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revision 1.1504 by heimbach, Mon Sep 26 18:24:26 2011 UTC revision 1.1661 by mlosch, Fri May 18 12:44:21 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      - add parameterisation of advective-diffusive flux into the ice shelf
9        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
10      - simply eps3/3a computation
11    o eesupp:
12     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
13       between tiles, just fill-in edges assuming locally periodic subdomain) and
14       add corresponding exchange subroutines (EXCH0);
15     - new CG-solver version (_EX0) for disconnected-tiles special case.
16    o model/src (CG-solvers):
17     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
18       (similar final residual output and max-Iter number as with standard version);
19     - allows to store and use lowest-residual solution (standard & _SR versions);
20     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
21     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
22    o eesup/src:
23     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
24       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
25    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
26    
27    checkpoint63m (2012/04/27)
28    o pkg/shelfice:
29     - account for partical cells in surface level below ice-shelf for hydrostatic
30       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
31    o ad test experiments:
32     - update and rename to "ad_optfile.local" local AD-optfile specific to a
33       particular adjoint verification experiment (in verification/*/code_ad/)
34    o pkg/seaice & pkg/exf:
35     - Part two of ECCO-CLIVAR code merges.
36       Completes merge of seaice area relax. code.
37       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
38       to be set in EXF_OPTIONS.h since this pkg controls its I/O
39       (and avoids second CPP option in SEAICE_OPTIONS.h)
40     - change default value of costIceStart & costIceEnd to a valid date.
41     - add snowPrecip to HSNOW in seaice_growth
42    o pkg/ptracers:
43     - move ptracers summary and setup check into separated S/R ; add a check for
44       valid PTRACERS_Iter0 value (error+stop or just warning).
45    o pkg/cal (+ pkg/ecco):
46     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
47       as input; and for AD, unless both are not differentiable (e.g., k index)).
48    o model/src:
49     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
50       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
51       temporary set to usingZCoords value (to be changed to F when using shelfice).
52     - hydrostatic pressure: implement partial cell near the surface also for
53       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
54       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
55    o pkg/ctrl/ctrl_init.F:
56     - add a formal parameter to s/r ctrl_init_rec to print
57       xx_$(ctrl_valiable)_file for easier debugging
58     - move call of cal_* routines into the if-block where they are really
59       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
60       to specify a startdate
61    o pkg/seaice:
62     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
63       global_ocean.cs32x15/code versions).
64     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
65       verification experiment global_ocean.cs32x15.seaice and update results.
66    o pkg/exf:
67     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
68       (according to useExfYearlyFields).
69    o pkg/cal:
70     - move calendar setting & summary (previously in cal_readparams.F) into new
71       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
72       length of the simulation is set (after SET_PARMS call); This is an attempt
73       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
74     - For safety: keep a record of pkg/cal parameter settings status
75               to allow to STOP if one pkg/cal S/R is called too early.
76     - add a stop in all basic pkg/cal subroutines if called before setting is done.
77     - modify cal_getdate.F: stop when nothing was returned;
78       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
79       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
80    
81    checkpoint63l (2012/04/04)
82    o pkg/bbl:
83      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
84        update global_with_exf output.yearly.txt file.
85    o pkg/cal:
86      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
87      - remove 2 unsused and very short (1 line only) functions ;
88      - remove unsused subroutines from AD-Diff list.
89    o model/src:
90      - start to implement clean wait to stop in initialization S/R (config_check.F,
91         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
92    o folowing PRINT_MESSAGE changes:
93      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
94    o pkg/bbl:
95      - modification so it can work with z*
96      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
97      - global_with_exf/input.yearly verification; changes output.yearly.txt
98    o eesupp/src:
99      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
100        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
101      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
102        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
103      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
104      - when using MPI, always set usingMPI=T ; set default accordingly and stop
105        if not consistent.
106      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
107        argument is zero (in case called within single-thread section).
108    o pkg/fizhi:
109        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
110        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
111    o pkg/exch2:
112      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
113        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
114      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
115        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
116        with bad ones coming from a not-yet-updated halo.
117        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
118    o pkg/frazil:
119        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
120        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
121    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
122    o verification/lab_sea
123      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
124      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
125      * nTimeSteps 3 -> 4
126      * changed reference output accordingly
127    o pkg/ctrl:
128      * fix ctrl_get_gen for xx_sst, xx_sss
129    o pkg/fizhi:
130      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
131        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
132      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
133        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
134        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
135    o pkg/gmredi:
136      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
137    o pkg/fizhi:
138      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
139        (old)aces open64 tuv test.
