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revision 1.1454 by jmc, Tue Jun 14 16:52:22 2011 UTC revision 1.1650 by jmc, Wed Apr 11 18:17:42 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 model/src:
8     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
9       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
10       temporary set to usingZCoords value (to be changed to F when using shelfice).
11     - hydrostatic pressure: implement partial cell near the surface also for
12       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
13       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
14    o pkg/ctrl/ctrl_init.F:
15     - add a formal parameter to s/r ctrl_init_rec to print
16       xx_$(ctrl_valiable)_file for easier debugging
17     - move call of cal_* routines into the if-block where they are really
18       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
19       to specify a startdate
20    o pkg/seaice:
21     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
22       global_ocean.cs32x15/code versions).
23     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
24       verification experiment global_ocean.cs32x15.seaice and update results.
25    o pkg/exf:
26     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
27       (according to useExfYearlyFields).
28    o pkg/cal:
29     - move calendar setting & summary (previously in cal_readparams.F) into new
30       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
31       length of the simulation is set (after SET_PARMS call); This is an attempt
32       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
33     - For safety: keep a record of pkg/cal parameter settings status
34               to allow to STOP if one pkg/cal S/R is called too early.
35     - add a stop in all basic pkg/cal subroutines if called before setting is done.
36     - modify cal_getdate.F: stop when nothing was returned;
37       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
38       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
39    
40    checkpoint63l (2012/04/04)
41    o pkg/bbl:
42      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
43        update global_with_exf output.yearly.txt file.
44    o pkg/cal:
45      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
46      - remove 2 unsused and very short (1 line only) functions ;
47      - remove unsused subroutines from AD-Diff list.
48    o model/src:
49      - start to implement clean wait to stop in initialization S/R (config_check.F,
50         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
51    o folowing PRINT_MESSAGE changes:
52      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
53    o pkg/bbl:
54      - modification so it can work with z*
55      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
56      - global_with_exf/input.yearly verification; changes output.yearly.txt
57    o eesupp/src:
58      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
59        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
60      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
61        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
62      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
63      - when using MPI, always set usingMPI=T ; set default accordingly and stop
64        if not consistent.
65      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
66        argument is zero (in case called within single-thread section).
67    o pkg/fizhi:
68        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
69        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
70    o pkg/exch2:
71      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
72        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
73      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
74        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
75        with bad ones coming from a not-yet-updated halo.
76        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
77    o pkg/frazil:
78        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
79        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
80    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
81    o verification/lab_sea
82      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
83      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
84      * nTimeSteps 3 -> 4
85      * changed reference output accordingly
86    o pkg/ctrl:
87      * fix ctrl_get_gen for xx_sst, xx_sss
88    o pkg/fizhi:
89      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
90        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
91      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
92        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
93        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
94    o pkg/gmredi:
95      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
96    o pkg/fizhi:
97      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
98        (old)aces open64 tuv test.
99    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
100    o pkg/mom_vecinv:
101      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
102        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
103        with non-lin free-surf).
104    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
105      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
106      some compilers (gfortran 4.6.0 on MacOS)
107    o momentum:
108      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
109        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
110        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
111    
112    checkpoint63k (2012/03/17)
113    o model/src:
114       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
115         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
116       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
117         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
118    o model/src: solve_*diagonal.F
119       - replace division with multiplication by inverse (similar to original version)
120         update output of AD exp. global_ocean.90x40x15.
121       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
122         to enable the use of the vectorized & differentiable solve_tridiagonal.F
123       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
124         vertical advection (to get solve_tridiagonal tested in AD mode).
