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revision 1.1557 by jmc, Wed Dec 21 17:31:53 2011 UTC revision 1.1645 by jmc, Wed Apr 4 16:18:50 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63l (2012/04/04)
8    o pkg/bbl:
9      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
10        update global_with_exf output.yearly.txt file.
11    o pkg/cal:
12      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
13      - remove 2 unsused and very short (1 line only) functions ;
14      - remove unsused subroutines from AD-Diff list.
15    o model/src:
16      - start to implement clean wait to stop in initialization S/R (config_check.F,
17         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
18    o folowing PRINT_MESSAGE changes:
19      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
20    o pkg/bbl:
21      - modification so it can work with z*
22      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
23      - global_with_exf/input.yearly verification; changes output.yearly.txt
24    o eesupp/src:
25      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
26        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
27      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
28        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
29      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
30      - when using MPI, always set usingMPI=T ; set default accordingly and stop
31        if not consistent.
32      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
33        argument is zero (in case called within single-thread section).
34    o pkg/fizhi:
35        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
36        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
37    o pkg/exch2:
38      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
39        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
40      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
41        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
42        with bad ones coming from a not-yet-updated halo.
43        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
44    o pkg/frazil:
45        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
46        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
47    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
48    o verification/lab_sea
49      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
50      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
51      * nTimeSteps 3 -> 4
52      * changed reference output accordingly
53    o pkg/ctrl:
54      * fix ctrl_get_gen for xx_sst, xx_sss
55    o pkg/fizhi:
56      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
57        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
58      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
59        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
60        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
61    o pkg/gmredi:
62      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
63    o pkg/fizhi:
64      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
65        (old)aces open64 tuv test.
66    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
67    o pkg/mom_vecinv:
68      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
69        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
70        with non-lin free-surf).
71    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
72      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
73      some compilers (gfortran 4.6.0 on MacOS)
74    o momentum:
75      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
76        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
77        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
78    
79    checkpoint63k (2012/03/17)
80    o model/src:
81       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
82         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
83       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
84         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
85    o model/src: solve_*diagonal.F
86       - replace division with multiplication by inverse (similar to original version)
87         update output of AD exp. global_ocean.90x40x15.
88       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
89         to enable the use of the vectorized & differentiable solve_tridiagonal.F
90       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
91         vertical advection (to get solve_tridiagonal tested in AD mode).
92    o pkg/seaice: ECCO-CLIVAR merge:
93      1. seaice AREA relaxation
94         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
95         * runtime flag: SEAICE_tauAreaObsRelax
96      2. modified global mean cost imbalance code: CPP option
97          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
98    o another iteration on solve_*diagonal.F
99       Make choices independent of AUTODIFF
100       Default will be the adjoinable vectorized version.
101       Alternative choices are:
102       * non-adjoinable original version with low memory footprint:
103         #define SOLVE_DIAGONAL_LOWMEMORY
104       * still adjoinable but does not vectorize (k as inner-most loop):
105         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
106    o testreport
107     - add option to use a home made wrapper around "make"
108     - remove MITGCM_IEEE env. variable (no longer active)
109    o pkg/shelfice
110     - improve computation of friction velocity for velocity dependent
111       exchange coefficients: include velocities into SHELFICEBoundaryLayer
112       block to average velocities vertically
113     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
114    o Modify diagonal solvers, now three versions (upon request):
115      #ifndef SOLVE_DIAGONAL_AUTODIFF
116        1. default version (dating back a while ago)
117      #else /* def SOLVE_DIAGONAL_AUTODIFF */
118      # ifdef SOLVE_DIAGONAL_KINNER
119        2. adjoinable version with k-innermost loop (G. Forget)
120      # else
121        3. adjoinable vectorized version of 2.
122      # endif
123      #endif /* SOLVE_DIAGONAL_AUTODIFF */
124      All flags are currently set within routines, but could/should be moved to CPP-options.
125      Array bounds for 1. are as before, for 2.,3. cover the entire domain
126      (could be changed for 1. too).
