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revision 1.1489 by dimitri, Sun Aug 7 07:08:14 2011 UTC revision 1.1649 by mlosch, Wed Apr 11 12:11:56 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/ctrl/ctrl_init.F:
8     - add a formal parameter to s/r ctrl_init_rec to print
9       xx_$(ctrl_valiable)_file for easier debugging
10     - move call of cal_* routines into the if-block where they are really
11       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
12       to specify a startdate
13    o pkg/seaice:
14     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
15       global_ocean.cs32x15/code versions).
16     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
17       verification experiment global_ocean.cs32x15.seaice and update results.
18    o pkg/exf:
19     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
20       (according to useExfYearlyFields).
21    o pkg/cal:
22     - move calendar setting & summary (previously in cal_readparams.F) into new
23       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
24       length of the simulation is set (after SET_PARMS call); This is an attempt
25       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
26     - For safety: keep a record of pkg/cal parameter settings status
27               to allow to STOP if one pkg/cal S/R is called too early.
28     - add a stop in all basic pkg/cal subroutines if called before setting is done.
29     - modify cal_getdate.F: stop when nothing was returned;
30       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
31       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
32    
33    checkpoint63l (2012/04/04)
34    o pkg/bbl:
35      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
36        update global_with_exf output.yearly.txt file.
37    o pkg/cal:
38      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
39      - remove 2 unsused and very short (1 line only) functions ;
40      - remove unsused subroutines from AD-Diff list.
41    o model/src:
42      - start to implement clean wait to stop in initialization S/R (config_check.F,
43         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
44    o folowing PRINT_MESSAGE changes:
45      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
46    o pkg/bbl:
47      - modification so it can work with z*
48      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
49      - global_with_exf/input.yearly verification; changes output.yearly.txt
50    o eesupp/src:
51      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
52        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
53      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
54        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
55      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
56      - when using MPI, always set usingMPI=T ; set default accordingly and stop
57        if not consistent.
58      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
59        argument is zero (in case called within single-thread section).
60    o pkg/fizhi:
61        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
62        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
63    o pkg/exch2:
64      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
65        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
66      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
67        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
68        with bad ones coming from a not-yet-updated halo.
69        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
70    o pkg/frazil:
71        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
72        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
73    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
74    o verification/lab_sea
75      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
76      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
77      * nTimeSteps 3 -> 4
78      * changed reference output accordingly
79    o pkg/ctrl:
80      * fix ctrl_get_gen for xx_sst, xx_sss
81    o pkg/fizhi:
82      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
83        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
84      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
85        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
86        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
87    o pkg/gmredi:
88      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
89    o pkg/fizhi:
90      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
91        (old)aces open64 tuv test.
92    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
93    o pkg/mom_vecinv:
94      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
95        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
96        with non-lin free-surf).
97    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
98      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
99      some compilers (gfortran 4.6.0 on MacOS)
100    o momentum:
101      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
102        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
103        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
104    
105    checkpoint63k (2012/03/17)
106    o model/src:
107       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
108         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
109       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
110         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
111    o model/src: solve_*diagonal.F
112       - replace division with multiplication by inverse (similar to original version)
113         update output of AD exp. global_ocean.90x40x15.
114       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
115         to enable the use of the vectorized & differentiable solve_tridiagonal.F
116       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
117         vertical advection (to get solve_tridiagonal tested in AD mode).
118    o pkg/seaice: ECCO-CLIVAR merge:
