.h files:
698      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
699        outside of the #ifdef ALLOW_THISPKG / #endif block.
700      - update verification/*/code/PKG_OPTIONS.h files.
701    o add a verification experiment (offline_exf_seaice/input.seaice) that test
702      the B-grid LSOR solver
703    o pkg/seaice: sort out emissivity and long wave radiation step 2:
704      - add emissivity for snow and ice as new run-time parameters
705        (unfortunately) that default to the corresponding exf values; this
706        changes results in most verification experiments so that for backward
707        compatibility these parameter have to be set explicitly to inconsistent
708        values (ugly);
709      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
710        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
711        until we agree how to handle this bug properly
712    o pkg/exf (interpolation):
713      - add a set of run-time param ({inputfield}_interpMethod), one for
714        each interpolated input field, to select the interpolation method
715        with a value of zero switching off the interpolation;
716      - print interpolation parameters to standard output;
717      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
718        (to use instead runoff_interpMethod=0 in data.exf).
719      - simplify default setting of interpolation parameters (for all fields,
720        set position to match model grid cell-center position, leading to trivial
721        interpolation in case of regular Lat-Lon grid) and fix for the case of
722        non-uniform delY.
723    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
724       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
725       this factor is absolutely required, because the lw exitance (= out-going
726       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
727       where the reflectivity rho = 1-emissivity for conservation reasons. Once
728       this is established, we can remove the CPP-Flag (if we want to).
729    o pkg/seaice:
730      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
731        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
732      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
733        what the name implies (and not emissivity*BoltzmannConstant), this means
734        the old default value of 5.5e-8 now means
735        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
736        S/R exf_readparms
737      - FV-discretization of the B-grid LSOR solver, turn on with
738        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
739        of the calling routine dynsolver, so that B and C-grid code look a
740        little more alike.
741      - fix index bugs in ostres.F (B-grid code)
742    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
743    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
744      default for SEAICE_emissivity, if useEXF; requires setting a wrong
745      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
746      backward compatiblity
747    o model/src: use sigmaR in calc_ivdc
748    
749    checkpoint63g (2011/12/16)
750    o pkg/seaice/seaice_growth.F:
751      fix heat conservation of the coupled ocean-seaice system.
752      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
753      solid vs liquid water treatment is resolved via QNET.
754    o pkg/seaice/seaice_growth.F:
755      add missing term for sublimation in saltFlux, which was breaking conservation.
756    o pkg/seaice/seaice_model.F:
757      Remove this patholigical case treatment in evolution branch,
758      where it is un-necessary and breaks conservation.
759      Update global_ocean.cs32x15/results accordingly for
760      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
761    o model/src:
762      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
763      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
764    o pkg/obcs:
765      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
766      tendency for temperature and salinity that is then applied to update
767      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
768      horizontal advection and diffusion contributions on the boundary (in
769      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
770      removing the mask in S/R timestep_tracer. The advantage of this approach is
771      that the updated tracer values include contributions from the surface
772      forcing and vertical diffusion.
773      This modification changes exp4.stevens because of vertical diffusion.
774    o model/src:
775      change non-curvilinear grid setting to also work with exch2 + blank tiles:
776      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
777        face dimensions.
778      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
779        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
780        and INI_SPHERICAL_POLAR_GRID.
781      change test-experiment global_ocean.90x40x15:
782      - split the domain in many more tiles (9x4 tiles of 10x10 each);
783      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
784      - update results of both test (std & dwnslp).
785    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
786       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
787    o model/src:
788      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
789        and fix initialisation when using sigma-coords.
790    o model/src:
791     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
792       to their current value at the beginning of forward_step.F": add a new run-time
793       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
794     - set doResetHFactors=T in the following test exp:
795        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
796        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
797        and tutorial_global_oce_in_p (nonLinFS in p)
798    o pkg/ecco
799      - added IES cost term
800    o verification/advect_xz
801      - scale down the depth by 1/100 (from 200 km to just 2.km)
802      - add secondary test using divergent flow, r-star and implicit vertical advection.
803      - add note (check_conserve_TS.txt) and matlab script to check global
804        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
805    o pkg/rbcs:
806      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
807    o pkg/obcs (Stevens BCs):
808      - fix various problems in the phase speed computations of the Stevens
809        boundary conditions:
810        - sign error for western and southern boundaries,
811        - time tendencies were underestimated by factor of dTracerLev and some just
812          zero (for multidim advection schemes) -> now estimate time tendencies
813          from difference between previous (n) time level and the one before (n-1);
814          this requires storing a field per tracer per boundary, also in the pickup
815          files.
816        - replace deltaTmom in cflMer/Zon computation with dTracerLev
817        - set default phase velocity to cflMer/Zon
818      - update verification experiment exp4.stevens
819    o pkg/generic_advdiff (implicit_r):
820      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
821        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
822      - fix implicit vertical diffusion or advection with NonLin FreeSurf
823        (was using current recip_hFacC instead of future recip_hFacC): set future
824        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
825        solver S/R ;
826      - fill diagnostics of vertical advective fluxes (computed from tendency)
827        when using implicit vert. advection;
828      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
829         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
830         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
831         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
832    o pkg/diagnostics:
833      - add diags for T & S tendency which goes through Adams-Bashforth.