140    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
141    o pkg/mom_vecinv:
142      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
143        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
144        with non-lin free-surf).
145    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
146      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
147      some compilers (gfortran 4.6.0 on MacOS)
148    o momentum:
149      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
150        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
151        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
152    
153    checkpoint63k (2012/03/17)
154    o model/src:
155       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
156         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
157       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
158         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
159    o model/src: solve_*diagonal.F
160       - replace division with multiplication by inverse (similar to original version)
161         update output of AD exp. global_ocean.90x40x15.
162       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
163         to enable the use of the vectorized & differentiable solve_tridiagonal.F
164       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
165         vertical advection (to get solve_tridiagonal tested in AD mode).
166    o pkg/seaice: ECCO-CLIVAR merge:
167      1. seaice AREA relaxation
168         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
169         * runtime flag: SEAICE_tauAreaObsRelax
170      2. modified global mean cost imbalance code: CPP option
171          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
172    o another iteration on solve_*diagonal.F
173       Make choices independent of AUTODIFF
174       Default will be the adjoinable vectorized version.
175       Alternative choices are:
176       * non-adjoinable original version with low memory footprint:
177         #define SOLVE_DIAGONAL_LOWMEMORY
178       * still adjoinable but does not vectorize (k as inner-most loop):
179         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
180    o testreport
181     - add option to use a home made wrapper around "make"
182     - remove MITGCM_IEEE env. variable (no longer active)
183    o pkg/shelfice
184     - improve computation of friction velocity for velocity dependent
185       exchange coefficients: include velocities into SHELFICEBoundaryLayer
186       block to average velocities vertically
187     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
188    o Modify diagonal solvers, now three versions (upon request):
189      #ifndef SOLVE_DIAGONAL_AUTODIFF
190        1. default version (dating back a while ago)
191      #else /* def SOLVE_DIAGONAL_AUTODIFF */
192      # ifdef SOLVE_DIAGONAL_KINNER
193        2. adjoinable version with k-innermost loop (G. Forget)
194      # else
195        3. adjoinable vectorized version of 2.
196      # endif
197      #endif /* SOLVE_DIAGONAL_AUTODIFF */
198      All flags are currently set within routines, but could/should be moved to CPP-options.
199      Array bounds for 1. are as before, for 2.,3. cover the entire domain
200      (could be changed for 1. too).
201    o verification/lab_sea (fwd):
202      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
203        use 7 categories (except hb87), new solve4temp params (except salt_plume),
204        constant salinity (=4) or variable salinity (salt_plume) done through
205        SItracer.
206    o pkg/seaice:
207      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
208      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
209         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
210        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
211        SEAICE_freeze got retired) but already better than previously with
212        SEAICE_freeze=123456.7 deg.C;
213      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
214        (safer multi-threaded setting); always set SEAICEuseEVP;
215      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
216        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
217        stop if multiple specifications for the same coeff; make sure default
218        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
219    o pkg/obcs:
220      - allow to switch to upwind 1rst order advection scheme for the advective
221        flux computation at the open-boundary; disabled for adjoint built.
222    o pkg/ptracers:
223      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
224      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
225      - add parameter to decide when to start a tracer; use internal flag to
226        know which tracer to step-forward; switch this internal flag at the top
227        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
228        for adjoint built.
229    o pkg/seaice:
230      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
231      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
232      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
233    o pkg/ecco:
234      - fix writing of output file DiagnosCost_ClimSalt/Theta
235        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
236    o pkg/seaice:
237      - add missing initialisation of COR_ICE array in dynsolver.F
238      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
239        compiled either way, and is tested in all exps (multidim was only tested
240        in lab_sea ad before).
241      - cosmetic change to prepare for future addition of ITD. no change to results.
242        no defaults change.
243      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
244      - by lack of adequate verification experiments, I further used custom versions
245        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
246        should be correct.
247      - avoid recomputations in ad.
248    o array initialisation in adjoint mode:
249      1) pkg/mom_common/mom_calc_ke.F:
250        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
251        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
252        part this initialisation is gone, resulting in Floating Point Exception
253        (caught by open64 compiler with debug option).
