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revision 1.1538 by mlosch, Tue Nov 29 17:43:32 2011 UTC revision 1.1639 by jmc, Fri Mar 30 18:48:32 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 eesupp/src:
8      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
9        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
10      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
11        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
12      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
13      - when using MPI, always set usingMPI=T ; set default accordingly and stop
14        if not consistent.
15      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
16        argument is zero (in case called within single-thread section).
17    o pkg/fizhi:
18        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
19        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
20    o pkg/exch2:
21      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
22        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
23      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
24        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
25        with bad ones coming from a not-yet-updated halo.
26        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
27    o pkg/frazil:
28        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
29        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
30    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
31    o verification/lab_sea
32      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
33      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
34      * nTimeSteps 3 -> 4
35      * changed reference output accordingly
36    o pkg/ctrl:
37      * fix ctrl_get_gen for xx_sst, xx_sss
38    o pkg/fizhi:
39      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
40        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
41      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
42        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
43        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
44    o pkg/gmredi:
45      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
46    o pkg/fizhi:
47      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
48        (old)aces open64 tuv test.
49    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
50    o pkg/mom_vecinv:
51      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
52        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
53        with non-lin free-surf).
54    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
55      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
56      some compilers (gfortran 4.6.0 on MacOS)
57    o momentum:
58      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
59        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
60        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
61    
62    checkpoint63k (2012/03/17)
63    o model/src:
64       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
65         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
66       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
67         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
68    o model/src: solve_*diagonal.F
69       - replace division with multiplication by inverse (similar to original version)
70         update output of AD exp. global_ocean.90x40x15.
71       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
72         to enable the use of the vectorized & differentiable solve_tridiagonal.F
73       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
74         vertical advection (to get solve_tridiagonal tested in AD mode).
75    o pkg/seaice: ECCO-CLIVAR merge:
76      1. seaice AREA relaxation
77         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
78         * runtime flag: SEAICE_tauAreaObsRelax
79      2. modified global mean cost imbalance code: CPP option
80          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
81    o another iteration on solve_*diagonal.F
82       Make choices independent of AUTODIFF
83       Default will be the adjoinable vectorized version.
84       Alternative choices are:
85       * non-adjoinable original version with low memory footprint:
86         #define SOLVE_DIAGONAL_LOWMEMORY
87       * still adjoinable but does not vectorize (k as inner-most loop):
88         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
89    o testreport
90     - add option to use a home made wrapper around "make"
91     - remove MITGCM_IEEE env. variable (no longer active)
92    o pkg/shelfice
93     - improve computation of friction velocity for velocity dependent
94       exchange coefficients: include velocities into SHELFICEBoundaryLayer
95       block to average velocities vertically
96     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
97    o Modify diagonal solvers, now three versions (upon request):
98      #ifndef SOLVE_DIAGONAL_AUTODIFF
99        1. default version (dating back a while ago)
100      #else /* def SOLVE_DIAGONAL_AUTODIFF */
101      # ifdef SOLVE_DIAGONAL_KINNER
102        2. adjoinable version with k-innermost loop (G. Forget)
103      # else
104        3. adjoinable vectorized version of 2.
105      # endif
106      #endif /* SOLVE_DIAGONAL_AUTODIFF */
107      All flags are currently set within routines, but could/should be moved to CPP-options.
108      Array bounds for 1. are as before, for 2.,3. cover the entire domain
109      (could be changed for 1. too).
110    o verification/lab_sea (fwd):
111      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
112        use 7 categories (except hb87), new solve4temp params (except salt_plume),
113        constant salinity (=4) or variable salinity (salt_plume) done through
114        SItracer.
115    o pkg/seaice:
116      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
117      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
118         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
119        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
120        SEAICE_freeze got retired) but already better than previously with
121        SEAICE_freeze=123456.7 deg.C;
122      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
123        (safer multi-threaded setting); always set SEAICEuseEVP;
124      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
125        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
126        stop if multiple specifications for the same coeff; make sure default
127        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
128    o pkg/obcs:
129      - allow to switch to upwind 1rst order advection scheme for the advective
130        flux computation at the open-boundary; disabled for adjoint built.