127    o verification/lab_sea (fwd):
128      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
129        use 7 categories (except hb87), new solve4temp params (except salt_plume),
130        constant salinity (=4) or variable salinity (salt_plume) done through
131        SItracer.
132    o pkg/seaice:
133      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
134      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
135         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
136        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
137        SEAICE_freeze got retired) but already better than previously with
138        SEAICE_freeze=123456.7 deg.C;
139      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
140        (safer multi-threaded setting); always set SEAICEuseEVP;
141      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
142        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
143        stop if multiple specifications for the same coeff; make sure default
144        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
145    o pkg/obcs:
146      - allow to switch to upwind 1rst order advection scheme for the advective
147        flux computation at the open-boundary; disabled for adjoint built.
148    o pkg/ptracers:
149      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
150      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
151      - add parameter to decide when to start a tracer; use internal flag to
152        know which tracer to step-forward; switch this internal flag at the top
153        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
154        for adjoint built.
155    o pkg/seaice:
156      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
157      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
158      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
159    o pkg/ecco:
160      - fix writing of output file DiagnosCost_ClimSalt/Theta
161        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
162    o pkg/seaice:
163      - add missing initialisation of COR_ICE array in dynsolver.F
164      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
165        compiled either way, and is tested in all exps (multidim was only tested
166        in lab_sea ad before).
167      - cosmetic change to prepare for future addition of ITD. no change to results.
168        no defaults change.
169      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
170      - by lack of adequate verification experiments, I further used custom versions
171        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
172        should be correct.
173      - avoid recomputations in ad.
174    o array initialisation in adjoint mode:
175      1) pkg/mom_common/mom_calc_ke.F:
176        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
177        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
178        part this initialisation is gone, resulting in Floating Point Exception
179        (caught by open64 compiler with debug option).
180      2) model/src/convective_weights.F
181        set output convectCount over the full array range (instead of doing
182        an update): this fix a similar issue when called within recomputation (adjoint)
183        which could by-pass the initialisation (normally done in the caller S/R).
184    o pkg/seaice:
185      - final version of turbulent flux params, as agreed at MIT ice meet:
186           SEAICE_mcPheePiston (default is ~ 0.000875)
187           SEAICE_mcPheeTaper (default is 0.)
188           SEAICE_frazilFrac (defualt is 1.)
189           SEAICE_mcPheeStepFunc (default is false)
190      - changes results at trunction error level
191      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
192    o added pkg/frazil:
193      - see frazil_description.tex for details
194      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
195    o pkg/shelfice/shelfice_thermodynamics.F
196      - fix exponents for velocity dependent exchange coefficients: change
197        from 2/3(=0) to 0.66666666666666667
198      - move computation of velocity dependent exchange coefficients into
199        separate loop, so that it applies to both thermodynamics
200      - move some divisions by constants out of loops
201    
202    checkpoint63j (2012/02/16)
203    o pkg/seaice:
204      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
205      - SItracer:  added run time params, and allow coupling to ocn salinity.
206    o pkg/seaice: remove (almost) all divisions by constants within loops
207      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
208      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
209      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
210      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
211    o pkg/seaice :
212      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
213        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
214      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
215      - add permanent SItflux diag that corresponds to TFLUX but includes
216        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
217      - allow activation/testing of a fix for suspected missing term in
218        ocn-ice heat budget (to be confirmed). To test this, you want to
219        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
220        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
221      - no change in results, fwd or ad.
222    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
223      - switch to variable freezing point.
224           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
225      - bug fix : the sublimation term that was missing is now activated.
226           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
227      - bug fix : flooding sign term for SIsal0.NE.0.
228           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
229    o pkg/seaice:
230      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
231        is now the default, and the old default constant freezing point is recovered
232        with SEAICE_tempFrz0    = -1.96,
233             SEAICE_dTempFrz_dS = 0.,
234      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
235      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
236      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
237        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
238      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
239        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
240      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
241        seaice_growth r149 for legacy branch (no results change).
242      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
243        from I. Fenty).
244      - results did not change except for global_ocean.cs32x15, mostly due to the
245        switch to variable freezing point (see above item for detail).
246    o pkg/thsice:
247      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
248        seawater freezing in thsice_calc_thickn (not used).
249    o pkg/seaice: turbulent flux term specification via run time params.