119      1. seaice AREA relaxation
120         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
121         * runtime flag: SEAICE_tauAreaObsRelax
122      2. modified global mean cost imbalance code: CPP option
123          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
124    o another iteration on solve_*diagonal.F
125       Make choices independent of AUTODIFF
126       Default will be the adjoinable vectorized version.
127       Alternative choices are:
128       * non-adjoinable original version with low memory footprint:
129         #define SOLVE_DIAGONAL_LOWMEMORY
130       * still adjoinable but does not vectorize (k as inner-most loop):
131         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
132    o testreport
133     - add option to use a home made wrapper around "make"
134     - remove MITGCM_IEEE env. variable (no longer active)
135    o pkg/shelfice
136     - improve computation of friction velocity for velocity dependent
137       exchange coefficients: include velocities into SHELFICEBoundaryLayer
138       block to average velocities vertically
139     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
140    o Modify diagonal solvers, now three versions (upon request):
141      #ifndef SOLVE_DIAGONAL_AUTODIFF
142        1. default version (dating back a while ago)
143      #else /* def SOLVE_DIAGONAL_AUTODIFF */
144      # ifdef SOLVE_DIAGONAL_KINNER
145        2. adjoinable version with k-innermost loop (G. Forget)
146      # else
147        3. adjoinable vectorized version of 2.
148      # endif
149      #endif /* SOLVE_DIAGONAL_AUTODIFF */
150      All flags are currently set within routines, but could/should be moved to CPP-options.
151      Array bounds for 1. are as before, for 2.,3. cover the entire domain
152      (could be changed for 1. too).
153    o verification/lab_sea (fwd):
154      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
155        use 7 categories (except hb87), new solve4temp params (except salt_plume),
156        constant salinity (=4) or variable salinity (salt_plume) done through
157        SItracer.
158    o pkg/seaice:
159      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
160      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
161         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
162        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
163        SEAICE_freeze got retired) but already better than previously with
164        SEAICE_freeze=123456.7 deg.C;
165      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
166        (safer multi-threaded setting); always set SEAICEuseEVP;
167      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
168        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
169        stop if multiple specifications for the same coeff; make sure default
170        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
171    o pkg/obcs:
172      - allow to switch to upwind 1rst order advection scheme for the advective
173        flux computation at the open-boundary; disabled for adjoint built.
174    o pkg/ptracers:
175      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
176      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
177      - add parameter to decide when to start a tracer; use internal flag to
178        know which tracer to step-forward; switch this internal flag at the top
179        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
180        for adjoint built.
181    o pkg/seaice:
182      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
183      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
184      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
185    o pkg/ecco:
186      - fix writing of output file DiagnosCost_ClimSalt/Theta
187        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
188    o pkg/seaice:
189      - add missing initialisation of COR_ICE array in dynsolver.F
190      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
191        compiled either way, and is tested in all exps (multidim was only tested
192        in lab_sea ad before).
193      - cosmetic change to prepare for future addition of ITD. no change to results.
194        no defaults change.
195      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
196      - by lack of adequate verification experiments, I further used custom versions
197        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
198        should be correct.
199      - avoid recomputations in ad.
200    o array initialisation in adjoint mode:
201      1) pkg/mom_common/mom_calc_ke.F:
202        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
203        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
204        part this initialisation is gone, resulting in Floating Point Exception
205        (caught by open64 compiler with debug option).
206      2) model/src/convective_weights.F
207        set output convectCount over the full array range (instead of doing
208        an update): this fix a similar issue when called within recomputation (adjoint)
209        which could by-pass the initialisation (normally done in the caller S/R).
210    o pkg/seaice:
211      - final version of turbulent flux params, as agreed at MIT ice meet:
212           SEAICE_mcPheePiston (default is ~ 0.000875)
213           SEAICE_mcPheeTaper (default is 0.)
214           SEAICE_frazilFrac (defualt is 1.)
215           SEAICE_mcPheeStepFunc (default is false)
216      - changes results at trunction error level
217      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
218    o added pkg/frazil:
219      - see frazil_description.tex for details
220      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
221    o pkg/shelfice/shelfice_thermodynamics.F
222      - fix exponents for velocity dependent exchange coefficients: change
223        from 2/3(=0) to 0.66666666666666667
224      - move computation of velocity dependent exchange coefficients into
225        separate loop, so that it applies to both thermodynamics
226      - move some divisions by constants out of loops
227    
228    checkpoint63j (2012/02/16)
229    o pkg/seaice:
230      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
231      - SItracer:  added run time params, and allow coupling to ocn salinity.
