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revision 1.1551 by jmc, Fri Dec 16 22:57:31 2011 UTC revision 1.1656 by jmc, Thu Apr 26 13:49:29 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/shelfice:
8     - account for partical cells in surface level below ice-shelf for hydrostatic
9       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
10    o ad test experiments:
11     - update and rename to "ad_optfile.local" local AD-optfile specific to a
12       particular adjoint verification experiment (in verification/*/code_ad/)
13    o pkg/seaice & pkg/exf:
14     - Part two of ECCO-CLIVAR code merges.
15       Completes merge of seaice area relax. code.
16       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
17       to be set in EXF_OPTIONS.h since this pkg controls its I/O
18       (and avoids second CPP option in SEAICE_OPTIONS.h)
19     - change default value of costIceStart & costIceEnd to a valid date.
20     - add snowPrecip to HSNOW in seaice_growth
21    o pkg/ptracers:
22     - move ptracers summary and setup check into separated S/R ; add a check for
23       valid PTRACERS_Iter0 value (error+stop or just warning).
24    o pkg/cal (+ pkg/ecco):
25     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
26       as input; and for AD, unless both are not differentiable (e.g., k index)).
27    o model/src:
28     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
29       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
30       temporary set to usingZCoords value (to be changed to F when using shelfice).
31     - hydrostatic pressure: implement partial cell near the surface also for
32       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
33       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
34    o pkg/ctrl/ctrl_init.F:
35     - add a formal parameter to s/r ctrl_init_rec to print
36       xx_$(ctrl_valiable)_file for easier debugging
37     - move call of cal_* routines into the if-block where they are really
38       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
39       to specify a startdate
40    o pkg/seaice:
41     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
42       global_ocean.cs32x15/code versions).
43     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
44       verification experiment global_ocean.cs32x15.seaice and update results.
45    o pkg/exf:
46     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
47       (according to useExfYearlyFields).
48    o pkg/cal:
49     - move calendar setting & summary (previously in cal_readparams.F) into new
50       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
51       length of the simulation is set (after SET_PARMS call); This is an attempt
52       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
53     - For safety: keep a record of pkg/cal parameter settings status
54               to allow to STOP if one pkg/cal S/R is called too early.
55     - add a stop in all basic pkg/cal subroutines if called before setting is done.
56     - modify cal_getdate.F: stop when nothing was returned;
57       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
58       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
59    
60    checkpoint63l (2012/04/04)
61    o pkg/bbl:
62      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
63        update global_with_exf output.yearly.txt file.
64    o pkg/cal:
65      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
66      - remove 2 unsused and very short (1 line only) functions ;
67      - remove unsused subroutines from AD-Diff list.
68    o model/src:
69      - start to implement clean wait to stop in initialization S/R (config_check.F,
70         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
71    o folowing PRINT_MESSAGE changes:
72      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
73    o pkg/bbl:
74      - modification so it can work with z*
75      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
76      - global_with_exf/input.yearly verification; changes output.yearly.txt
77    o eesupp/src:
78      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
79        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
80      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
81        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
82      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
83      - when using MPI, always set usingMPI=T ; set default accordingly and stop
84        if not consistent.
85      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
86        argument is zero (in case called within single-thread section).
87    o pkg/fizhi:
88        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
89        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
90    o pkg/exch2:
91      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
92        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
93      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
94        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
95        with bad ones coming from a not-yet-updated halo.
96        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
97    o pkg/frazil:
98        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
99        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
100    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
101    o verification/lab_sea
102      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
103      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
104      * nTimeSteps 3 -> 4
105      * changed reference output accordingly
106    o pkg/ctrl:
107      * fix ctrl_get_gen for xx_sst, xx_sss
108    o pkg/fizhi:
109      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
110        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
111      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
112        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
113        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
114    o pkg/gmredi:
115      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
116    o pkg/fizhi:
117      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
118        (old)aces open64 tuv test.
119    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
120    o pkg/mom_vecinv:
121      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
122        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
123        with non-lin free-surf).