834    
835    checkpoint63f (2011/11/30)
836    o pkg/obcs/obcs_calc_stevens.F:
837      - join some loops to reduce number of if-statements
838      - fix a bug in code for northern and southern boundaries.
839    o pkg/seaice/seaice_init_varia.F
840      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
841        caused zero ice-velocities for the B-grid code
842    o pkg/seaice/seaice_init_fixed.F
843      - fix a bug in the initialisation of the second metric terms
844        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
845      - this affects all seaice configurations with useCurviLinearGrid = .true.
846        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
847        = .true. (default)
848      - the only verification experiment affected is global_ocean.cs32x15:
849        icedyn, seaice, and seaice_dynmix (AD)
850    o pkg/thsice/thsice_diagnostics_state.F
851      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
852        not contain garbage that can lead to surprises in diagstats_calc.F
853    o model/src:
854      - move bi,bj loops inside INTEGR_CONTINUITY ;
855      - call INTEGR_CONTINUITY directly from forward_step.F
856        (previously called from momentum_correction_step.F)
857      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
858        forward_step.F and pkg/ecco/the_main_loop.F
859    o model/src/do_oceanic_phys.F:
860      - reset addMass to zero only if useICEFRONT ;
861      - separated k-loop for rhoInSitu calculation ;
862      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
863        and at constant T,S (= WdRHOdP);
864      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
865        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
866        transport of locally-referenced potential density);
867        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
868    o gluemnc:
869      - replace ncrcat with ncks when adding variables to *.glob.nc
870      - change the way variables without record dimensions are handled so that
871        files that have variables with and without record variables can be glued:
872        add a record dimension with a new unique name to be able to differentiate
873        between variable with and without a-prior record dimensions. Remove
874        this record dimension before adding the variable to the *.glob.nc file.
875        This procedure automatically works also for grid.*.nc files that do not
876        have any record dimension.
877    o verification/cpl_aim+ocn:
878      - generate new reference output on baudelaire (gfortran, mpich2) (previously
879        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
880    o pkg/obcs/obcs_calc_stevens.F:
881      - add code for northern and southern boundaries.
882      - reorder some loops to save some operations and so that drFBar can be scalar
883    o model/src:
884      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
885        truncation) and add diagnostics for Adams-Bashforth tendency increment.
886      - update test-exp. AD output:
887        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
888      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
889        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
890        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
891        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
892        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
893        tutorial_plume_on_slope.
894    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
895      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
896      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
897      does not even come with an F77 compiler anymore, this should not be
898      a limitation
899    
900    checkpoint63e (2011/11/06)
901    o pkg/seaice adjoint of LSR:
902      - substantially rework STORE dirs.
903      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
904        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
905        and only perform SOLV_MAX_FIXED adjoint iters.
906        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
907        always goes to same record, meaning that the last forward field will be
908        the one used in the adjoint - an approximation.
909      - now produces non-zero LSR-related gradients, and acceptable gradients for
910        An's zonal (x-z) test case (to be checked in)
911      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
912        (but these are screwed up by the thermodynamics in the first place);
913        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
914        output_adm.txt also reflects changes to seaice_lsr
915      - global_ocean.cs32x15:
916        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
917          (output_adm.seaice.txt was updated)
918        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
919          (output_adm.seaice_dynmix.txt)
920    o test-exp. exp4+stevens:
921      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
922    o pkg/seaice (lsr solver):
923      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
924        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
925      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
926      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
927        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
928      - compute (with new S/R) and print initial (+ free-driff sol. if available)
929        and final residual of linearised system.
930    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
931      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
932    o pkg/obcs: Stevens BCs (still only for east and west)
933      - fix Stevens BCs by using intermediate velocities of previous
934        time step as "baroclinic" contribution rather velocity of one grid cell
935        inside the boundaries; more consistent but makes the entire treatment
936        more complicated, requires new pickup files and two new S/Rs:
937        obcs_copy_uv_n and obcs_save_uv_n
938        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
939        (undefined by default)
940      - silently move computation of some grid factors into separate loops to
941        save some recomputations
942      - add a hack for non-linear free surface
943      - add a verification experiment to exp4 that tests this code
944    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
945    
946    checkpoint63d (2011/10/25)
947  o pkg/obcs + seaice-dynamics:  o pkg/obcs + seaice-dynamics:
948    - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before    - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
949      solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB      solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
# Line 25  o pkg/dic: Line 965  o pkg/dic:
965    - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add    - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
966      carbonate computation/output to CALC_PCO2_APPROX      carbonate computation/output to CALC_PCO2_APPROX
967  o pkg/generic_advdiff  o pkg/generic_advdiff
968    - make TAF generate code that vectorizes:    - make TAF generate code that vectorizes:
969      gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F      gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
970  o model/src:  o model/src:
971    - improve vectorization also for adjoint code of    - improve vectorization also for adjoint code of
972      solve_tridiagonal and solve_pentadiagonal. As this requires up to      solve_tridiagonal and solve_pentadiagonal. As this requires up to
973      5 new 3D-fields, this code is only turned on for the combination of      5 new 3D-fields, this code is only turned on for the combination of
974      ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message      ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
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