232    o pkg/seaice: remove (almost) all divisions by constants within loops
233      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
234      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
235      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
236      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
237    o pkg/seaice :
238      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
239        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
240      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
241      - add permanent SItflux diag that corresponds to TFLUX but includes
242        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
243      - allow activation/testing of a fix for suspected missing term in
244        ocn-ice heat budget (to be confirmed). To test this, you want to
245        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
246        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
247      - no change in results, fwd or ad.
248    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
249      - switch to variable freezing point.
250           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
251      - bug fix : the sublimation term that was missing is now activated.
252           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
253      - bug fix : flooding sign term for SIsal0.NE.0.
254           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
255    o pkg/seaice:
256      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
257        is now the default, and the old default constant freezing point is recovered
258        with SEAICE_tempFrz0    = -1.96,
259             SEAICE_dTempFrz_dS = 0.,
260      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
261      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
262      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
263        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
264      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
265        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
266      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
267        seaice_growth r149 for legacy branch (no results change).
268      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
269        from I. Fenty).
270      - results did not change except for global_ocean.cs32x15, mostly due to the
271        switch to variable freezing point (see above item for detail).
272    o pkg/thsice:
273      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
274        seawater freezing in thsice_calc_thickn (not used).
275    o pkg/seaice: turbulent flux term specification via run time params.
276      - replace CPP switches with run time switches to facilitate testing
277      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
278                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
279      - added runtime parameter : SEAICEturbFluxFormula
280      - move Mcphee constants to SEAICE_PARAMS.h
281      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
282                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
283                 remove seaice_summary call (moved to seaice_init_fixed)
284      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
285        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
286      - seaice_summary.F : add missing report of read turbulent flux term set up
287                           and SITRACER.
288      - seaice_check.F : check range; inform and stop if retired CPPs are used
289                         (incl. SEAICE_AGE).
290      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
291             CPP switch, same computation as before for the different options.
292      - change results at the truncation level.
293    o pkg/seaice:
294      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
295        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
296        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
297      - update verification/*/input*/data.seaice:
298        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
299        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
300        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
301        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
302    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
303      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
304        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
305        difference in results only due to machine truncation.
306      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
307        MaykutPolySatVap; keep MIN_LWDOWN.
308      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
309      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
310        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
311    o pkg/salt_plume:
312      - isolate saltPlumeFlux array exch into a specific S/R called from
313        do_oceanic_phys.F
314      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
315    o verification:
316      - move untested set-up to MITgcm_contrib/verification_other.
317    o pkg/seaice:
318      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
319    o pkg/seaice:
320      - seaice_solve4temp.F (keeping results unchanged):
321        * add 2 future run-time params to select which saturation vapor pressure
322          formula is used and how post-iteration fluxes are set.
323          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
324        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
325          the linearized expression to stay consistent with tsurf finding.
326      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
327        can be < 0.
328    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
329      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
330        conductive heat flux F_c , and add it explicitly when updating tsurf as
331        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
332        so that now F_ia has a consistent meaning through the entire routine.
333        This causes differences at truncation level: update output of fwd exp.
334        global_ocean.cs32x15.seaice.
335    o pkg/seaice:
336      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
337        of arrays, sign/direction of fluxes; no effect on results.
338      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
339        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
340        note: this should have been done before changing celsius2K default.
341      - to keep results unchanged, add back old value of celsius2K in verification
342        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
343      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
344        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
345        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
346        freezing temp is consistent with value in seaice_growth.F ; this causes
347        differences at machine truncation level: update lab_sea AD output (3/4).
348    o pkg/seaice:
349      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
350        and climsst/sss even when using seaice (to prevent calculation that might
351        use SST on land); does not affect any verification exp.
352      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
353        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
354    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
355      over land (non-legacy code)
356    o vectorize salt_plume package:
357      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
358      - this code computes plumebk everywhere (also over land), thus requires
359        code to avoid divisions by zero and catch the case of kLev=Nr.
360      - efficiency of salt_plume_frac is still sub-optimal
361    o tools (genmake2):
362      - fix makefile NAME specification (option: -makefile NAME) by adding
363        "-f $MAKEFILE" in few places where it was missing including makedepend
364        command (contribution from Paul).