131    o pkg/ptracers:
132      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
133      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
134      - add parameter to decide when to start a tracer; use internal flag to
135        know which tracer to step-forward; switch this internal flag at the top
136        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
137        for adjoint built.
138    o pkg/seaice:
139      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
140      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
141      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
142    o pkg/ecco:
143      - fix writing of output file DiagnosCost_ClimSalt/Theta
144        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
145    o pkg/seaice:
146      - add missing initialisation of COR_ICE array in dynsolver.F
147      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
148        compiled either way, and is tested in all exps (multidim was only tested
149        in lab_sea ad before).
150      - cosmetic change to prepare for future addition of ITD. no change to results.
151        no defaults change.
152      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
153      - by lack of adequate verification experiments, I further used custom versions
154        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
155        should be correct.
156      - avoid recomputations in ad.
157    o array initialisation in adjoint mode:
158      1) pkg/mom_common/mom_calc_ke.F:
159        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
160        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
161        part this initialisation is gone, resulting in Floating Point Exception
162        (caught by open64 compiler with debug option).
163      2) model/src/convective_weights.F
164        set output convectCount over the full array range (instead of doing
165        an update): this fix a similar issue when called within recomputation (adjoint)
166        which could by-pass the initialisation (normally done in the caller S/R).
167    o pkg/seaice:
168      - final version of turbulent flux params, as agreed at MIT ice meet:
169           SEAICE_mcPheePiston (default is ~ 0.000875)
170           SEAICE_mcPheeTaper (default is 0.)
171           SEAICE_frazilFrac (defualt is 1.)
172           SEAICE_mcPheeStepFunc (default is false)
173      - changes results at trunction error level
174      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
175    o added pkg/frazil:
176      - see frazil_description.tex for details
177      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
178    o pkg/shelfice/shelfice_thermodynamics.F
179      - fix exponents for velocity dependent exchange coefficients: change
180        from 2/3(=0) to 0.66666666666666667
181      - move computation of velocity dependent exchange coefficients into
182        separate loop, so that it applies to both thermodynamics
183      - move some divisions by constants out of loops
184    
185    checkpoint63j (2012/02/16)
186    o pkg/seaice:
187      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
188      - SItracer:  added run time params, and allow coupling to ocn salinity.
189    o pkg/seaice: remove (almost) all divisions by constants within loops
190      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
191      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
192      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
193      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
194    o pkg/seaice :
195      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
196        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
197      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
198      - add permanent SItflux diag that corresponds to TFLUX but includes
199        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
200      - allow activation/testing of a fix for suspected missing term in
201        ocn-ice heat budget (to be confirmed). To test this, you want to
202        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
203        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
204      - no change in results, fwd or ad.
205    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
206      - switch to variable freezing point.
207           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
208      - bug fix : the sublimation term that was missing is now activated.
209           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
210      - bug fix : flooding sign term for SIsal0.NE.0.
211           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
212    o pkg/seaice:
213      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
214        is now the default, and the old default constant freezing point is recovered
215        with SEAICE_tempFrz0    = -1.96,
216             SEAICE_dTempFrz_dS = 0.,
217      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
218      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
219      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
220        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
221      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
222        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
223      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
224        seaice_growth r149 for legacy branch (no results change).
225      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
226        from I. Fenty).
227      - results did not change except for global_ocean.cs32x15, mostly due to the
228        switch to variable freezing point (see above item for detail).
229    o pkg/thsice:
230      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
231        seawater freezing in thsice_calc_thickn (not used).
232    o pkg/seaice: turbulent flux term specification via run time params.
233      - replace CPP switches with run time switches to facilitate testing
234      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
235                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
236      - added runtime parameter : SEAICEturbFluxFormula
237      - move Mcphee constants to SEAICE_PARAMS.h
238      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
239                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
240                 remove seaice_summary call (moved to seaice_init_fixed)
241      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
242        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
243      - seaice_summary.F : add missing report of read turbulent flux term set up
244                           and SITRACER.
245      - seaice_check.F : check range; inform and stop if retired CPPs are used
246                         (incl. SEAICE_AGE).