124    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
125      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
126      some compilers (gfortran 4.6.0 on MacOS)
127    o momentum:
128      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
129        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
130        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
131    
132    checkpoint63k (2012/03/17)
133    o model/src:
134       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
135         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
136       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
137         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
138    o model/src: solve_*diagonal.F
139       - replace division with multiplication by inverse (similar to original version)
140         update output of AD exp. global_ocean.90x40x15.
141       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
142         to enable the use of the vectorized & differentiable solve_tridiagonal.F
143       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
144         vertical advection (to get solve_tridiagonal tested in AD mode).
145    o pkg/seaice: ECCO-CLIVAR merge:
146      1. seaice AREA relaxation
147         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
148         * runtime flag: SEAICE_tauAreaObsRelax
149      2. modified global mean cost imbalance code: CPP option
150          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
151    o another iteration on solve_*diagonal.F
152       Make choices independent of AUTODIFF
153       Default will be the adjoinable vectorized version.
154       Alternative choices are:
155       * non-adjoinable original version with low memory footprint:
156         #define SOLVE_DIAGONAL_LOWMEMORY
157       * still adjoinable but does not vectorize (k as inner-most loop):
158         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
159    o testreport
160     - add option to use a home made wrapper around "make"
161     - remove MITGCM_IEEE env. variable (no longer active)
162    o pkg/shelfice
163     - improve computation of friction velocity for velocity dependent
164       exchange coefficients: include velocities into SHELFICEBoundaryLayer
165       block to average velocities vertically
166     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
167    o Modify diagonal solvers, now three versions (upon request):
168      #ifndef SOLVE_DIAGONAL_AUTODIFF
169        1. default version (dating back a while ago)
170      #else /* def SOLVE_DIAGONAL_AUTODIFF */
171      # ifdef SOLVE_DIAGONAL_KINNER
172        2. adjoinable version with k-innermost loop (G. Forget)
173      # else
174        3. adjoinable vectorized version of 2.
175      # endif
176      #endif /* SOLVE_DIAGONAL_AUTODIFF */
177      All flags are currently set within routines, but could/should be moved to CPP-options.
178      Array bounds for 1. are as before, for 2.,3. cover the entire domain
179      (could be changed for 1. too).
180    o verification/lab_sea (fwd):
181      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
182        use 7 categories (except hb87), new solve4temp params (except salt_plume),
183        constant salinity (=4) or variable salinity (salt_plume) done through
184        SItracer.
185    o pkg/seaice:
186      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
187      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
188         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
189        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
190        SEAICE_freeze got retired) but already better than previously with
191        SEAICE_freeze=123456.7 deg.C;
192      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
193        (safer multi-threaded setting); always set SEAICEuseEVP;
194      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
195        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
196        stop if multiple specifications for the same coeff; make sure default
197        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
198    o pkg/obcs:
199      - allow to switch to upwind 1rst order advection scheme for the advective
200        flux computation at the open-boundary; disabled for adjoint built.
201    o pkg/ptracers:
202      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
203      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
204      - add parameter to decide when to start a tracer; use internal flag to
205        know which tracer to step-forward; switch this internal flag at the top
206        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
207        for adjoint built.
208    o pkg/seaice:
209      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
210      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
211      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
212    o pkg/ecco:
213      - fix writing of output file DiagnosCost_ClimSalt/Theta
214        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
215    o pkg/seaice:
216      - add missing initialisation of COR_ICE array in dynsolver.F
217      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
218        compiled either way, and is tested in all exps (multidim was only tested
219        in lab_sea ad before).
220      - cosmetic change to prepare for future addition of ITD. no change to results.
221        no defaults change.
222      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
223      - by lack of adequate verification experiments, I further used custom versions
224        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
225        should be correct.
226      - avoid recomputations in ad.
227    o array initialisation in adjoint mode:
228      1) pkg/mom_common/mom_calc_ke.F:
229        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
230        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
231        part this initialisation is gone, resulting in Floating Point Exception
232        (caught by open64 compiler with debug option).