365    
366    checkpoint63i (2012/01/24)
367    o model/src:
368      - add factorized versions of some EOS code to find_rho.F,
369        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
370    o model/src:
371      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
372      - change default celsius2K from 273.16 to 273.15
373      - to keep results unchanged, add back old value of celsius2K in verification
374        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
375         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
376    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
377      to make TAF generate vectorizable code
378    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
379       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
380       have flags that do this more efficiently.
381    o pkg/diagnostics/diagstats_calc.F
382      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
383    o pkg/obcs (with exch2):
384      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
385        and remove code (in obcs_readparms.F) which was based on EXCH of indices
386        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
387    o pkg/exf and seaice exp:
388      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
389        so that switching off area & heff advection flags does not affect results.
390      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
391      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
392        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
393        results of verification experiments: 1D_ocean_ice_column(fwd),
394        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
395        and offline_exf_seaice (all 4).
396    o pkg/seaice:
397      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
398        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
399      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
400        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
401        not multi-dim advection;
402      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
403        SHORTWAVE_HEATING #undef.
404    o optim: make Makefile more robust (?)
405    o pkg/obcs:
406      * fix treatment of obcs_read_pickup for TAF
407    o pkg/shelfice:
408      * add missing initialisation of num_shifwflx
409      * new adjoint verification exp. for isomip
410      * change Prandtl and Schmidt numbers from generic formulations
411        (in terms of model diffus. and visc.) to separate runtime
412        parameters, with Holland and Jenkins (1999) default values.
413    o pkg/exf (interpolation):
414      - extended input field (2 rows) near the N & S poles:
415        * fill in with the symetric value (when even Nb of data in longitude)
416        * add average value at the poles only for scalar quantities ; for vector
417          component interpolation, skip the averaging and keep duplicated values,
418          unless the 2 components have same location (uvInterp=T) in which case
419          interpolate the 2 components together using S/R EXF_INTERP_UV.
420      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
421        together: this allows to account properly for local orientation when
422        averaging at N & S pole.
423      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
424        exf-interpolation near N & S poles. Undef by default.
425      - add debug check/print on 1rst iter if debugLevel >=2.
426    o pkg/exf:
427      - change masking flags definition (no longer "parameter"), put them in
428        common block and set them in S/R EXF_INIT_FIXED.
429      - change recognized masking flag from s,u,v to c,w,s since the mask
430        to use (maskC,W,S) depends on position on model grid and has little to
431        do with scalar/vector difference; fix masking if using P-coordinates.
432      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
433        and update results of exp. global_with_exf (x2).
434      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
435    o pkg/obcs
436      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
437    o pkg/exf (interpolation):
438      - assume periodicity in X only if input field cover full longitude range.
439      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
440        and should vectorise).
441      - fix input lat of the 2 added row (in case we provide N.pole data).
442    
443    checkpoint63h (2011/12/30)
444    o pkg/seaice:
445      - change declaration of UVM from _RL to _RS in order to get B-grid
446        uIce,vIce monitor when _RS = real*4
447    o pkg/offline:
448      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
449      - compute vertical velocity if not read from file (switch on exactConserv
450        & staggerTimeStep);
451      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
452    o verification:
453      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
454        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
455        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
456      - update output of exp. global_ocean.cs32x15.viscA4 after changing
457        grid-file angles (used here for coriolis-3d);
458      - remove (or gzip) few files not needed to run fizhi-cs experiments.
459    o pkg/exf (vector interpolation):
460      - rotate vector component toward local grid-axis orientation using grid-angles
461        (stored in GRID.h) instead of locally computed rotation angle; keep old code
462        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
463    o pkg/seaice:
464      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
465        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
466    o pkg/PKG_OPTIONS.h files:
467      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
468        outside of the #ifdef ALLOW_THISPKG / #endif block.
469      - update verification/*/code/PKG_OPTIONS.h files.