247      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
248             CPP switch, same computation as before for the different options.
249      - change results at the truncation level.
250    o pkg/seaice:
251      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
252        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
253        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
254      - update verification/*/input*/data.seaice:
255        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
256        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
257        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
258        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
259    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
260      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
261        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
262        difference in results only due to machine truncation.
263      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
264        MaykutPolySatVap; keep MIN_LWDOWN.
265      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
266      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
267        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
268    o pkg/salt_plume:
269      - isolate saltPlumeFlux array exch into a specific S/R called from
270        do_oceanic_phys.F
271      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
272    o verification:
273      - move untested set-up to MITgcm_contrib/verification_other.
274    o pkg/seaice:
275      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
276    o pkg/seaice:
277      - seaice_solve4temp.F (keeping results unchanged):
278        * add 2 future run-time params to select which saturation vapor pressure
279          formula is used and how post-iteration fluxes are set.
280          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
281        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
282          the linearized expression to stay consistent with tsurf finding.
283      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
284        can be < 0.
285    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
286      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
287        conductive heat flux F_c , and add it explicitly when updating tsurf as
288        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
289        so that now F_ia has a consistent meaning through the entire routine.
290        This causes differences at truncation level: update output of fwd exp.
291        global_ocean.cs32x15.seaice.
292    o pkg/seaice:
293      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
294        of arrays, sign/direction of fluxes; no effect on results.
295      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
296        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
297        note: this should have been done before changing celsius2K default.
298      - to keep results unchanged, add back old value of celsius2K in verification
299        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
300      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
301        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
302        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
303        freezing temp is consistent with value in seaice_growth.F ; this causes
304        differences at machine truncation level: update lab_sea AD output (3/4).
305    o pkg/seaice:
306      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
307        and climsst/sss even when using seaice (to prevent calculation that might
308        use SST on land); does not affect any verification exp.
309      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
310        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
311    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
312      over land (non-legacy code)
313    o vectorize salt_plume package:
314      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
315      - this code computes plumebk everywhere (also over land), thus requires
316        code to avoid divisions by zero and catch the case of kLev=Nr.
317      - efficiency of salt_plume_frac is still sub-optimal
318    o tools (genmake2):
319      - fix makefile NAME specification (option: -makefile NAME) by adding
320        "-f $MAKEFILE" in few places where it was missing including makedepend
321        command (contribution from Paul).
322    
323    checkpoint63i (2012/01/24)
324    o model/src:
325      - add factorized versions of some EOS code to find_rho.F,
326        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
327    o model/src:
328      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
329      - change default celsius2K from 273.16 to 273.15
330      - to keep results unchanged, add back old value of celsius2K in verification
331        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
332         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
333    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
334      to make TAF generate vectorizable code
335    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
336       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
337       have flags that do this more efficiently.
338    o pkg/diagnostics/diagstats_calc.F
339      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
340    o pkg/obcs (with exch2):
341      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
342        and remove code (in obcs_readparms.F) which was based on EXCH of indices
343        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
344    o pkg/exf and seaice exp:
345      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
346        so that switching off area & heff advection flags does not affect results.
347      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
348      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
349        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
350        results of verification experiments: 1D_ocean_ice_column(fwd),
351        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
352        and offline_exf_seaice (all 4).
353    o pkg/seaice:
354      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
355        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
356      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
357        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
358        not multi-dim advection;
359      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
360        SHORTWAVE_HEATING #undef.
361    o optim: make Makefile more robust (?)
362    o pkg/obcs:
363      * fix treatment of obcs_read_pickup for TAF
364    o pkg/shelfice:
365      * add missing initialisation of num_shifwflx
366      * new adjoint verification exp. for isomip
367      * change Prandtl and Schmidt numbers from generic formulations
368        (in terms of model diffus. and visc.) to separate runtime
369        parameters, with Holland and Jenkins (1999) default values.
370    o pkg/exf (interpolation):
371      - extended input field (2 rows) near the N & S poles:
372        * fill in with the symetric value (when even Nb of data in longitude)
373        * add average value at the poles only for scalar quantities ; for vector
374          component interpolation, skip the averaging and keep duplicated values,
375          unless the 2 components have same location (uvInterp=T) in which case
376          interpolate the 2 components together using S/R EXF_INTERP_UV.
