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revision 1.1543 by mmazloff, Tue Dec 6 04:19:24 2011 UTC revision 1.1650 by jmc, Wed Apr 11 18:17:42 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
9       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
10       temporary set to usingZCoords value (to be changed to F when using shelfice).
11     - hydrostatic pressure: implement partial cell near the surface also for
12       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
13       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
14    o pkg/ctrl/ctrl_init.F:
15     - add a formal parameter to s/r ctrl_init_rec to print
16       xx_$(ctrl_valiable)_file for easier debugging
17     - move call of cal_* routines into the if-block where they are really
18       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
19       to specify a startdate
20    o pkg/seaice:
21     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
22       global_ocean.cs32x15/code versions).
23     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
24       verification experiment global_ocean.cs32x15.seaice and update results.
25    o pkg/exf:
26     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
27       (according to useExfYearlyFields).
28    o pkg/cal:
29     - move calendar setting & summary (previously in cal_readparams.F) into new
30       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
31       length of the simulation is set (after SET_PARMS call); This is an attempt
32       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
33     - For safety: keep a record of pkg/cal parameter settings status
34               to allow to STOP if one pkg/cal S/R is called too early.
35     - add a stop in all basic pkg/cal subroutines if called before setting is done.
36     - modify cal_getdate.F: stop when nothing was returned;
37       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
38       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
39    
40    checkpoint63l (2012/04/04)
41    o pkg/bbl:
42      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
43        update global_with_exf output.yearly.txt file.
44    o pkg/cal:
45      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
46      - remove 2 unsused and very short (1 line only) functions ;
47      - remove unsused subroutines from AD-Diff list.
48    o model/src:
49      - start to implement clean wait to stop in initialization S/R (config_check.F,
50         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
51    o folowing PRINT_MESSAGE changes:
52      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
53    o pkg/bbl:
54      - modification so it can work with z*
55      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
56      - global_with_exf/input.yearly verification; changes output.yearly.txt
57    o eesupp/src:
58      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
59        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
60      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
61        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
62      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
63      - when using MPI, always set usingMPI=T ; set default accordingly and stop
64        if not consistent.
65      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
66        argument is zero (in case called within single-thread section).
67    o pkg/fizhi:
68        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
69        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
70    o pkg/exch2:
71      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
72        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
73      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
74        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
75        with bad ones coming from a not-yet-updated halo.
76        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
77    o pkg/frazil:
78        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
79        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
80    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
81    o verification/lab_sea
82      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
83      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
84      * nTimeSteps 3 -> 4
85      * changed reference output accordingly
86    o pkg/ctrl:
87      * fix ctrl_get_gen for xx_sst, xx_sss
88    o pkg/fizhi:
89      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
90        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
91      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
92        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
93        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
94    o pkg/gmredi:
95      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
96    o pkg/fizhi:
97      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
98        (old)aces open64 tuv test.
99    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
100    o pkg/mom_vecinv:
101      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
102        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
103        with non-lin free-surf).
104    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
105      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
106      some compilers (gfortran 4.6.0 on MacOS)
107    o momentum:
108      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
109        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
110        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
111    
112    checkpoint63k (2012/03/17)
113    o model/src:
114       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
115         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
116       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
117         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
118    o model/src: solve_*diagonal.F
119       - replace division with multiplication by inverse (similar to original version)
120         update output of AD exp. global_ocean.90x40x15.
121       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
122         to enable the use of the vectorized & differentiable solve_tridiagonal.F
123       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
124         vertical advection (to get solve_tridiagonal tested in AD mode).