470    o add a verification experiment (offline_exf_seaice/input.seaice) that test
471      the B-grid LSOR solver
472    o pkg/seaice: sort out emissivity and long wave radiation step 2:
473      - add emissivity for snow and ice as new run-time parameters
474        (unfortunately) that default to the corresponding exf values; this
475        changes results in most verification experiments so that for backward
476        compatibility these parameter have to be set explicitly to inconsistent
477        values (ugly);
478      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
479        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
480        until we agree how to handle this bug properly
481    o pkg/exf (interpolation):
482      - add a set of run-time param ({inputfield}_interpMethod), one for
483        each interpolated input field, to select the interpolation method
484        with a value of zero switching off the interpolation;
485      - print interpolation parameters to standard output;
486      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
487        (to use instead runoff_interpMethod=0 in data.exf).
488      - simplify default setting of interpolation parameters (for all fields,
489        set position to match model grid cell-center position, leading to trivial
490        interpolation in case of regular Lat-Lon grid) and fix for the case of
491        non-uniform delY.
492    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
493       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
494       this factor is absolutely required, because the lw exitance (= out-going
495       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
496       where the reflectivity rho = 1-emissivity for conservation reasons. Once
497       this is established, we can remove the CPP-Flag (if we want to).
498    o pkg/seaice:
499      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
500        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
501      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
502        what the name implies (and not emissivity*BoltzmannConstant), this means
503        the old default value of 5.5e-8 now means
504        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
505        S/R exf_readparms
506      - FV-discretization of the B-grid LSOR solver, turn on with
507        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
508        of the calling routine dynsolver, so that B and C-grid code look a
509        little more alike.
510      - fix index bugs in ostres.F (B-grid code)
511    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
512    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
513      default for SEAICE_emissivity, if useEXF; requires setting a wrong
514      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
515      backward compatiblity
516    o model/src: use sigmaR in calc_ivdc
517    
518    checkpoint63g (2011/12/16)
519    o pkg/seaice/seaice_growth.F:
520      fix heat conservation of the coupled ocean-seaice system.
521      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
522      solid vs liquid water treatment is resolved via QNET.
523    o pkg/seaice/seaice_growth.F:
524      add missing term for sublimation in saltFlux, which was breaking conservation.
525    o pkg/seaice/seaice_model.F:
526      Remove this patholigical case treatment in evolution branch,
527      where it is un-necessary and breaks conservation.
528      Update global_ocean.cs32x15/results accordingly for
529      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
530    o model/src:
531      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
532      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
533    o pkg/obcs:
534      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
535      tendency for temperature and salinity that is then applied to update
536      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
537      horizontal advection and diffusion contributions on the boundary (in
538      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
539      removing the mask in S/R timestep_tracer. The advantage of this approach is
540      that the updated tracer values include contributions from the surface
541      forcing and vertical diffusion.
542      This modification changes exp4.stevens because of vertical diffusion.
543    o model/src:
544      change non-curvilinear grid setting to also work with exch2 + blank tiles:
545      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
546        face dimensions.
547      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
548        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
549        and INI_SPHERICAL_POLAR_GRID.
550      change test-experiment global_ocean.90x40x15:
551      - split the domain in many more tiles (9x4 tiles of 10x10 each);
552      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
553      - update results of both test (std & dwnslp).
554    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
555       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
556    o model/src:
557      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
558        and fix initialisation when using sigma-coords.
559    o model/src:
560     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
561       to their current value at the beginning of forward_step.F": add a new run-time
562       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
563     - set doResetHFactors=T in the following test exp:
564        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
565        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
566        and tutorial_global_oce_in_p (nonLinFS in p)
567    o pkg/ecco
568      - added IES cost term
569    o verification/advect_xz
570      - scale down the depth by 1/100 (from 200 km to just 2.km)
571      - add secondary test using divergent flow, r-star and implicit vertical advection.
572      - add note (check_conserve_TS.txt) and matlab script to check global
573        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
574    o pkg/rbcs:
575      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
576    o pkg/obcs (Stevens BCs):
577      - fix various problems in the phase speed computations of the Stevens
578        boundary conditions:
579        - sign error for western and southern boundaries,
580        - time tendencies were underestimated by factor of dTracerLev and some just
581          zero (for multidim advection schemes) -> now estimate time tendencies
582          from difference between previous (n) time level and the one before (n-1);
583          this requires storing a field per tracer per boundary, also in the pickup
584          files.