250      - replace CPP switches with run time switches to facilitate testing
251      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
252                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
253      - added runtime parameter : SEAICEturbFluxFormula
254      - move Mcphee constants to SEAICE_PARAMS.h
255      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
256                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
257                 remove seaice_summary call (moved to seaice_init_fixed)
258      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
259        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
260      - seaice_summary.F : add missing report of read turbulent flux term set up
261                           and SITRACER.
262      - seaice_check.F : check range; inform and stop if retired CPPs are used
263                         (incl. SEAICE_AGE).
264      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
265             CPP switch, same computation as before for the different options.
266      - change results at the truncation level.
267    o pkg/seaice:
268      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
269        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
270        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
271      - update verification/*/input*/data.seaice:
272        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
273        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
274        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
275        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
276    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
277      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
278        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
279        difference in results only due to machine truncation.
280      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
281        MaykutPolySatVap; keep MIN_LWDOWN.
282      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
283      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
284        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
285    o pkg/salt_plume:
286      - isolate saltPlumeFlux array exch into a specific S/R called from
287        do_oceanic_phys.F
288      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
289    o verification:
290      - move untested set-up to MITgcm_contrib/verification_other.
291    o pkg/seaice:
292      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
293    o pkg/seaice:
294      - seaice_solve4temp.F (keeping results unchanged):
295        * add 2 future run-time params to select which saturation vapor pressure
296          formula is used and how post-iteration fluxes are set.
297          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
298        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
299          the linearized expression to stay consistent with tsurf finding.
300      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
301        can be < 0.
302    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
303      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
304        conductive heat flux F_c , and add it explicitly when updating tsurf as
305        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
306        so that now F_ia has a consistent meaning through the entire routine.
307        This causes differences at truncation level: update output of fwd exp.
308        global_ocean.cs32x15.seaice.
309    o pkg/seaice:
310      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
311        of arrays, sign/direction of fluxes; no effect on results.
312      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
313        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
314        note: this should have been done before changing celsius2K default.
315      - to keep results unchanged, add back old value of celsius2K in verification
316        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
317      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
318        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
319        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
320        freezing temp is consistent with value in seaice_growth.F ; this causes
321        differences at machine truncation level: update lab_sea AD output (3/4).
322    o pkg/seaice:
323      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
324        and climsst/sss even when using seaice (to prevent calculation that might
325        use SST on land); does not affect any verification exp.
326      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
327        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
328    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
329      over land (non-legacy code)
330    o vectorize salt_plume package:
331      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
332      - this code computes plumebk everywhere (also over land), thus requires
333        code to avoid divisions by zero and catch the case of kLev=Nr.
334      - efficiency of salt_plume_frac is still sub-optimal
335    o tools (genmake2):
336      - fix makefile NAME specification (option: -makefile NAME) by adding
337        "-f $MAKEFILE" in few places where it was missing including makedepend
338        command (contribution from Paul).
339    
340    checkpoint63i (2012/01/24)
341    o model/src:
342      - add factorized versions of some EOS code to find_rho.F,
343        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
344    o model/src:
345      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
346      - change default celsius2K from 273.16 to 273.15
347      - to keep results unchanged, add back old value of celsius2K in verification
348        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
349         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
350    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
351      to make TAF generate vectorizable code
352    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
353       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
354       have flags that do this more efficiently.
355    o pkg/diagnostics/diagstats_calc.F
356      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
357    o pkg/obcs (with exch2):
358      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
359        and remove code (in obcs_readparms.F) which was based on EXCH of indices
360        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
361    o pkg/exf and seaice exp:
362      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
363        so that switching off area & heff advection flags does not affect results.
364      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
365      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
366        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
367        results of verification experiments: 1D_ocean_ice_column(fwd),
368        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
369        and offline_exf_seaice (all 4).
370    o pkg/seaice:
371      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
372        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
373      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
374        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
375        not multi-dim advection;
376      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
377        SHORTWAVE_HEATING #undef.
378    o optim: make Makefile more robust (?)