233      2) model/src/convective_weights.F
234        set output convectCount over the full array range (instead of doing
235        an update): this fix a similar issue when called within recomputation (adjoint)
236        which could by-pass the initialisation (normally done in the caller S/R).
237    o pkg/seaice:
238      - final version of turbulent flux params, as agreed at MIT ice meet:
239           SEAICE_mcPheePiston (default is ~ 0.000875)
240           SEAICE_mcPheeTaper (default is 0.)
241           SEAICE_frazilFrac (defualt is 1.)
242           SEAICE_mcPheeStepFunc (default is false)
243      - changes results at trunction error level
244      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
245    o added pkg/frazil:
246      - see frazil_description.tex for details
247      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
248    o pkg/shelfice/shelfice_thermodynamics.F
249      - fix exponents for velocity dependent exchange coefficients: change
250        from 2/3(=0) to 0.66666666666666667
251      - move computation of velocity dependent exchange coefficients into
252        separate loop, so that it applies to both thermodynamics
253      - move some divisions by constants out of loops
254    
255    checkpoint63j (2012/02/16)
256    o pkg/seaice:
257      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
258      - SItracer:  added run time params, and allow coupling to ocn salinity.
259    o pkg/seaice: remove (almost) all divisions by constants within loops
260      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
261      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
262      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
263      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
264    o pkg/seaice :
265      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
266        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
267      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
268      - add permanent SItflux diag that corresponds to TFLUX but includes
269        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
270      - allow activation/testing of a fix for suspected missing term in
271        ocn-ice heat budget (to be confirmed). To test this, you want to
272        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
273        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
274      - no change in results, fwd or ad.
275    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
276      - switch to variable freezing point.
277           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
278      - bug fix : the sublimation term that was missing is now activated.
279           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
280      - bug fix : flooding sign term for SIsal0.NE.0.
281           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
282    o pkg/seaice:
283      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
284        is now the default, and the old default constant freezing point is recovered
285        with SEAICE_tempFrz0    = -1.96,
286             SEAICE_dTempFrz_dS = 0.,
287      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
288      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
289      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
290        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
291      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
292        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
293      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
294        seaice_growth r149 for legacy branch (no results change).
295      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
296        from I. Fenty).
297      - results did not change except for global_ocean.cs32x15, mostly due to the
298        switch to variable freezing point (see above item for detail).
299    o pkg/thsice:
300      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
301        seawater freezing in thsice_calc_thickn (not used).
302    o pkg/seaice: turbulent flux term specification via run time params.
303      - replace CPP switches with run time switches to facilitate testing
304      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
305                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
306      - added runtime parameter : SEAICEturbFluxFormula
307      - move Mcphee constants to SEAICE_PARAMS.h
308      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
309                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
310                 remove seaice_summary call (moved to seaice_init_fixed)
311      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
312        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
313      - seaice_summary.F : add missing report of read turbulent flux term set up
314                           and SITRACER.
315      - seaice_check.F : check range; inform and stop if retired CPPs are used
316                         (incl. SEAICE_AGE).
317      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
318             CPP switch, same computation as before for the different options.
319      - change results at the truncation level.
320    o pkg/seaice:
321      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
322        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
323        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
324      - update verification/*/input*/data.seaice:
325        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
326        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
327        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
328        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
329    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
330      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
331        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
332        difference in results only due to machine truncation.
333      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
334        MaykutPolySatVap; keep MIN_LWDOWN.
335      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
336      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
337        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
338    o pkg/salt_plume:
339      - isolate saltPlumeFlux array exch into a specific S/R called from
340        do_oceanic_phys.F
341      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
342    o verification:
343      - move untested set-up to MITgcm_contrib/verification_other.
344    o pkg/seaice:
345      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
346    o pkg/seaice:
347      - seaice_solve4temp.F (keeping results unchanged):
348        * add 2 future run-time params to select which saturation vapor pressure
349          formula is used and how post-iteration fluxes are set.
350          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
351        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
352          the linearized expression to stay consistent with tsurf finding.