585        - replace deltaTmom in cflMer/Zon computation with dTracerLev
586        - set default phase velocity to cflMer/Zon
587      - update verification experiment exp4.stevens
588    o pkg/generic_advdiff (implicit_r):
589      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
590        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
591      - fix implicit vertical diffusion or advection with NonLin FreeSurf
592        (was using current recip_hFacC instead of future recip_hFacC): set future
593        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
594        solver S/R ;
595      - fill diagnostics of vertical advective fluxes (computed from tendency)
596        when using implicit vert. advection;
597      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
598         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
599         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
600         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
601    o pkg/diagnostics:
602      - add diags for T & S tendency which goes through Adams-Bashforth.
603    
604    checkpoint63f (2011/11/30)
605    o pkg/obcs/obcs_calc_stevens.F:
606      - join some loops to reduce number of if-statements
607      - fix a bug in code for northern and southern boundaries.
608    o pkg/seaice/seaice_init_varia.F
609      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
610        caused zero ice-velocities for the B-grid code
611    o pkg/seaice/seaice_init_fixed.F
612      - fix a bug in the initialisation of the second metric terms
613        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
614      - this affects all seaice configurations with useCurviLinearGrid = .true.
615        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
616        = .true. (default)
617      - the only verification experiment affected is global_ocean.cs32x15:
618        icedyn, seaice, and seaice_dynmix (AD)
619    o pkg/thsice/thsice_diagnostics_state.F
620      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
621        not contain garbage that can lead to surprises in diagstats_calc.F
622    o model/src:
623      - move bi,bj loops inside INTEGR_CONTINUITY ;
624      - call INTEGR_CONTINUITY directly from forward_step.F
625        (previously called from momentum_correction_step.F)
626      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
627        forward_step.F and pkg/ecco/the_main_loop.F
628    o model/src/do_oceanic_phys.F:
629      - reset addMass to zero only if useICEFRONT ;
630      - separated k-loop for rhoInSitu calculation ;
631      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
632        and at constant T,S (= WdRHOdP);
633      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
634        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
635        transport of locally-referenced potential density);
636        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
637    o gluemnc:
638      - replace ncrcat with ncks when adding variables to *.glob.nc
639      - change the way variables without record dimensions are handled so that
640        files that have variables with and without record variables can be glued:
641        add a record dimension with a new unique name to be able to differentiate
642        between variable with and without a-prior record dimensions. Remove
643        this record dimension before adding the variable to the *.glob.nc file.
644        This procedure automatically works also for grid.*.nc files that do not
645        have any record dimension.
646    o verification/cpl_aim+ocn:
647      - generate new reference output on baudelaire (gfortran, mpich2) (previously
648        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
649    o pkg/obcs/obcs_calc_stevens.F:
650      - add code for northern and southern boundaries.
651      - reorder some loops to save some operations and so that drFBar can be scalar
652    o model/src:
653      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
654        truncation) and add diagnostics for Adams-Bashforth tendency increment.
655      - update test-exp. AD output:
656        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
657      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
658        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
659        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
660        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
661        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
662        tutorial_plume_on_slope.
663    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
664      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
665      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
666      does not even come with an F77 compiler anymore, this should not be
667      a limitation
668    
669    checkpoint63e (2011/11/06)
670    o pkg/seaice adjoint of LSR:
671      - substantially rework STORE dirs.
672      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
673        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
674        and only perform SOLV_MAX_FIXED adjoint iters.
675        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
676        always goes to same record, meaning that the last forward field will be
677        the one used in the adjoint - an approximation.
678      - now produces non-zero LSR-related gradients, and acceptable gradients for
679        An's zonal (x-z) test case (to be checked in)
680      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
681        (but these are screwed up by the thermodynamics in the first place);
682        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
683        output_adm.txt also reflects changes to seaice_lsr
684      - global_ocean.cs32x15:
685        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
686          (output_adm.seaice.txt was updated)
687        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
688          (output_adm.seaice_dynmix.txt)
689    o test-exp. exp4+stevens:
690      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
691    o pkg/seaice (lsr solver):
692      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
693        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
694      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
695      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
696        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
697      - compute (with new S/R) and print initial (+ free-driff sol. if available)
698        and final residual of linearised system.
