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revision 1.1578 by mlosch, Fri Jan 20 15:49:11 2012 UTC revision 1.1702 by jmc, Thu Aug 2 22:48:11 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/autodiff:
8      re-write active I/O high-level (control) S/R:
9      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
10      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
11      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
12        MDS_READ/WRITE_FIELD); change loops to multi-threads.
13      - update and merge active_file_control_slice.flow into active_file_control.flow
14      - update the calls in lower level S/R (active_file.F, active_file_g.F and
15        active_file_ad.F) keeping the argument list and function unchanged.
16    o autodiff and RS=real*4:
17      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
18        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
19      - change argument type of 3-D mask argument to _RS to match type in the call
20        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
21    o pkg/thsice:
22      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
23      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
24        fresh-water flux: uniform correction or proportional to local precip.
25    o pkg/ctrl:
26      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
27      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
28                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
29      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
30    
31    checkpoint63q (2012/07/30)
32    o pkg/autodiff:
33      note about monitor and snap-shot of ad-variables:
34      a) need to apply ADEXCH before monitor or output of ad-vars to include
35       overlap contributions (was done for adjDump but missing for monitor).
36      b) since ADEXCH implies adding overlap values to interior array, machine
37       truncation error is expected when adding an ADEXCH call in the middle of
38       the time-stepping (although mathematically identical).
39      modifs:
40      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
41        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
42      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
43        apply ADEXCH before monitor or snap-shot of ad-variables:
44           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
45      - implement new method (copy+adexch) for snap-shot and monitor of main model
46        ad-vars (initially not used by default -> output unchanged).
47      - change default (set to 2) to use new method and update few output_adm.txt
48        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
49        and both tutorial_tracer_adjsens tests).
50      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
51        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
52    o pkg/ctrl:
53      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
54      generic control variables via
55      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
56      Only required customization should be S/R ctrl_map_ini_genarr.F
57      (routine in repository contains example)
58    o pkg/exf:
59      - fix and refine checking of surface-relaxation setting when using EXF
60    o verification (adjoint exp):
61      - reduce length of simulation by half for experiment global_ocean.cs32x15
62        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
63    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
64      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
65        of KE that can occur with aggressive optimization
66      + put quadratic bottom drag calculation in separated loops (only done if
67        using bottomDragQuadratic)
68    o model/src: CG2D_NSA
69      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
70         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
71      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
72         change cg2d residual target to be expressed in Wunits (=> do not normalise
73         RHS ; this fix global_max Pb with TAF); update output.
74    o verification/tutorial_tracer_adjsens:
75       improve parameter consistency (and get rid of warnings):
76       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
77       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
78       - use staggerTimeStep (for stability) in som81; use default rotation period.
79    o pkg/exch2:
80      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
81        reset to 0 = 1 long line in X)
82    o pkg/mdsio:
83      - fix reading of dimensions from meta file for large-size domain
84    o model/src:
85      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
86      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
87        Cubed-Sphere Exch with CS-corners inside the domain;
88        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
89        globalArea and to set hasWetCSCorners.
90      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
91        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
92      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
93        useCDscheme and useCubedSphereExchange).
94    o pkg/seaice/seaice_growth.F :
95      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
96        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
97        when the previous code was not correct.
98      - in all cases diagnoze the boundary condition mismatch to SIaaflux
99      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
100        that term to QNET (essentially to set the melt/freeze water to 0degC).
101        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
102    o verification/global_ocean.cs32x15/input.seaice :
103      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
104      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
105      - update results (output.seaice.txt) accordingly.
106    o verification/lab_sea/input/data.seaice :
107      - remove SEAICEheatConsFix, which is now be tested
108        in global_ocean.cs32x15. The presently coded fix
109        is only consistent with real fresh water + nlfs.
110      - update results (output.txt) accordingly.
111    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
112    o AD_CONFIG.h file:
113      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
114      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
115        add it explicitly in each fortran src file where it is needed.
116        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
117        thus introducing potentially wrong dependency; therefore, better to include
118        it only where it's really needed, and after any other included OPTIONS file
119        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
120        or ALLOW_TANGENTLINEAR_RUN).
121    
122    checkpoint63p (2012/07/06)
123    o pkg/autodiff:
124      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
125      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
126        which are now read from new parameter file "data.autodiff" (inAdExact
127        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
128      - add file "data.autodiff" in all verification/*/input_ad/ directories.