377      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
378        together: this allows to account properly for local orientation when
379        averaging at N & S pole.
380      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
381        exf-interpolation near N & S poles. Undef by default.
382      - add debug check/print on 1rst iter if debugLevel >=2.
383    o pkg/exf:
384      - change masking flags definition (no longer "parameter"), put them in
385        common block and set them in S/R EXF_INIT_FIXED.
386      - change recognized masking flag from s,u,v to c,w,s since the mask
387        to use (maskC,W,S) depends on position on model grid and has little to
388        do with scalar/vector difference; fix masking if using P-coordinates.
389      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
390        and update results of exp. global_with_exf (x2).
391      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
392    o pkg/obcs
393      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
394    o pkg/exf (interpolation):
395      - assume periodicity in X only if input field cover full longitude range.
396      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
397        and should vectorise).
398      - fix input lat of the 2 added row (in case we provide N.pole data).
399    
400    checkpoint63h (2011/12/30)
401    o pkg/seaice:
402      - change declaration of UVM from _RL to _RS in order to get B-grid
403        uIce,vIce monitor when _RS = real*4
404    o pkg/offline:
405      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
406      - compute vertical velocity if not read from file (switch on exactConserv
407        & staggerTimeStep);
408      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
409    o verification:
410      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
411        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
412        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
413      - update output of exp. global_ocean.cs32x15.viscA4 after changing
414        grid-file angles (used here for coriolis-3d);
415      - remove (or gzip) few files not needed to run fizhi-cs experiments.
416    o pkg/exf (vector interpolation):
417      - rotate vector component toward local grid-axis orientation using grid-angles
418        (stored in GRID.h) instead of locally computed rotation angle; keep old code
419        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
420    o pkg/seaice:
421      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
422        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
423    o pkg/PKG_OPTIONS.h files:
424      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
425        outside of the #ifdef ALLOW_THISPKG / #endif block.
426      - update verification/*/code/PKG_OPTIONS.h files.
427    o add a verification experiment (offline_exf_seaice/input.seaice) that test
428      the B-grid LSOR solver
429    o pkg/seaice: sort out emissivity and long wave radiation step 2:
430      - add emissivity for snow and ice as new run-time parameters
431        (unfortunately) that default to the corresponding exf values; this
432        changes results in most verification experiments so that for backward
433        compatibility these parameter have to be set explicitly to inconsistent
434        values (ugly);
435      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
436        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
437        until we agree how to handle this bug properly
438    o pkg/exf (interpolation):
439      - add a set of run-time param ({inputfield}_interpMethod), one for
440        each interpolated input field, to select the interpolation method
441        with a value of zero switching off the interpolation;
442      - print interpolation parameters to standard output;
443      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
444        (to use instead runoff_interpMethod=0 in data.exf).
445      - simplify default setting of interpolation parameters (for all fields,
446        set position to match model grid cell-center position, leading to trivial
447        interpolation in case of regular Lat-Lon grid) and fix for the case of
448        non-uniform delY.
449    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
450       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
451       this factor is absolutely required, because the lw exitance (= out-going
452       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
453       where the reflectivity rho = 1-emissivity for conservation reasons. Once
454       this is established, we can remove the CPP-Flag (if we want to).
455    o pkg/seaice:
456      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
457        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
458      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
459        what the name implies (and not emissivity*BoltzmannConstant), this means
460        the old default value of 5.5e-8 now means
461        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
462        S/R exf_readparms
463      - FV-discretization of the B-grid LSOR solver, turn on with
464        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
465        of the calling routine dynsolver, so that B and C-grid code look a
466        little more alike.
467      - fix index bugs in ostres.F (B-grid code)
468    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
469    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
470      default for SEAICE_emissivity, if useEXF; requires setting a wrong
471      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
472      backward compatiblity
473    o model/src: use sigmaR in calc_ivdc
474    
475    checkpoint63g (2011/12/16)
476    o pkg/seaice/seaice_growth.F:
477      fix heat conservation of the coupled ocean-seaice system.