699    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
700      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
701    o pkg/obcs: Stevens BCs (still only for east and west)
702      - fix Stevens BCs by using intermediate velocities of previous
703        time step as "baroclinic" contribution rather velocity of one grid cell
704        inside the boundaries; more consistent but makes the entire treatment
705        more complicated, requires new pickup files and two new S/Rs:
706        obcs_copy_uv_n and obcs_save_uv_n
707        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
708        (undefined by default)
709      - silently move computation of some grid factors into separate loops to
710        save some recomputations
711      - add a hack for non-linear free surface
712      - add a verification experiment to exp4 that tests this code
713    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
714    
715    checkpoint63d (2011/10/25)
716    o pkg/obcs + seaice-dynamics:
717      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
718        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
719        values (consistent with an implicit method).
720      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
721        return to older implementation (same results as before); note that none of
722        the "experimental" OBCS_SEAICE options are implemented in the new version.
723      - switch test exp. seaice_obcs to use new version (update output).
724    o pkg/seaice:
725      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
726      - add parenthesis in Water-Ice drag calculations (evp & lsr);
727      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
728        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
729      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
730        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
731    o pkg/layers:
732      - Include potential density as new coordinate (Thanks to David Munday)
733    o pkg/dic:
734      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
735        carbonate computation/output to CALC_PCO2_APPROX
736    o pkg/generic_advdiff
737      - make TAF generate code that vectorizes:
738        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
739    o model/src:
740      - improve vectorization also for adjoint code of
741        solve_tridiagonal and solve_pentadiagonal. As this requires up to
742        5 new 3D-fields, this code is only turned on for the combination of
743        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
744        for singular matrix check (only for TARGET_NEC_SX).
745      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
746        ALLOW_AUTODIFF. This flag now needs to be set outside of
747        solve_tri/pentadiagonal.F
748    o pkg/exf:
749      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
750        optional namelist EXF_NML_OBCS).
751      - add many debug-print (to trace down where pkg/cal error msg comes from)
752    o pkg/mom_vecinv/mom_vi_hdissip.F
753      - rearrange loops so that vectorization is improved and in particular
754        the adjoint routine vectorizes. The code is a little longer now, but I
755        think easier to read.
756        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
757    o pkg/seaice:
758      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
759    o pkg/exch2:
760      - alternative code (without tile x tile matrix) for cumulated (global) sum;
761        used as default; keep using matrix version in adjustment.cs-32x32x1.
762    o tools/build_options:
763      - after merging some MPI and/or multi-threads specific optfiles so that
764        the modified default optfile support both built (using genmake2 -mpi
765        for the MPI built, using genmake2 -omp for OpenMP built),
766        move now obsolete optfiles to tools/build_options/unsupported/
767       (add copy of email sent to support list in doc/optfiles_changes.txt)
768    
769    checkpoint63c (2011/09/28)
770    o pkg/ebm:
771      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
772        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
773    o pkg/seaice (SItracer pickup)
774    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
775      To be done:
776      - thorough testing of missing fields in S/R seaice_read_pickup
777      - thorough matching between generic tracers and specific fields used
778        (e.g. volume-weighted age, area-weighted age, salinity, ...)
779    o pkg/grdchk:
780      - all procs calculate and print finite-difference gradient (for testreport)
781      - change description output used by testreport;
782      - AD testing: also compare and report Finite-difference gradient;
783        => update all output_adm*.txt
784    o test exp. global_ocean_ebm:
785      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
786        and turn on exactConserve; update (fwd) output.
787    o pkg/seaice (LSR):
788      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
789      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
790        * identical results with non-CS topology (but save up to half of EXCH calls)
791        * no much changes in cs-32 verification tests since no ice at face edges
792         (differences due to convergence criteria, since nb of iterations changed)
793        * expect some differences on lat-lon-cap grid.
794        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
795    o pkg/exch2:
796      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
797        many tiles); until alternative coding is added, just add a stop.