254      2) model/src/convective_weights.F
255        set output convectCount over the full array range (instead of doing
256        an update): this fix a similar issue when called within recomputation (adjoint)
257        which could by-pass the initialisation (normally done in the caller S/R).
258    o pkg/seaice:
259      - final version of turbulent flux params, as agreed at MIT ice meet:
260           SEAICE_mcPheePiston (default is ~ 0.000875)
261           SEAICE_mcPheeTaper (default is 0.)
262           SEAICE_frazilFrac (defualt is 1.)
263           SEAICE_mcPheeStepFunc (default is false)
264      - changes results at trunction error level
265      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
266    o added pkg/frazil:
267      - see frazil_description.tex for details
268      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
269    o pkg/shelfice/shelfice_thermodynamics.F
270      - fix exponents for velocity dependent exchange coefficients: change
271        from 2/3(=0) to 0.66666666666666667
272      - move computation of velocity dependent exchange coefficients into
273        separate loop, so that it applies to both thermodynamics
274      - move some divisions by constants out of loops
275    
276    checkpoint63j (2012/02/16)
277    o pkg/seaice:
278      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
279      - SItracer:  added run time params, and allow coupling to ocn salinity.
280    o pkg/seaice: remove (almost) all divisions by constants within loops
281      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
282      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
283      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
284      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
285    o pkg/seaice :
286      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
287        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
288      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
289      - add permanent SItflux diag that corresponds to TFLUX but includes
290        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
291      - allow activation/testing of a fix for suspected missing term in
292        ocn-ice heat budget (to be confirmed). To test this, you want to
293        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
294        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
295      - no change in results, fwd or ad.
296    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
297      - switch to variable freezing point.
298           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
299      - bug fix : the sublimation term that was missing is now activated.
300           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
301      - bug fix : flooding sign term for SIsal0.NE.0.
302           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
303    o pkg/seaice:
304      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
305        is now the default, and the old default constant freezing point is recovered
306        with SEAICE_tempFrz0    = -1.96,
307             SEAICE_dTempFrz_dS = 0.,
308      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
309      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
310      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
311        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
312      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
313        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
314      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
315        seaice_growth r149 for legacy branch (no results change).
316      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
317        from I. Fenty).
318      - results did not change except for global_ocean.cs32x15, mostly due to the
319        switch to variable freezing point (see above item for detail).
320    o pkg/thsice:
321      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
322        seawater freezing in thsice_calc_thickn (not used).
323    o pkg/seaice: turbulent flux term specification via run time params.
324      - replace CPP switches with run time switches to facilitate testing
325      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
326                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
327      - added runtime parameter : SEAICEturbFluxFormula
328      - move Mcphee constants to SEAICE_PARAMS.h
329      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
330                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
331                 remove seaice_summary call (moved to seaice_init_fixed)
332      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
333        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
334      - seaice_summary.F : add missing report of read turbulent flux term set up
335                           and SITRACER.
336      - seaice_check.F : check range; inform and stop if retired CPPs are used
337                         (incl. SEAICE_AGE).
338      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
339             CPP switch, same computation as before for the different options.
340      - change results at the truncation level.
341    o pkg/seaice:
342      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
343        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
344        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
345      - update verification/*/input*/data.seaice:
346        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
347        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
348        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
349        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
350    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
351      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
352        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
353        difference in results only due to machine truncation.
354      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
355        MaykutPolySatVap; keep MIN_LWDOWN.
356      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
357      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
358        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
359    o pkg/salt_plume:
360      - isolate saltPlumeFlux array exch into a specific S/R called from
361        do_oceanic_phys.F
362      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
363    o verification:
364      - move untested set-up to MITgcm_contrib/verification_other.
365    o pkg/seaice:
366      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
367    o pkg/seaice:
368      - seaice_solve4temp.F (keeping results unchanged):
369        * add 2 future run-time params to select which saturation vapor pressure
370          formula is used and how post-iteration fluxes are set.
371          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
372        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
373          the linearized expression to stay consistent with tsurf finding.
374      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
375        can be < 0.
376    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
377      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
378        conductive heat flux F_c , and add it explicitly when updating tsurf as
379        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
380        so that now F_ia has a consistent meaning through the entire routine.
381        This causes differences at truncation level: update output of fwd exp.
382        global_ocean.cs32x15.seaice.
383    o pkg/seaice:
384      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
385        of arrays, sign/direction of fluxes; no effect on results.