125    o pkg/seaice: ECCO-CLIVAR merge:
126      1. seaice AREA relaxation
127         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
128         * runtime flag: SEAICE_tauAreaObsRelax
129      2. modified global mean cost imbalance code: CPP option
130          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
131    o another iteration on solve_*diagonal.F
132       Make choices independent of AUTODIFF
133       Default will be the adjoinable vectorized version.
134       Alternative choices are:
135       * non-adjoinable original version with low memory footprint:
136         #define SOLVE_DIAGONAL_LOWMEMORY
137       * still adjoinable but does not vectorize (k as inner-most loop):
138         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
139    o testreport
140     - add option to use a home made wrapper around "make"
141     - remove MITGCM_IEEE env. variable (no longer active)
142    o pkg/shelfice
143     - improve computation of friction velocity for velocity dependent
144       exchange coefficients: include velocities into SHELFICEBoundaryLayer
145       block to average velocities vertically
146     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
147    o Modify diagonal solvers, now three versions (upon request):
148      #ifndef SOLVE_DIAGONAL_AUTODIFF
149        1. default version (dating back a while ago)
150      #else /* def SOLVE_DIAGONAL_AUTODIFF */
151      # ifdef SOLVE_DIAGONAL_KINNER
152        2. adjoinable version with k-innermost loop (G. Forget)
153      # else
154        3. adjoinable vectorized version of 2.
155      # endif
156      #endif /* SOLVE_DIAGONAL_AUTODIFF */
157      All flags are currently set within routines, but could/should be moved to CPP-options.
158      Array bounds for 1. are as before, for 2.,3. cover the entire domain
159      (could be changed for 1. too).
160    o verification/lab_sea (fwd):
161      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
162        use 7 categories (except hb87), new solve4temp params (except salt_plume),
163        constant salinity (=4) or variable salinity (salt_plume) done through
164        SItracer.
165    o pkg/seaice:
166      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
167      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
168         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
169        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
170        SEAICE_freeze got retired) but already better than previously with
171        SEAICE_freeze=123456.7 deg.C;
172      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
173        (safer multi-threaded setting); always set SEAICEuseEVP;
174      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
175        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
176        stop if multiple specifications for the same coeff; make sure default
177        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
178    o pkg/obcs:
179      - allow to switch to upwind 1rst order advection scheme for the advective
180        flux computation at the open-boundary; disabled for adjoint built.
181    o pkg/ptracers:
182      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
183      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
184      - add parameter to decide when to start a tracer; use internal flag to
185        know which tracer to step-forward; switch this internal flag at the top
186        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
187        for adjoint built.
188    o pkg/seaice:
189      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
190      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
191      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
192    o pkg/ecco:
193      - fix writing of output file DiagnosCost_ClimSalt/Theta
194        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
195    o pkg/seaice:
196      - add missing initialisation of COR_ICE array in dynsolver.F
197      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
198        compiled either way, and is tested in all exps (multidim was only tested
199        in lab_sea ad before).
200      - cosmetic change to prepare for future addition of ITD. no change to results.
201        no defaults change.
202      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
203      - by lack of adequate verification experiments, I further used custom versions
204        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
205        should be correct.
206      - avoid recomputations in ad.
207    o array initialisation in adjoint mode:
208      1) pkg/mom_common/mom_calc_ke.F:
209        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
210        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
211        part this initialisation is gone, resulting in Floating Point Exception
212        (caught by open64 compiler with debug option).
213      2) model/src/convective_weights.F
214        set output convectCount over the full array range (instead of doing
215        an update): this fix a similar issue when called within recomputation (adjoint)
216        which could by-pass the initialisation (normally done in the caller S/R).
217    o pkg/seaice:
218      - final version of turbulent flux params, as agreed at MIT ice meet:
219           SEAICE_mcPheePiston (default is ~ 0.000875)
220           SEAICE_mcPheeTaper (default is 0.)
221           SEAICE_frazilFrac (defualt is 1.)
222           SEAICE_mcPheeStepFunc (default is false)
223      - changes results at trunction error level
224      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
225    o added pkg/frazil:
226      - see frazil_description.tex for details
227      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
228    o pkg/shelfice/shelfice_thermodynamics.F
229      - fix exponents for velocity dependent exchange coefficients: change
230        from 2/3(=0) to 0.66666666666666667
231      - move computation of velocity dependent exchange coefficients into
232        separate loop, so that it applies to both thermodynamics
233      - move some divisions by constants out of loops
234    
235    checkpoint63j (2012/02/16)
236    o pkg/seaice:
237      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
238      - SItracer:  added run time params, and allow coupling to ocn salinity.