353      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
354        can be < 0.
355    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
356      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
357        conductive heat flux F_c , and add it explicitly when updating tsurf as
358        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
359        so that now F_ia has a consistent meaning through the entire routine.
360        This causes differences at truncation level: update output of fwd exp.
361        global_ocean.cs32x15.seaice.
362    o pkg/seaice:
363      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
364        of arrays, sign/direction of fluxes; no effect on results.
365      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
366        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
367        note: this should have been done before changing celsius2K default.
368      - to keep results unchanged, add back old value of celsius2K in verification
369        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
370      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
371        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
372        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
373        freezing temp is consistent with value in seaice_growth.F ; this causes
374        differences at machine truncation level: update lab_sea AD output (3/4).
375    o pkg/seaice:
376      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
377        and climsst/sss even when using seaice (to prevent calculation that might
378        use SST on land); does not affect any verification exp.
379      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
380        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
381    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
382      over land (non-legacy code)
383    o vectorize salt_plume package:
384      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
385      - this code computes plumebk everywhere (also over land), thus requires
386        code to avoid divisions by zero and catch the case of kLev=Nr.
387      - efficiency of salt_plume_frac is still sub-optimal
388    o tools (genmake2):
389      - fix makefile NAME specification (option: -makefile NAME) by adding
390        "-f $MAKEFILE" in few places where it was missing including makedepend
391        command (contribution from Paul).
392    
393    checkpoint63i (2012/01/24)
394    o model/src:
395      - add factorized versions of some EOS code to find_rho.F,
396        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
397    o model/src:
398      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
399      - change default celsius2K from 273.16 to 273.15
400      - to keep results unchanged, add back old value of celsius2K in verification
401        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
402         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
403    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
404      to make TAF generate vectorizable code
405    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
406       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
407       have flags that do this more efficiently.
408    o pkg/diagnostics/diagstats_calc.F
409      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
410    o pkg/obcs (with exch2):
411      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
412        and remove code (in obcs_readparms.F) which was based on EXCH of indices
413        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
414    o pkg/exf and seaice exp:
415      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
416        so that switching off area & heff advection flags does not affect results.
417      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
418      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
419        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
420        results of verification experiments: 1D_ocean_ice_column(fwd),
421        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
422        and offline_exf_seaice (all 4).
423    o pkg/seaice:
424      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
425        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
426      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
427        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
428        not multi-dim advection;
429      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
430        SHORTWAVE_HEATING #undef.
431    o optim: make Makefile more robust (?)
432    o pkg/obcs:
433      * fix treatment of obcs_read_pickup for TAF
434    o pkg/shelfice:
435      * add missing initialisation of num_shifwflx
436      * new adjoint verification exp. for isomip
437      * change Prandtl and Schmidt numbers from generic formulations
438        (in terms of model diffus. and visc.) to separate runtime
439        parameters, with Holland and Jenkins (1999) default values.
440    o pkg/exf (interpolation):
441      - extended input field (2 rows) near the N & S poles:
442        * fill in with the symetric value (when even Nb of data in longitude)
443        * add average value at the poles only for scalar quantities ; for vector
444          component interpolation, skip the averaging and keep duplicated values,
445          unless the 2 components have same location (uvInterp=T) in which case
446          interpolate the 2 components together using S/R EXF_INTERP_UV.
447      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
448        together: this allows to account properly for local orientation when
449        averaging at N & S pole.
450      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
451        exf-interpolation near N & S poles. Undef by default.
452      - add debug check/print on 1rst iter if debugLevel >=2.
453    o pkg/exf:
454      - change masking flags definition (no longer "parameter"), put them in
455        common block and set them in S/R EXF_INIT_FIXED.
456      - change recognized masking flag from s,u,v to c,w,s since the mask
457        to use (maskC,W,S) depends on position on model grid and has little to
458        do with scalar/vector difference; fix masking if using P-coordinates.
459      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
460        and update results of exp. global_with_exf (x2).