386      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
387        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
388        note: this should have been done before changing celsius2K default.
389      - to keep results unchanged, add back old value of celsius2K in verification
390        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
391      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
392        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
393        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
394        freezing temp is consistent with value in seaice_growth.F ; this causes
395        differences at machine truncation level: update lab_sea AD output (3/4).
396    o pkg/seaice:
397      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
398        and climsst/sss even when using seaice (to prevent calculation that might
399        use SST on land); does not affect any verification exp.
400      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
401        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
402    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
403      over land (non-legacy code)
404    o vectorize salt_plume package:
405      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
406      - this code computes plumebk everywhere (also over land), thus requires
407        code to avoid divisions by zero and catch the case of kLev=Nr.
408      - efficiency of salt_plume_frac is still sub-optimal
409    o tools (genmake2):
410      - fix makefile NAME specification (option: -makefile NAME) by adding
411        "-f $MAKEFILE" in few places where it was missing including makedepend
412        command (contribution from Paul).
413    
414    checkpoint63i (2012/01/24)
415    o model/src:
416      - add factorized versions of some EOS code to find_rho.F,
417        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
418    o model/src:
419      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
420      - change default celsius2K from 273.16 to 273.15
421      - to keep results unchanged, add back old value of celsius2K in verification
422        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
423         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
424    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
425      to make TAF generate vectorizable code
426    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
427       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
428       have flags that do this more efficiently.
429    o pkg/diagnostics/diagstats_calc.F
430      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
431    o pkg/obcs (with exch2):
432      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
433        and remove code (in obcs_readparms.F) which was based on EXCH of indices
434        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
435    o pkg/exf and seaice exp:
436      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
437        so that switching off area & heff advection flags does not affect results.
438      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
439      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
440        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
441        results of verification experiments: 1D_ocean_ice_column(fwd),
442        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
443        and offline_exf_seaice (all 4).
444    o pkg/seaice:
445      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
446        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
447      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
448        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
449        not multi-dim advection;
450      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
451        SHORTWAVE_HEATING #undef.
452    o optim: make Makefile more robust (?)
453    o pkg/obcs:
454      * fix treatment of obcs_read_pickup for TAF
455    o pkg/shelfice:
456      * add missing initialisation of num_shifwflx
457      * new adjoint verification exp. for isomip
458      * change Prandtl and Schmidt numbers from generic formulations
459        (in terms of model diffus. and visc.) to separate runtime
460        parameters, with Holland and Jenkins (1999) default values.
461    o pkg/exf (interpolation):
462      - extended input field (2 rows) near the N & S poles:
463        * fill in with the symetric value (when even Nb of data in longitude)
464        * add average value at the poles only for scalar quantities ; for vector
465          component interpolation, skip the averaging and keep duplicated values,
466          unless the 2 components have same location (uvInterp=T) in which case
467          interpolate the 2 components together using S/R EXF_INTERP_UV.
468      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
469        together: this allows to account properly for local orientation when
470        averaging at N & S pole.
471      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
472        exf-interpolation near N & S poles. Undef by default.
473      - add debug check/print on 1rst iter if debugLevel >=2.
474    o pkg/exf:
475      - change masking flags definition (no longer "parameter"), put them in
476        common block and set them in S/R EXF_INIT_FIXED.
477      - change recognized masking flag from s,u,v to c,w,s since the mask
478        to use (maskC,W,S) depends on position on model grid and has little to
479        do with scalar/vector difference; fix masking if using P-coordinates.
480      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
481        and update results of exp. global_with_exf (x2).
482      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
483    o pkg/obcs
484      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
485    o pkg/exf (interpolation):
486      - assume periodicity in X only if input field cover full longitude range.
487      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
488        and should vectorise).
489      - fix input lat of the 2 added row (in case we provide N.pole data).
490    
491    checkpoint63h (2011/12/30)
492    o pkg/seaice:
493      - change declaration of UVM from _RL to _RS in order to get B-grid
494        uIce,vIce monitor when _RS = real*4
495    o pkg/offline:
496      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
497      - compute vertical velocity if not read from file (switch on exactConserv
498        & staggerTimeStep);
499      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
500    o verification:
501      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
502        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
503        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
504      - update output of exp. global_ocean.cs32x15.viscA4 after changing
505        grid-file angles (used here for coriolis-3d);
506      - remove (or gzip) few files not needed to run fizhi-cs experiments.