129      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
130        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
131    o verification/tutorial_tracer_adjsens/
132      - add extra sub-verification which uses "SOM" advection scheme
133        (2nd Order-Moment Advection Scheme, Prather Limiter) with
134          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
135        and in data:
136          multiDimAdvection=.TRUE.,
137          tempAdvScheme=81,
138          saltAdvScheme=81,
139    o model/src:
140      - introduce ALLOW_BALANCE_RELAX which allow the removal
141       of the global mean of relaxation terms by setting
142       balanceThetaClimRelax and balanceSaltClimRelax
143      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
144       This case is now treated appropriately in seaice_growth.F
145    o pkg/seaice:
146      - do balanceEmPmR and balanceQnet based on the net fluxes
147        (SItflux) that enter the ocean+ice system rather than QNET
148        and EMPMR. Works best in real fresh water.
149      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
150        out of the diagnotics bloc, and stored in global arrays.
151    
152    checkpoint63o (2012/06/29)
153    o vertical mixing schemes:
154      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
155      - replace computation of density (in Function STATE1, opps_calc.F) by a call
156        to S/R FIND_RHO_SCALAR
157      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
158        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
159        affects output (vermix.ggl90) at truncation level.
160    o testreport:
161      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
162        (nSx,nSy) for the number of threads (from eedata.mth)
163    o model/src:
164      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
165        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
166    o verification/tutorial_tracer_adjsens/
167      - compile with ALLOW_CG2D_NSA
168      - run with nonlinFreeSurf=3
169      - update reference output_adm.txt
170    o tools/genmake2:
171      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
172        refine usePROFILES switching off (only when NetCDF is not available).
173    o verification (atmospheric set-up):
174      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
175    o pkg/profiles : refine profiles and files handling.
176    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
177    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
178      - changes to use model/src/the_main_loop.F rather than the ecco version
179        in ecco type adjoint runs.
180    o model/src:
181      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
182      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
183      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
184    o model/src:
185      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
186        update output of test experiment bottom_ctrl_5x5.
187    o pkg/generic_advdiff:
188      - implement vertical bi-harmonic diffusion (for now, only for T & S and
189        only explicitly).
190    o verification/bottom_ctrl_5x5/
191      update reference output (results changed quite some time ago,
192      not sure when; but new reference results look ok in terms of grdchk)
193    o verification/1D_ocean_ice_column/
194      For verification purposes, the exact adjoint rather than an approx.
195      should be used (e.g., to comare against F.D. or TLM).
196      removed autodiff_inadmode*_ad.F routines in code_ad/
197      Update results/ accordingly.
198    o pkg/cal:
199      - change cal_getdate.F so that output date is function of input time only
200        (less ambiguous, not mixed up with input iteration number).
201      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
202    o pkg/diagnostics:
203      - implement calendarDumps also for stats-diags
204      - implement calendarDumps also for snap-shot output (negative freq)
205      - for now, ignores calendarDumps if non-zero phase-lag.
206    
207    checkpoint63n (2012/06/04)
208    o model/src:
209      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
210        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
211      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
212        similar to calc_r_star.F); update results of experiment internal_wave and
213        tutorial_global_oce_in_p (affected @ truncation level).
214    o pkg/shelfice:
215      - add parameterisation of advective-diffusive flux into the ice shelf
216        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
217      - simply eps3/3a computation
218    o eesupp:
219     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
220       between tiles, just fill-in edges assuming locally periodic subdomain) and
221       add corresponding exchange subroutines (EXCH0);
222     - new CG-solver version (_EX0) for disconnected-tiles special case.
223    o model/src (CG-solvers):
224     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
225       (similar final residual output and max-Iter number as with standard version);
226     - allows to store and use lowest-residual solution (standard & _SR versions);
227     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
228     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
229    o eesup/src:
230     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
231       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
232    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
233    
234    checkpoint63m (2012/04/27)
235    o pkg/shelfice:
236     - account for partical cells in surface level below ice-shelf for hydrostatic
237       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
238    o ad test experiments:
239     - update and rename to "ad_optfile.local" local AD-optfile specific to a
240       particular adjoint verification experiment (in verification/*/code_ad/)
241    o pkg/seaice & pkg/exf:
242     - Part two of ECCO-CLIVAR code merges.