239    o pkg/seaice: remove (almost) all divisions by constants within loops
240      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
241      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
242      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
243      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
244    o pkg/seaice :
245      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
246        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
247      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
248      - add permanent SItflux diag that corresponds to TFLUX but includes
249        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
250      - allow activation/testing of a fix for suspected missing term in
251        ocn-ice heat budget (to be confirmed). To test this, you want to
252        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
253        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
254      - no change in results, fwd or ad.
255    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
256      - switch to variable freezing point.
257           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
258      - bug fix : the sublimation term that was missing is now activated.
259           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
260      - bug fix : flooding sign term for SIsal0.NE.0.
261           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
262    o pkg/seaice:
263      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
264        is now the default, and the old default constant freezing point is recovered
265        with SEAICE_tempFrz0    = -1.96,
266             SEAICE_dTempFrz_dS = 0.,
267      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
268      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
269      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
270        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
271      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
272        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
273      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
274        seaice_growth r149 for legacy branch (no results change).
275      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
276        from I. Fenty).
277      - results did not change except for global_ocean.cs32x15, mostly due to the
278        switch to variable freezing point (see above item for detail).
279    o pkg/thsice:
280      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
281        seawater freezing in thsice_calc_thickn (not used).
282    o pkg/seaice: turbulent flux term specification via run time params.
283      - replace CPP switches with run time switches to facilitate testing
284      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
285                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
286      - added runtime parameter : SEAICEturbFluxFormula
287      - move Mcphee constants to SEAICE_PARAMS.h
288      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
289                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
290                 remove seaice_summary call (moved to seaice_init_fixed)
291      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
292        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
293      - seaice_summary.F : add missing report of read turbulent flux term set up
294                           and SITRACER.
295      - seaice_check.F : check range; inform and stop if retired CPPs are used
296                         (incl. SEAICE_AGE).
297      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
298             CPP switch, same computation as before for the different options.
299      - change results at the truncation level.
300    o pkg/seaice:
301      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
302        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
303        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
304      - update verification/*/input*/data.seaice:
305        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
306        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
307        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
308        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
309    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
310      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
311        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
312        difference in results only due to machine truncation.
313      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
314        MaykutPolySatVap; keep MIN_LWDOWN.
315      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
316      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
317        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
318    o pkg/salt_plume:
319      - isolate saltPlumeFlux array exch into a specific S/R called from
320        do_oceanic_phys.F
321      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
322    o verification:
323      - move untested set-up to MITgcm_contrib/verification_other.
324    o pkg/seaice:
325      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
326    o pkg/seaice:
327      - seaice_solve4temp.F (keeping results unchanged):
328        * add 2 future run-time params to select which saturation vapor pressure
329          formula is used and how post-iteration fluxes are set.
330          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
331        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
332          the linearized expression to stay consistent with tsurf finding.
333      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
334        can be < 0.
335    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
336      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
337        conductive heat flux F_c , and add it explicitly when updating tsurf as
338        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
339        so that now F_ia has a consistent meaning through the entire routine.
340        This causes differences at truncation level: update output of fwd exp.
341        global_ocean.cs32x15.seaice.
342    o pkg/seaice:
343      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
344        of arrays, sign/direction of fluxes; no effect on results.
345      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
346        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
347        note: this should have been done before changing celsius2K default.
348      - to keep results unchanged, add back old value of celsius2K in verification
349        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
350      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
351        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
352        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
353        freezing temp is consistent with value in seaice_growth.F ; this causes
354        differences at machine truncation level: update lab_sea AD output (3/4).
355    o pkg/seaice:
356      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
357        and climsst/sss even when using seaice (to prevent calculation that might
358        use SST on land); does not affect any verification exp.
359      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
360        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
361    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
362      over land (non-legacy code)
363    o vectorize salt_plume package:
364      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
365      - this code computes plumebk everywhere (also over land), thus requires
366        code to avoid divisions by zero and catch the case of kLev=Nr.
367      - efficiency of salt_plume_frac is still sub-optimal
368    o tools (genmake2):
369      - fix makefile NAME specification (option: -makefile NAME) by adding
370        "-f $MAKEFILE" in few places where it was missing including makedepend
371        command (contribution from Paul).