507    o pkg/exf (vector interpolation):
508      - rotate vector component toward local grid-axis orientation using grid-angles
509        (stored in GRID.h) instead of locally computed rotation angle; keep old code
510        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
511    o pkg/seaice:
512      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
513        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
514    o pkg/PKG_OPTIONS.h files:
515      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
516        outside of the #ifdef ALLOW_THISPKG / #endif block.
517      - update verification/*/code/PKG_OPTIONS.h files.
518    o add a verification experiment (offline_exf_seaice/input.seaice) that test
519      the B-grid LSOR solver
520    o pkg/seaice: sort out emissivity and long wave radiation step 2:
521      - add emissivity for snow and ice as new run-time parameters
522        (unfortunately) that default to the corresponding exf values; this
523        changes results in most verification experiments so that for backward
524        compatibility these parameter have to be set explicitly to inconsistent
525        values (ugly);
526      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
527        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
528        until we agree how to handle this bug properly
529    o pkg/exf (interpolation):
530      - add a set of run-time param ({inputfield}_interpMethod), one for
531        each interpolated input field, to select the interpolation method
532        with a value of zero switching off the interpolation;
533      - print interpolation parameters to standard output;
534      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
535        (to use instead runoff_interpMethod=0 in data.exf).
536      - simplify default setting of interpolation parameters (for all fields,
537        set position to match model grid cell-center position, leading to trivial
538        interpolation in case of regular Lat-Lon grid) and fix for the case of
539        non-uniform delY.
540    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
541       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
542       this factor is absolutely required, because the lw exitance (= out-going
543       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
544       where the reflectivity rho = 1-emissivity for conservation reasons. Once
545       this is established, we can remove the CPP-Flag (if we want to).
546    o pkg/seaice:
547      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
548        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
549      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
550        what the name implies (and not emissivity*BoltzmannConstant), this means
551        the old default value of 5.5e-8 now means
552        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
553        S/R exf_readparms
554      - FV-discretization of the B-grid LSOR solver, turn on with
555        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
556        of the calling routine dynsolver, so that B and C-grid code look a
557        little more alike.
558      - fix index bugs in ostres.F (B-grid code)
559    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
560    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
561      default for SEAICE_emissivity, if useEXF; requires setting a wrong
562      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
563      backward compatiblity
564    o model/src: use sigmaR in calc_ivdc
565    
566    checkpoint63g (2011/12/16)
567    o pkg/seaice/seaice_growth.F:
568      fix heat conservation of the coupled ocean-seaice system.
569      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
570      solid vs liquid water treatment is resolved via QNET.
571    o pkg/seaice/seaice_growth.F:
572      add missing term for sublimation in saltFlux, which was breaking conservation.
573    o pkg/seaice/seaice_model.F:
574      Remove this patholigical case treatment in evolution branch,
575      where it is un-necessary and breaks conservation.
576      Update global_ocean.cs32x15/results accordingly for
577      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
578    o model/src:
579      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
580      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
581    o pkg/obcs:
582      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
583      tendency for temperature and salinity that is then applied to update
584      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
585      horizontal advection and diffusion contributions on the boundary (in
586      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
587      removing the mask in S/R timestep_tracer. The advantage of this approach is
588      that the updated tracer values include contributions from the surface
589      forcing and vertical diffusion.
590      This modification changes exp4.stevens because of vertical diffusion.
591    o model/src:
592      change non-curvilinear grid setting to also work with exch2 + blank tiles:
593      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
594        face dimensions.
595      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
596        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
597        and INI_SPHERICAL_POLAR_GRID.
598      change test-experiment global_ocean.90x40x15:
599      - split the domain in many more tiles (9x4 tiles of 10x10 each);
600      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
601      - update results of both test (std & dwnslp).
602    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
603       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
604    o model/src:
605      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
606        and fix initialisation when using sigma-coords.
607    o model/src:
608     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
609       to their current value at the beginning of forward_step.F": add a new run-time
610       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
611     - set doResetHFactors=T in the following test exp:
612        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
613        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
614        and tutorial_global_oce_in_p (nonLinFS in p)
615    o pkg/ecco
616      - added IES cost term
617    o verification/advect_xz
618      - scale down the depth by 1/100 (from 200 km to just 2.km)
619      - add secondary test using divergent flow, r-star and implicit vertical advection.