125    o pkg/seaice: ECCO-CLIVAR merge:
126      1. seaice AREA relaxation
127         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
128         * runtime flag: SEAICE_tauAreaObsRelax
129      2. modified global mean cost imbalance code: CPP option
130          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
131    o another iteration on solve_*diagonal.F
132       Make choices independent of AUTODIFF
133       Default will be the adjoinable vectorized version.
134       Alternative choices are:
135       * non-adjoinable original version with low memory footprint:
136         #define SOLVE_DIAGONAL_LOWMEMORY
137       * still adjoinable but does not vectorize (k as inner-most loop):
138         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
139    o testreport
140     - add option to use a home made wrapper around "make"
141     - remove MITGCM_IEEE env. variable (no longer active)
142    o pkg/shelfice
143     - improve computation of friction velocity for velocity dependent
144       exchange coefficients: include velocities into SHELFICEBoundaryLayer
145       block to average velocities vertically
146     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
147    o Modify diagonal solvers, now three versions (upon request):
148      #ifndef SOLVE_DIAGONAL_AUTODIFF
149        1. default version (dating back a while ago)
150      #else /* def SOLVE_DIAGONAL_AUTODIFF */
151      # ifdef SOLVE_DIAGONAL_KINNER
152        2. adjoinable version with k-innermost loop (G. Forget)
153      # else
154        3. adjoinable vectorized version of 2.
155      # endif
156      #endif /* SOLVE_DIAGONAL_AUTODIFF */
157      All flags are currently set within routines, but could/should be moved to CPP-options.
158      Array bounds for 1. are as before, for 2.,3. cover the entire domain
159      (could be changed for 1. too).
160    o verification/lab_sea (fwd):
161      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
162        use 7 categories (except hb87), new solve4temp params (except salt_plume),
163        constant salinity (=4) or variable salinity (salt_plume) done through
164        SItracer.
165    o pkg/seaice:
166      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
167      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
168         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
169        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
170        SEAICE_freeze got retired) but already better than previously with
171        SEAICE_freeze=123456.7 deg.C;
172      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
173        (safer multi-threaded setting); always set SEAICEuseEVP;
174      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
175        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
176        stop if multiple specifications for the same coeff; make sure default
177        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
178    o pkg/obcs:
179      - allow to switch to upwind 1rst order advection scheme for the advective
180        flux computation at the open-boundary; disabled for adjoint built.
181    o pkg/ptracers:
182      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
183      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
184      - add parameter to decide when to start a tracer; use internal flag to
185        know which tracer to step-forward; switch this internal flag at the top
186        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
187        for adjoint built.
188    o pkg/seaice:
189      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
190      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
191      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
192    o pkg/ecco:
193      - fix writing of output file DiagnosCost_ClimSalt/Theta
194        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
195    o pkg/seaice:
196      - add missing initialisation of COR_ICE array in dynsolver.F
197      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
198        compiled either way, and is tested in all exps (multidim was only tested
199        in lab_sea ad before).
200      - cosmetic change to prepare for future addition of ITD. no change to results.
201        no defaults change.
202      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
203      - by lack of adequate verification experiments, I further used custom versions
204        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
205        should be correct.
206      - avoid recomputations in ad.
207    o array initialisation in adjoint mode:
208      1) pkg/mom_common/mom_calc_ke.F:
209        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
210        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
211        part this initialisation is gone, resulting in Floating Point Exception
212        (caught by open64 compiler with debug option).
213      2) model/src/convective_weights.F
214        set output convectCount over the full array range (instead of doing
215        an update): this fix a similar issue when called within recomputation (adjoint)
216        which could by-pass the initialisation (normally done in the caller S/R).
217    o pkg/seaice:
218      - final version of turbulent flux params, as agreed at MIT ice meet:
219           SEAICE_mcPheePiston (default is ~ 0.000875)
220           SEAICE_mcPheeTaper (default is 0.)
221           SEAICE_frazilFrac (defualt is 1.)
222           SEAICE_mcPheeStepFunc (default is false)
223      - changes results at trunction error level
224      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
225    o added pkg/frazil:
226      - see frazil_description.tex for details
227      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
228    o pkg/shelfice/shelfice_thermodynamics.F
229      - fix exponents for velocity dependent exchange coefficients: change
230        from 2/3(=0) to 0.66666666666666667
231      - move computation of velocity dependent exchange coefficients into
232        separate loop, so that it applies to both thermodynamics
233      - move some divisions by constants out of loops
234    
235    checkpoint63j (2012/02/16)
236    o pkg/seaice:
237      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
238      - SItracer:  added run time params, and allow coupling to ocn salinity.