461      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
462    o pkg/obcs
463      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
464    o pkg/exf (interpolation):
465      - assume periodicity in X only if input field cover full longitude range.
466      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
467        and should vectorise).
468      - fix input lat of the 2 added row (in case we provide N.pole data).
469    
470    checkpoint63h (2011/12/30)
471    o pkg/seaice:
472      - change declaration of UVM from _RL to _RS in order to get B-grid
473        uIce,vIce monitor when _RS = real*4
474    o pkg/offline:
475      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
476      - compute vertical velocity if not read from file (switch on exactConserv
477        & staggerTimeStep);
478      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
479    o verification:
480      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
481        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
482        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
483      - update output of exp. global_ocean.cs32x15.viscA4 after changing
484        grid-file angles (used here for coriolis-3d);
485      - remove (or gzip) few files not needed to run fizhi-cs experiments.
486    o pkg/exf (vector interpolation):
487      - rotate vector component toward local grid-axis orientation using grid-angles
488        (stored in GRID.h) instead of locally computed rotation angle; keep old code
489        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
490    o pkg/seaice:
491      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
492        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
493    o pkg/PKG_OPTIONS.h files:
494      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
495        outside of the #ifdef ALLOW_THISPKG / #endif block.
496      - update verification/*/code/PKG_OPTIONS.h files.
497    o add a verification experiment (offline_exf_seaice/input.seaice) that test
498      the B-grid LSOR solver
499    o pkg/seaice: sort out emissivity and long wave radiation step 2:
500      - add emissivity for snow and ice as new run-time parameters
501        (unfortunately) that default to the corresponding exf values; this
502        changes results in most verification experiments so that for backward
503        compatibility these parameter have to be set explicitly to inconsistent
504        values (ugly);
505      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
506        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
507        until we agree how to handle this bug properly
508    o pkg/exf (interpolation):
509      - add a set of run-time param ({inputfield}_interpMethod), one for
510        each interpolated input field, to select the interpolation method
511        with a value of zero switching off the interpolation;
512      - print interpolation parameters to standard output;
513      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
514        (to use instead runoff_interpMethod=0 in data.exf).
515      - simplify default setting of interpolation parameters (for all fields,
516        set position to match model grid cell-center position, leading to trivial
517        interpolation in case of regular Lat-Lon grid) and fix for the case of
518        non-uniform delY.
519    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
520       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
521       this factor is absolutely required, because the lw exitance (= out-going
522       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
523       where the reflectivity rho = 1-emissivity for conservation reasons. Once
524       this is established, we can remove the CPP-Flag (if we want to).
525    o pkg/seaice:
526      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
527        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
528      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
529        what the name implies (and not emissivity*BoltzmannConstant), this means
530        the old default value of 5.5e-8 now means
531        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
532        S/R exf_readparms
533      - FV-discretization of the B-grid LSOR solver, turn on with
534        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
535        of the calling routine dynsolver, so that B and C-grid code look a
536        little more alike.
537      - fix index bugs in ostres.F (B-grid code)
538    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
539    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
540      default for SEAICE_emissivity, if useEXF; requires setting a wrong
541      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
542      backward compatiblity
543    o model/src: use sigmaR in calc_ivdc
544    
545  checkpoint63g (2011/12/16)  checkpoint63g (2011/12/16)
546  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
547    fix heat conservation of the coupled ocean-seaice system.    fix heat conservation of the coupled ocean-seaice system.
# Line 14  o pkg/seaice/seaice_growth.F: Line 552  o pkg/seaice/seaice_growth.F:
552  o pkg/seaice/seaice_model.F:  o pkg/seaice/seaice_model.F:
553    Remove this patholigical case treatment in evolution branch,    Remove this patholigical case treatment in evolution branch,
554    where it is un-necessary and breaks conservation.    where it is un-necessary and breaks conservation.
555    Update global_ocean.cs32x15/results accordingly for    Update global_ocean.cs32x15/results accordingly for
556    output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt    output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
557  o model/src:  o model/src:
558    useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in    useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
559    external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.    external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
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