620      - add note (check_conserve_TS.txt) and matlab script to check global
621        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
622    o pkg/rbcs:
623      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
624    o pkg/obcs (Stevens BCs):
625      - fix various problems in the phase speed computations of the Stevens
626        boundary conditions:
627        - sign error for western and southern boundaries,
628        - time tendencies were underestimated by factor of dTracerLev and some just
629          zero (for multidim advection schemes) -> now estimate time tendencies
630          from difference between previous (n) time level and the one before (n-1);
631          this requires storing a field per tracer per boundary, also in the pickup
632          files.
633        - replace deltaTmom in cflMer/Zon computation with dTracerLev
634        - set default phase velocity to cflMer/Zon
635      - update verification experiment exp4.stevens
636    o pkg/generic_advdiff (implicit_r):
637      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
638        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
639      - fix implicit vertical diffusion or advection with NonLin FreeSurf
640        (was using current recip_hFacC instead of future recip_hFacC): set future
641        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
642        solver S/R ;
643      - fill diagnostics of vertical advective fluxes (computed from tendency)
644        when using implicit vert. advection;
645      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
646         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
647         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
648         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
649    o pkg/diagnostics:
650      - add diags for T & S tendency which goes through Adams-Bashforth.
651    
652    checkpoint63f (2011/11/30)
653    o pkg/obcs/obcs_calc_stevens.F:
654      - join some loops to reduce number of if-statements
655      - fix a bug in code for northern and southern boundaries.
656    o pkg/seaice/seaice_init_varia.F
657      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
658        caused zero ice-velocities for the B-grid code
659    o pkg/seaice/seaice_init_fixed.F
660      - fix a bug in the initialisation of the second metric terms
661        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
662      - this affects all seaice configurations with useCurviLinearGrid = .true.
663        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
664        = .true. (default)
665      - the only verification experiment affected is global_ocean.cs32x15:
666        icedyn, seaice, and seaice_dynmix (AD)
667    o pkg/thsice/thsice_diagnostics_state.F
668      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
669        not contain garbage that can lead to surprises in diagstats_calc.F
670    o model/src:
671      - move bi,bj loops inside INTEGR_CONTINUITY ;
672      - call INTEGR_CONTINUITY directly from forward_step.F
673        (previously called from momentum_correction_step.F)
674      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
675        forward_step.F and pkg/ecco/the_main_loop.F
676    o model/src/do_oceanic_phys.F:
677      - reset addMass to zero only if useICEFRONT ;
678      - separated k-loop for rhoInSitu calculation ;
679      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
680        and at constant T,S (= WdRHOdP);
681      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
682        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
683        transport of locally-referenced potential density);
684        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
685    o gluemnc:
686      - replace ncrcat with ncks when adding variables to *.glob.nc
687      - change the way variables without record dimensions are handled so that
688        files that have variables with and without record variables can be glued:
689        add a record dimension with a new unique name to be able to differentiate
690        between variable with and without a-prior record dimensions. Remove
691        this record dimension before adding the variable to the *.glob.nc file.
692        This procedure automatically works also for grid.*.nc files that do not
693        have any record dimension.
694    o verification/cpl_aim+ocn:
695      - generate new reference output on baudelaire (gfortran, mpich2) (previously
696        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
697    o pkg/obcs/obcs_calc_stevens.F:
698      - add code for northern and southern boundaries.
699      - reorder some loops to save some operations and so that drFBar can be scalar
700    o model/src:
701      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
702        truncation) and add diagnostics for Adams-Bashforth tendency increment.
703      - update test-exp. AD output:
704        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
705      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
706        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
707        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
708        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
709        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
710        tutorial_plume_on_slope.
711    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
712      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
713      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
714      does not even come with an F77 compiler anymore, this should not be
715      a limitation
716    
717    checkpoint63e (2011/11/06)
718    o pkg/seaice adjoint of LSR:
719      - substantially rework STORE dirs.
720      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
721        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
722        and only perform SOLV_MAX_FIXED adjoint iters.
723        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
724        always goes to same record, meaning that the last forward field will be
725        the one used in the adjoint - an approximation.