478      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
479      solid vs liquid water treatment is resolved via QNET.
480    o pkg/seaice/seaice_growth.F:
481      add missing term for sublimation in saltFlux, which was breaking conservation.
482    o pkg/seaice/seaice_model.F:
483      Remove this patholigical case treatment in evolution branch,
484      where it is un-necessary and breaks conservation.
485      Update global_ocean.cs32x15/results accordingly for
486      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
487    o model/src:
488      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
489      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
490    o pkg/obcs:
491      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
492      tendency for temperature and salinity that is then applied to update
493      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
494      horizontal advection and diffusion contributions on the boundary (in
495      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
496      removing the mask in S/R timestep_tracer. The advantage of this approach is
497      that the updated tracer values include contributions from the surface
498      forcing and vertical diffusion.
499      This modification changes exp4.stevens because of vertical diffusion.
500    o model/src:
501      change non-curvilinear grid setting to also work with exch2 + blank tiles:
502      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
503        face dimensions.
504      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
505        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
506        and INI_SPHERICAL_POLAR_GRID.
507      change test-experiment global_ocean.90x40x15:
508      - split the domain in many more tiles (9x4 tiles of 10x10 each);
509      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
510      - update results of both test (std & dwnslp).
511    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
512       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
513    o model/src:
514      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
515        and fix initialisation when using sigma-coords.
516    o model/src:
517     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
518       to their current value at the beginning of forward_step.F": add a new run-time
519       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
520     - set doResetHFactors=T in the following test exp:
521        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
522        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
523        and tutorial_global_oce_in_p (nonLinFS in p)
524    o pkg/ecco
525      - added IES cost term
526    o verification/advect_xz
527      - scale down the depth by 1/100 (from 200 km to just 2.km)
528      - add secondary test using divergent flow, r-star and implicit vertical advection.
529      - add note (check_conserve_TS.txt) and matlab script to check global
530        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
531    o pkg/rbcs:
532      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
533    o pkg/obcs (Stevens BCs):
534      - fix various problems in the phase speed computations of the Stevens
535        boundary conditions:
536        - sign error for western and southern boundaries,
537        - time tendencies were underestimated by factor of dTracerLev and some just
538          zero (for multidim advection schemes) -> now estimate time tendencies
539          from difference between previous (n) time level and the one before (n-1);
540          this requires storing a field per tracer per boundary, also in the pickup
541          files.
542        - replace deltaTmom in cflMer/Zon computation with dTracerLev
543        - set default phase velocity to cflMer/Zon
544      - update verification experiment exp4.stevens
545    o pkg/generic_advdiff (implicit_r):
546      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
547        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
548      - fix implicit vertical diffusion or advection with NonLin FreeSurf
549        (was using current recip_hFacC instead of future recip_hFacC): set future
550        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
551        solver S/R ;
552      - fill diagnostics of vertical advective fluxes (computed from tendency)
553        when using implicit vert. advection;
554      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
555         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
556         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
557         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
558    o pkg/diagnostics:
559      - add diags for T & S tendency which goes through Adams-Bashforth.
560    
561    checkpoint63f (2011/11/30)
562  o pkg/obcs/obcs_calc_stevens.F:  o pkg/obcs/obcs_calc_stevens.F:
563    - join some loops to reduce number of if-statements    - join some loops to reduce number of if-statements
564    - fix a bug in code for northern and southern boundaries.    - fix a bug in code for northern and southern boundaries.
565  o pkg/seaice/seaice_init_varia.F  o pkg/seaice/seaice_init_varia.F
566    - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and    - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
567      caused zero ice-velocities for the B-grid code      caused zero ice-velocities for the B-grid code
568  o pkg/seaice/seaice_init_fixed.F  o pkg/seaice/seaice_init_fixed.F
569    - fix a bug in the initialisation of the second metric terms    - fix a bug in the initialisation of the second metric terms
570      k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.      k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
571    - this affects all seaice configurations with useCurviLinearGrid = .true.    - this affects all seaice configurations with useCurviLinearGrid = .true.
572      and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms      and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
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