372    
373    checkpoint63i (2012/01/24)
374    o model/src:
375      - add factorized versions of some EOS code to find_rho.F,
376        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
377    o model/src:
378      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
379      - change default celsius2K from 273.16 to 273.15
380      - to keep results unchanged, add back old value of celsius2K in verification
381        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
382         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
383    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
384      to make TAF generate vectorizable code
385    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
386       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
387       have flags that do this more efficiently.
388    o pkg/diagnostics/diagstats_calc.F
389      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
390    o pkg/obcs (with exch2):
391      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
392        and remove code (in obcs_readparms.F) which was based on EXCH of indices
393        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
394    o pkg/exf and seaice exp:
395      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
396        so that switching off area & heff advection flags does not affect results.
397      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
398      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
399        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
400        results of verification experiments: 1D_ocean_ice_column(fwd),
401        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
402        and offline_exf_seaice (all 4).
403    o pkg/seaice:
404      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
405        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
406      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
407        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
408        not multi-dim advection;
409      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
410        SHORTWAVE_HEATING #undef.
411    o optim: make Makefile more robust (?)
412    o pkg/obcs:
413      * fix treatment of obcs_read_pickup for TAF
414    o pkg/shelfice:
415      * add missing initialisation of num_shifwflx
416      * new adjoint verification exp. for isomip
417      * change Prandtl and Schmidt numbers from generic formulations
418        (in terms of model diffus. and visc.) to separate runtime
419        parameters, with Holland and Jenkins (1999) default values.
420    o pkg/exf (interpolation):
421      - extended input field (2 rows) near the N & S poles:
422        * fill in with the symetric value (when even Nb of data in longitude)
423        * add average value at the poles only for scalar quantities ; for vector
424          component interpolation, skip the averaging and keep duplicated values,
425          unless the 2 components have same location (uvInterp=T) in which case
426          interpolate the 2 components together using S/R EXF_INTERP_UV.
427      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
428        together: this allows to account properly for local orientation when
429        averaging at N & S pole.
430      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
431        exf-interpolation near N & S poles. Undef by default.
432      - add debug check/print on 1rst iter if debugLevel >=2.
433    o pkg/exf:
434      - change masking flags definition (no longer "parameter"), put them in
435        common block and set them in S/R EXF_INIT_FIXED.
436      - change recognized masking flag from s,u,v to c,w,s since the mask
437        to use (maskC,W,S) depends on position on model grid and has little to
438        do with scalar/vector difference; fix masking if using P-coordinates.
439      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
440        and update results of exp. global_with_exf (x2).
441      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
442    o pkg/obcs
443      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
444    o pkg/exf (interpolation):
445      - assume periodicity in X only if input field cover full longitude range.
446      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
447        and should vectorise).
448      - fix input lat of the 2 added row (in case we provide N.pole data).
449    
450    checkpoint63h (2011/12/30)
451    o pkg/seaice:
452      - change declaration of UVM from _RL to _RS in order to get B-grid
453        uIce,vIce monitor when _RS = real*4
454    o pkg/offline:
455      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
456      - compute vertical velocity if not read from file (switch on exactConserv
457        & staggerTimeStep);
458      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
459    o verification:
460      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
461        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
462        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
463      - update output of exp. global_ocean.cs32x15.viscA4 after changing
464        grid-file angles (used here for coriolis-3d);
465      - remove (or gzip) few files not needed to run fizhi-cs experiments.
466    o pkg/exf (vector interpolation):
467      - rotate vector component toward local grid-axis orientation using grid-angles
468        (stored in GRID.h) instead of locally computed rotation angle; keep old code
469        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
470    o pkg/seaice:
471      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
472        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
473    o pkg/PKG_OPTIONS.h files:
474      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
475        outside of the #ifdef ALLOW_THISPKG / #endif block.
476      - update verification/*/code/PKG_OPTIONS.h files.