243       Completes merge of seaice area relax. code.
244       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
245       to be set in EXF_OPTIONS.h since this pkg controls its I/O
246       (and avoids second CPP option in SEAICE_OPTIONS.h)
247     - change default value of costIceStart & costIceEnd to a valid date.
248     - add snowPrecip to HSNOW in seaice_growth
249    o pkg/ptracers:
250     - move ptracers summary and setup check into separated S/R ; add a check for
251       valid PTRACERS_Iter0 value (error+stop or just warning).
252    o pkg/cal (+ pkg/ecco):
253     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
254       as input; and for AD, unless both are not differentiable (e.g., k index)).
255    o model/src:
256     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
257       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
258       temporary set to usingZCoords value (to be changed to F when using shelfice).
259     - hydrostatic pressure: implement partial cell near the surface also for
260       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
261       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
262    o pkg/ctrl/ctrl_init.F:
263     - add a formal parameter to s/r ctrl_init_rec to print
264       xx_$(ctrl_valiable)_file for easier debugging
265     - move call of cal_* routines into the if-block where they are really
266       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
267       to specify a startdate
268    o pkg/seaice:
269     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
270       global_ocean.cs32x15/code versions).
271     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
272       verification experiment global_ocean.cs32x15.seaice and update results.
273    o pkg/exf:
274     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
275       (according to useExfYearlyFields).
276    o pkg/cal:
277     - move calendar setting & summary (previously in cal_readparams.F) into new
278       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
279       length of the simulation is set (after SET_PARMS call); This is an attempt
280       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
281     - For safety: keep a record of pkg/cal parameter settings status
282               to allow to STOP if one pkg/cal S/R is called too early.
283     - add a stop in all basic pkg/cal subroutines if called before setting is done.
284     - modify cal_getdate.F: stop when nothing was returned;
285       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
286       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
287    
288    checkpoint63l (2012/04/04)
289    o pkg/bbl:
290      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
291        update global_with_exf output.yearly.txt file.
292    o pkg/cal:
293      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
294      - remove 2 unsused and very short (1 line only) functions ;
295      - remove unsused subroutines from AD-Diff list.
296    o model/src:
297      - start to implement clean wait to stop in initialization S/R (config_check.F,
298         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
299    o folowing PRINT_MESSAGE changes:
300      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
301    o pkg/bbl:
302      - modification so it can work with z*
303      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
304      - global_with_exf/input.yearly verification; changes output.yearly.txt
305    o eesupp/src:
306      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
307        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
308      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
309        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
310      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
311      - when using MPI, always set usingMPI=T ; set default accordingly and stop
312        if not consistent.
313      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
314        argument is zero (in case called within single-thread section).
315    o pkg/fizhi:
316        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
317        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
318    o pkg/exch2:
319      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
320        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
321      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
322        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
323        with bad ones coming from a not-yet-updated halo.
324        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
325    o pkg/frazil:
326        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
327        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
328    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
329    o verification/lab_sea
330      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
331      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
332      * nTimeSteps 3 -> 4
333      * changed reference output accordingly
334    o pkg/ctrl:
335      * fix ctrl_get_gen for xx_sst, xx_sss
336    o pkg/fizhi:
337      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
338        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
339      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
340        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
341        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
342    o pkg/gmredi:
343      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
344    o pkg/fizhi:
345      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
346        (old)aces open64 tuv test.
347    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
348    o pkg/mom_vecinv:
349      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
350        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
351        with non-lin free-surf).
352    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
353      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
354      some compilers (gfortran 4.6.0 on MacOS)
355    o momentum:
356      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
357        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
358        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
359    
360    checkpoint63k (2012/03/17)
361    o model/src:
362       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
363         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
364       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
365         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
366    o model/src: solve_*diagonal.F
367       - replace division with multiplication by inverse (similar to original version)
368         update output of AD exp. global_ocean.90x40x15.
369       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
370         to enable the use of the vectorized & differentiable solve_tridiagonal.F
371       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
372         vertical advection (to get solve_tridiagonal tested in AD mode).