379    o pkg/obcs:
380      * fix treatment of obcs_read_pickup for TAF
381    o pkg/shelfice:
382      * add missing initialisation of num_shifwflx
383      * new adjoint verification exp. for isomip
384      * change Prandtl and Schmidt numbers from generic formulations
385        (in terms of model diffus. and visc.) to separate runtime
386        parameters, with Holland and Jenkins (1999) default values.
387    o pkg/exf (interpolation):
388      - extended input field (2 rows) near the N & S poles:
389        * fill in with the symetric value (when even Nb of data in longitude)
390        * add average value at the poles only for scalar quantities ; for vector
391          component interpolation, skip the averaging and keep duplicated values,
392          unless the 2 components have same location (uvInterp=T) in which case
393          interpolate the 2 components together using S/R EXF_INTERP_UV.
394      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
395        together: this allows to account properly for local orientation when
396        averaging at N & S pole.
397      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
398        exf-interpolation near N & S poles. Undef by default.
399      - add debug check/print on 1rst iter if debugLevel >=2.
400    o pkg/exf:
401      - change masking flags definition (no longer "parameter"), put them in
402        common block and set them in S/R EXF_INIT_FIXED.
403      - change recognized masking flag from s,u,v to c,w,s since the mask
404        to use (maskC,W,S) depends on position on model grid and has little to
405        do with scalar/vector difference; fix masking if using P-coordinates.
406      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
407        and update results of exp. global_with_exf (x2).
408      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
409    o pkg/obcs
410      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
411    o pkg/exf (interpolation):
412      - assume periodicity in X only if input field cover full longitude range.
413      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
414        and should vectorise).
415      - fix input lat of the 2 added row (in case we provide N.pole data).
416    
417    checkpoint63h (2011/12/30)
418    o pkg/seaice:
419      - change declaration of UVM from _RL to _RS in order to get B-grid
420        uIce,vIce monitor when _RS = real*4
421    o pkg/offline:
422      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
423      - compute vertical velocity if not read from file (switch on exactConserv
424        & staggerTimeStep);
425      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
426    o verification:
427      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
428        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
429        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
430      - update output of exp. global_ocean.cs32x15.viscA4 after changing
431        grid-file angles (used here for coriolis-3d);
432      - remove (or gzip) few files not needed to run fizhi-cs experiments.
433    o pkg/exf (vector interpolation):
434      - rotate vector component toward local grid-axis orientation using grid-angles
435        (stored in GRID.h) instead of locally computed rotation angle; keep old code
436        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
437    o pkg/seaice:
438      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
439        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
440    o pkg/PKG_OPTIONS.h files:
441      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
442        outside of the #ifdef ALLOW_THISPKG / #endif block.
443      - update verification/*/code/PKG_OPTIONS.h files.
444    o add a verification experiment (offline_exf_seaice/input.seaice) that test
445      the B-grid LSOR solver
446    o pkg/seaice: sort out emissivity and long wave radiation step 2:
447      - add emissivity for snow and ice as new run-time parameters
448        (unfortunately) that default to the corresponding exf values; this
449        changes results in most verification experiments so that for backward
450        compatibility these parameter have to be set explicitly to inconsistent
451        values (ugly);
452      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
453        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
454        until we agree how to handle this bug properly
455  o pkg/exf (interpolation):  o pkg/exf (interpolation):
456    - add a set of run-time param ({inputfield}_interpMethod), one for    - add a set of run-time param ({inputfield}_interpMethod), one for
457      each interpolated input field, to select the interpolation method      each interpolated input field, to select the interpolation method
# Line 11  o pkg/exf (interpolation): Line 459  o pkg/exf (interpolation):
459    - print interpolation parameters to standard output;    - print interpolation parameters to standard output;
460    - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined    - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
461      (to use instead runoff_interpMethod=0 in data.exf).      (to use instead runoff_interpMethod=0 in data.exf).
462      - simplify default setting of interpolation parameters (for all fields,
463        set position to match model grid cell-center position, leading to trivial
464        interpolation in case of regular Lat-Lon grid) and fix for the case of
465        non-uniform delY.
466  o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for  o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
467     within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.     within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
468     this factor is absolutely required, because the lw exitance (= out-going     this factor is absolutely required, because the lw exitance (= out-going
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