798    o pkg/kpp:
799      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
800        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
801    o optfiles:
802      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
803        into corresponding standard one, which now support different build:
804        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
805      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
806    o pkg/obcs (seaice):
807      - add missing EXCH for uIce,vIce after applying OBCS;
808      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
809        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
810        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
811      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
812      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
813        and eedata.mth for MPI and mutlti-threaded testing.
814    o pkg/flt:
815      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
816      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
817      - fix pickup and trajectories + profiles output with multi-threads;
818      - add parameter to select group of fields to write along trajectory and
819        profile (default unchanged);
820      - only call PORT_RAND* function when flt_noise <> 0;
821      - add multi-threaded test for verification exp. flt_example.
822    o eesupp/src:
823      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
824      - USE_OMP_THREADING: check that number of threads (from eedata) matches
825        actual number (from env.var. setting).
826    o pkg/ebm:
827      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
828      - add multi-threaded test for verification exp. global_ocean_ebm
829    
830    checkpoint63b (2011/08/29)
831    o pkg/ebm:
832      - fix sign of runoff;
833      - update directly forcing fields (Qnet,EmPmR) to use standard
834        external_forcing_surf.F (remove ebm_forcing_surf.F);
835      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
836      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
837        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
838      - update global_ocean_ebm parameters file data and update output (fwd+ad).
839    o verification/matrix_example:
840      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
841        MPI and mutlti-threaded testing.
842    o pkg/matrix:
843      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
844      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
845      - fix for multi-threaded (remove DATA statement);
846      - use standard DIFFERENT_MULTIPLE function;
847      - add MATRIX_OPTIONS.h
848    o verification/matrix_example:
849       To allow to split the domain in several tiles, change the domain size
850        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
851        Western side) of land points.
852    o (*_)write_pickup:
853      - fix few bugs in mypackage_read/write_pickup.F
854      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
855        array of length 1 (was caught by compiler syntax-check).
856    o pkg/diagnostics (velocity potential solver):
857      - fix initialisation of main diagonal matrix (for overlap values)
858    o tools/build_options:
859      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
860        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
861      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
862        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
863        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
864        and use "-devel" testreport option for standard testing on baudelaire.
865    o pkg/grdchk:
866      - Assume that all gradient-check position are within the same tile
867        corresponding to global indices (iGloTile,jGloTile) and that
868        positions (i,j indices or nbeg) are local to this tile;
869      - set tile local-indices and proc. number according to tile global-indices;
870      - remove grdchkwhichproc from namelist (retired param);
871      - send adjoint gradient to all procs so that all procs print it to STDOUT;
872      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
873  o adding package bbl (Bottom Boundary Layer)  o adding package bbl (Bottom Boundary Layer)
874    description in MITgcm/pkg/bbl/bbl_description.tex    description in MITgcm/pkg/bbl/bbl_description.tex
875    example/test experiment in MITgcm_contrib/bbl    example/test experiment in MITgcm_contrib/bbl
   
876  o adjoint verifications  o adjoint verifications
877    - changed 5 experiments to multi-threaded    - changed 5 experiments to multi-tiles
878      * global_ocean.90x40x15      * global_ocean.90x40x15
879      * obcs_ctrl      * obcs_ctrl
880      * offline_exf_seaice      * offline_exf_seaice
# Line 17  o adjoint verifications Line 882  o adjoint verifications
882      * tutorial_tracer_adjsens      * tutorial_tracer_adjsens
883      changed reference output for those that crossed tile boundaries      changed reference output for those that crossed tile boundaries
884      (changed choices of gradient check positions)      (changed choices of gradient check positions)
885      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
886    - temporary bug fix in grdchk_loc.F for obcs    - temporary bug fix in grdchk_loc.F for obcs
   
887  o genmake2 & testreport  o genmake2 & testreport
888    - add target "obj" (just for OBJFILES files) to Makefile;    - add target "obj" (just for OBJFILES files) to Makefile;
889    - add option to specify FEXTRAFLAGS on command line.    - add option to specify FEXTRAFLAGS on command line.
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