477    o add a verification experiment (offline_exf_seaice/input.seaice) that test
478      the B-grid LSOR solver
479    o pkg/seaice: sort out emissivity and long wave radiation step 2:
480      - add emissivity for snow and ice as new run-time parameters
481        (unfortunately) that default to the corresponding exf values; this
482        changes results in most verification experiments so that for backward
483        compatibility these parameter have to be set explicitly to inconsistent
484        values (ugly);
485      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
486        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
487        until we agree how to handle this bug properly
488    o pkg/exf (interpolation):
489      - add a set of run-time param ({inputfield}_interpMethod), one for
490        each interpolated input field, to select the interpolation method
491        with a value of zero switching off the interpolation;
492      - print interpolation parameters to standard output;
493      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
494        (to use instead runoff_interpMethod=0 in data.exf).
495      - simplify default setting of interpolation parameters (for all fields,
496        set position to match model grid cell-center position, leading to trivial
497        interpolation in case of regular Lat-Lon grid) and fix for the case of
498        non-uniform delY.
499    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
500       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
501       this factor is absolutely required, because the lw exitance (= out-going
502       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
503       where the reflectivity rho = 1-emissivity for conservation reasons. Once
504       this is established, we can remove the CPP-Flag (if we want to).
505    o pkg/seaice:
506      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
507        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
508      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
509        what the name implies (and not emissivity*BoltzmannConstant), this means
510        the old default value of 5.5e-8 now means
511        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
512        S/R exf_readparms
513      - FV-discretization of the B-grid LSOR solver, turn on with
514        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
515        of the calling routine dynsolver, so that B and C-grid code look a
516        little more alike.
517      - fix index bugs in ostres.F (B-grid code)
518    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
519    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
520      default for SEAICE_emissivity, if useEXF; requires setting a wrong
521      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
522      backward compatiblity
523    o model/src: use sigmaR in calc_ivdc
524    
525    checkpoint63g (2011/12/16)
526    o pkg/seaice/seaice_growth.F:
527      fix heat conservation of the coupled ocean-seaice system.
528      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
529      solid vs liquid water treatment is resolved via QNET.
530    o pkg/seaice/seaice_growth.F:
531      add missing term for sublimation in saltFlux, which was breaking conservation.
532    o pkg/seaice/seaice_model.F:
533      Remove this patholigical case treatment in evolution branch,
534      where it is un-necessary and breaks conservation.
535      Update global_ocean.cs32x15/results accordingly for
536      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
537    o model/src:
538      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
539      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
540    o pkg/obcs:
541      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
542      tendency for temperature and salinity that is then applied to update
543      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
544      horizontal advection and diffusion contributions on the boundary (in
545      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
546      removing the mask in S/R timestep_tracer. The advantage of this approach is
547      that the updated tracer values include contributions from the surface
548      forcing and vertical diffusion.
549      This modification changes exp4.stevens because of vertical diffusion.
550    o model/src:
551      change non-curvilinear grid setting to also work with exch2 + blank tiles:
552      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
553        face dimensions.
554      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
555        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
556        and INI_SPHERICAL_POLAR_GRID.
557      change test-experiment global_ocean.90x40x15:
558      - split the domain in many more tiles (9x4 tiles of 10x10 each);
559      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
560      - update results of both test (std & dwnslp).
561    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
562       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
563    o model/src:
564      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
565        and fix initialisation when using sigma-coords.
566    o model/src:
567     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
568       to their current value at the beginning of forward_step.F": add a new run-time
569       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
570     - set doResetHFactors=T in the following test exp:
571        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
572        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
573        and tutorial_global_oce_in_p (nonLinFS in p)
574  o pkg/ecco  o pkg/ecco
575    - added IES cost term    - added IES cost term
576  o verification/advect_xz  o verification/advect_xz
577    - scale down the depth by 1/100 (from 200 km to just 2.km)    - scale down the depth by 1/100 (from 200 km to just 2.km)
578    - add secondary test using divergent flow, r-star and implicit vertical advection.    - add secondary test using divergent flow, r-star and implicit vertical advection.
579      - add note (check_conserve_TS.txt) and matlab script to check global
580        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
581  o pkg/rbcs:  o pkg/rbcs:
582    - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).    - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
583  o pkg/obcs (Stevens BCs):  o pkg/obcs (Stevens BCs):
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