373    o pkg/seaice: ECCO-CLIVAR merge:
374      1. seaice AREA relaxation
375         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
376         * runtime flag: SEAICE_tauAreaObsRelax
377      2. modified global mean cost imbalance code: CPP option
378          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
379    o another iteration on solve_*diagonal.F
380       Make choices independent of AUTODIFF
381       Default will be the adjoinable vectorized version.
382       Alternative choices are:
383       * non-adjoinable original version with low memory footprint:
384         #define SOLVE_DIAGONAL_LOWMEMORY
385       * still adjoinable but does not vectorize (k as inner-most loop):
386         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
387    o testreport
388     - add option to use a home made wrapper around "make"
389     - remove MITGCM_IEEE env. variable (no longer active)
390    o pkg/shelfice
391     - improve computation of friction velocity for velocity dependent
392       exchange coefficients: include velocities into SHELFICEBoundaryLayer
393       block to average velocities vertically
394     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
395    o Modify diagonal solvers, now three versions (upon request):
396      #ifndef SOLVE_DIAGONAL_AUTODIFF
397        1. default version (dating back a while ago)
398      #else /* def SOLVE_DIAGONAL_AUTODIFF */
399      # ifdef SOLVE_DIAGONAL_KINNER
400        2. adjoinable version with k-innermost loop (G. Forget)
401      # else
402        3. adjoinable vectorized version of 2.
403      # endif
404      #endif /* SOLVE_DIAGONAL_AUTODIFF */
405      All flags are currently set within routines, but could/should be moved to CPP-options.
406      Array bounds for 1. are as before, for 2.,3. cover the entire domain
407      (could be changed for 1. too).
408    o verification/lab_sea (fwd):
409      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
410        use 7 categories (except hb87), new solve4temp params (except salt_plume),
411        constant salinity (=4) or variable salinity (salt_plume) done through
412        SItracer.
413    o pkg/seaice:
414      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
415      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
416         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
417        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
418        SEAICE_freeze got retired) but already better than previously with
419        SEAICE_freeze=123456.7 deg.C;
420      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
421        (safer multi-threaded setting); always set SEAICEuseEVP;
422      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
423        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
424        stop if multiple specifications for the same coeff; make sure default
425        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
426    o pkg/obcs:
427      - allow to switch to upwind 1rst order advection scheme for the advective
428        flux computation at the open-boundary; disabled for adjoint built.
429    o pkg/ptracers:
430      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
431      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
432      - add parameter to decide when to start a tracer; use internal flag to
433        know which tracer to step-forward; switch this internal flag at the top
434        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
435        for adjoint built.
436    o pkg/seaice:
437      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
438      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
439      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
440    o pkg/ecco:
441      - fix writing of output file DiagnosCost_ClimSalt/Theta
442        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
443    o pkg/seaice:
444      - add missing initialisation of COR_ICE array in dynsolver.F
445      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
446        compiled either way, and is tested in all exps (multidim was only tested
447        in lab_sea ad before).
448      - cosmetic change to prepare for future addition of ITD. no change to results.
449        no defaults change.
450      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
451      - by lack of adequate verification experiments, I further used custom versions
452        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
453        should be correct.
454      - avoid recomputations in ad.
455    o array initialisation in adjoint mode:
456      1) pkg/mom_common/mom_calc_ke.F:
457        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
458        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
459        part this initialisation is gone, resulting in Floating Point Exception
460        (caught by open64 compiler with debug option).
461      2) model/src/convective_weights.F
462        set output convectCount over the full array range (instead of doing
463        an update): this fix a similar issue when called within recomputation (adjoint)
464        which could by-pass the initialisation (normally done in the caller S/R).
465    o pkg/seaice:
466      - final version of turbulent flux params, as agreed at MIT ice meet:
467           SEAICE_mcPheePiston (default is ~ 0.000875)
468           SEAICE_mcPheeTaper (default is 0.)
469           SEAICE_frazilFrac (defualt is 1.)
470           SEAICE_mcPheeStepFunc (default is false)
471      - changes results at trunction error level
472      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
473    o added pkg/frazil:
474      - see frazil_description.tex for details
475      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
476    o pkg/shelfice/shelfice_thermodynamics.F
477      - fix exponents for velocity dependent exchange coefficients: change
478        from 2/3(=0) to 0.66666666666666667
479      - move computation of velocity dependent exchange coefficients into
480        separate loop, so that it applies to both thermodynamics
481      - move some divisions by constants out of loops
482    
483    checkpoint63j (2012/02/16)
484    o pkg/seaice:
485      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
486      - SItracer:  added run time params, and allow coupling to ocn salinity.
487    o pkg/seaice: remove (almost) all divisions by constants within loops
488      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
489      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
490      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
491      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
492    o pkg/seaice :
493      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
494        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
495      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
496      - add permanent SItflux diag that corresponds to TFLUX but includes
497        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
498      - allow activation/testing of a fix for suspected missing term in
499        ocn-ice heat budget (to be confirmed). To test this, you want to
500        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
501        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
502      - no change in results, fwd or ad.