726      - now produces non-zero LSR-related gradients, and acceptable gradients for
727        An's zonal (x-z) test case (to be checked in)
728      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
729        (but these are screwed up by the thermodynamics in the first place);
730        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
731        output_adm.txt also reflects changes to seaice_lsr
732      - global_ocean.cs32x15:
733        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
734          (output_adm.seaice.txt was updated)
735        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
736          (output_adm.seaice_dynmix.txt)
737    o test-exp. exp4+stevens:
738      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
739    o pkg/seaice (lsr solver):
740      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
741        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
742      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
743      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
744        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
745      - compute (with new S/R) and print initial (+ free-driff sol. if available)
746        and final residual of linearised system.
747    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
748      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
749    o pkg/obcs: Stevens BCs (still only for east and west)
750      - fix Stevens BCs by using intermediate velocities of previous
751        time step as "baroclinic" contribution rather velocity of one grid cell
752        inside the boundaries; more consistent but makes the entire treatment
753        more complicated, requires new pickup files and two new S/Rs:
754        obcs_copy_uv_n and obcs_save_uv_n
755        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
756        (undefined by default)
757      - silently move computation of some grid factors into separate loops to
758        save some recomputations
759      - add a hack for non-linear free surface
760      - add a verification experiment to exp4 that tests this code
761    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
762    
763    checkpoint63d (2011/10/25)
764    o pkg/obcs + seaice-dynamics:
765      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
766        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
767        values (consistent with an implicit method).
768      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
769        return to older implementation (same results as before); note that none of
770        the "experimental" OBCS_SEAICE options are implemented in the new version.
771      - switch test exp. seaice_obcs to use new version (update output).
772    o pkg/seaice:
773      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
774      - add parenthesis in Water-Ice drag calculations (evp & lsr);
775      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
776        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
777      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
778        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
779    o pkg/layers:
780      - Include potential density as new coordinate (Thanks to David Munday)
781    o pkg/dic:
782      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
783        carbonate computation/output to CALC_PCO2_APPROX
784    o pkg/generic_advdiff
785      - make TAF generate code that vectorizes:
786        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
787    o model/src:
788      - improve vectorization also for adjoint code of
789        solve_tridiagonal and solve_pentadiagonal. As this requires up to
790        5 new 3D-fields, this code is only turned on for the combination of
791        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
792        for singular matrix check (only for TARGET_NEC_SX).
793      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
794        ALLOW_AUTODIFF. This flag now needs to be set outside of
795        solve_tri/pentadiagonal.F
796    o pkg/exf:
797      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
798        optional namelist EXF_NML_OBCS).
799      - add many debug-print (to trace down where pkg/cal error msg comes from)
800    o pkg/mom_vecinv/mom_vi_hdissip.F
801      - rearrange loops so that vectorization is improved and in particular
802        the adjoint routine vectorizes. The code is a little longer now, but I
803        think easier to read.
804        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
805    o pkg/seaice:
806      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
807    o pkg/exch2:
808      - alternative code (without tile x tile matrix) for cumulated (global) sum;
809        used as default; keep using matrix version in adjustment.cs-32x32x1.
810    o tools/build_options:
811      - after merging some MPI and/or multi-threads specific optfiles so that
812        the modified default optfile support both built (using genmake2 -mpi
813        for the MPI built, using genmake2 -omp for OpenMP built),
814        move now obsolete optfiles to tools/build_options/unsupported/
815       (add copy of email sent to support list in doc/optfiles_changes.txt)
816    
817    checkpoint63c (2011/09/28)
818    o pkg/ebm:
819      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
820        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
821  o pkg/seaice (SItracer pickup)  o pkg/seaice (SItracer pickup)
822  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
823    To be done:    To be done:
824    - thorough testing of missing fields in S/R seaice_read_pickup    - thorough testing of missing fields in S/R seaice_read_pickup
825    - thorough matching between generic tracers and specific fields used    - thorough matching between generic tracers and specific fields used
826      (e.g. volume-weighted age, area-weighted age, salinity, ...)      (e.g. volume-weighted age, area-weighted age, salinity, ...)
827    o pkg/grdchk:
828      - all procs calculate and print finite-difference gradient (for testreport)
829      - change description output used by testreport;
830      - AD testing: also compare and report Finite-difference gradient;
831        => update all output_adm*.txt
832    o test exp. global_ocean_ebm:
833      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
834        and turn on exactConserve; update (fwd) output.
835  o pkg/seaice (LSR):  o pkg/seaice (LSR):
836    - print to STDOUT number of solver iterations at SEAICE_monFreq interval.    - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
837    - modify solver to deal cleanly with u/v switch at face edges (CS-grid):    - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
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