503    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
504      - switch to variable freezing point.
505           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
506      - bug fix : the sublimation term that was missing is now activated.
507           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
508      - bug fix : flooding sign term for SIsal0.NE.0.
509           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
510    o pkg/seaice:
511      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
512        is now the default, and the old default constant freezing point is recovered
513        with SEAICE_tempFrz0    = -1.96,
514             SEAICE_dTempFrz_dS = 0.,
515      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
516      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
517      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
518        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
519      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
520        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
521      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
522        seaice_growth r149 for legacy branch (no results change).
523      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
524        from I. Fenty).
525      - results did not change except for global_ocean.cs32x15, mostly due to the
526        switch to variable freezing point (see above item for detail).
527    o pkg/thsice:
528      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
529        seawater freezing in thsice_calc_thickn (not used).
530    o pkg/seaice: turbulent flux term specification via run time params.
531      - replace CPP switches with run time switches to facilitate testing
532      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
533                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
534      - added runtime parameter : SEAICEturbFluxFormula
535      - move Mcphee constants to SEAICE_PARAMS.h
536      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
537                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
538                 remove seaice_summary call (moved to seaice_init_fixed)
539      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
540        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
541      - seaice_summary.F : add missing report of read turbulent flux term set up
542                           and SITRACER.
543      - seaice_check.F : check range; inform and stop if retired CPPs are used
544                         (incl. SEAICE_AGE).
545      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
546             CPP switch, same computation as before for the different options.
547      - change results at the truncation level.
548    o pkg/seaice:
549      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
550        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
551        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
552      - update verification/*/input*/data.seaice:
553        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
554        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
555        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
556        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
557    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
558      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
559        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
560        difference in results only due to machine truncation.
561      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
562        MaykutPolySatVap; keep MIN_LWDOWN.
563      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
564      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
565        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
566    o pkg/salt_plume:
567      - isolate saltPlumeFlux array exch into a specific S/R called from
568        do_oceanic_phys.F
569      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
570    o verification:
571      - move untested set-up to MITgcm_contrib/verification_other.
572    o pkg/seaice:
573      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
574    o pkg/seaice:
575      - seaice_solve4temp.F (keeping results unchanged):
576        * add 2 future run-time params to select which saturation vapor pressure
577          formula is used and how post-iteration fluxes are set.
578          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
579        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
580          the linearized expression to stay consistent with tsurf finding.
581      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
582        can be < 0.
583    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
584      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
585        conductive heat flux F_c , and add it explicitly when updating tsurf as
586        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
587        so that now F_ia has a consistent meaning through the entire routine.
588        This causes differences at truncation level: update output of fwd exp.
589        global_ocean.cs32x15.seaice.
590    o pkg/seaice:
591      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
592        of arrays, sign/direction of fluxes; no effect on results.
593      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
594        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
595        note: this should have been done before changing celsius2K default.
596      - to keep results unchanged, add back old value of celsius2K in verification
597        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
598      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
599        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
600        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
601        freezing temp is consistent with value in seaice_growth.F ; this causes
602        differences at machine truncation level: update lab_sea AD output (3/4).
603    o pkg/seaice:
604      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
605        and climsst/sss even when using seaice (to prevent calculation that might
606        use SST on land); does not affect any verification exp.
607      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
608        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
609    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
610      over land (non-legacy code)
611    o vectorize salt_plume package:
612      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
613      - this code computes plumebk everywhere (also over land), thus requires
614        code to avoid divisions by zero and catch the case of kLev=Nr.
615      - efficiency of salt_plume_frac is still sub-optimal
616    o tools (genmake2):
617      - fix makefile NAME specification (option: -makefile NAME) by adding
618        "-f $MAKEFILE" in few places where it was missing including makedepend
619        command (contribution from Paul).
620    
621    checkpoint63i (2012/01/24)
622    o model/src:
623      - add factorized versions of some EOS code to find_rho.F,
624        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
625    o model/src:
626      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
627      - change default celsius2K from 273.16 to 273.15
628      - to keep results unchanged, add back old value of celsius2K in verification
629        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
630         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
631  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
632    to make TAF generate vectorizable code    to make TAF generate vectorizable code
633  o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.  o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.

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