239    o pkg/seaice: remove (almost) all divisions by constants within loops
240      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
241      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
242      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
243      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
244    o pkg/seaice :
245      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
246        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
247      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
248      - add permanent SItflux diag that corresponds to TFLUX but includes
249        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
250      - allow activation/testing of a fix for suspected missing term in
251        ocn-ice heat budget (to be confirmed). To test this, you want to
252        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
253        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
254      - no change in results, fwd or ad.
255    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
256      - switch to variable freezing point.
257           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
258      - bug fix : the sublimation term that was missing is now activated.
259           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
260      - bug fix : flooding sign term for SIsal0.NE.0.
261           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
262    o pkg/seaice:
263      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
264        is now the default, and the old default constant freezing point is recovered
265        with SEAICE_tempFrz0    = -1.96,
266             SEAICE_dTempFrz_dS = 0.,
267      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
268      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
269      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
270        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
271      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
272        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
273      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
274        seaice_growth r149 for legacy branch (no results change).
275      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
276        from I. Fenty).
277      - results did not change except for global_ocean.cs32x15, mostly due to the
278        switch to variable freezing point (see above item for detail).
279    o pkg/thsice:
280      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
281        seawater freezing in thsice_calc_thickn (not used).
282    o pkg/seaice: turbulent flux term specification via run time params.
283      - replace CPP switches with run time switches to facilitate testing
284      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
285                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
286      - added runtime parameter : SEAICEturbFluxFormula
287      - move Mcphee constants to SEAICE_PARAMS.h
288      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
289                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
290                 remove seaice_summary call (moved to seaice_init_fixed)
291      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
292        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
293      - seaice_summary.F : add missing report of read turbulent flux term set up
294                           and SITRACER.
295      - seaice_check.F : check range; inform and stop if retired CPPs are used
296                         (incl. SEAICE_AGE).
297      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
298             CPP switch, same computation as before for the different options.
299      - change results at the truncation level.
300    o pkg/seaice:
301      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
302        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
303        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
304      - update verification/*/input*/data.seaice:
305        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
306        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
307        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
308        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
309    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
310      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
311        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
312        difference in results only due to machine truncation.
313      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
314        MaykutPolySatVap; keep MIN_LWDOWN.
315      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
316      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
317        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
318    o pkg/salt_plume:
319      - isolate saltPlumeFlux array exch into a specific S/R called from
320        do_oceanic_phys.F
321      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
322    o verification:
323      - move untested set-up to MITgcm_contrib/verification_other.
324    o pkg/seaice:
325      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
326    o pkg/seaice:
327      - seaice_solve4temp.F (keeping results unchanged):
328        * add 2 future run-time params to select which saturation vapor pressure
329          formula is used and how post-iteration fluxes are set.
330          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
331        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
332          the linearized expression to stay consistent with tsurf finding.
333      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
334        can be < 0.
335    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
336      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
337        conductive heat flux F_c , and add it explicitly when updating tsurf as
338        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
339        so that now F_ia has a consistent meaning through the entire routine.
340        This causes differences at truncation level: update output of fwd exp.
341        global_ocean.cs32x15.seaice.
342    o pkg/seaice:
343      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
344        of arrays, sign/direction of fluxes; no effect on results.
345      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
346        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
347        note: this should have been done before changing celsius2K default.
348      - to keep results unchanged, add back old value of celsius2K in verification
349        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
350      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
351        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
352        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
353        freezing temp is consistent with value in seaice_growth.F ; this causes
354        differences at machine truncation level: update lab_sea AD output (3/4).
355    o pkg/seaice:
356      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
357        and climsst/sss even when using seaice (to prevent calculation that might
358        use SST on land); does not affect any verification exp.
359      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
360        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
361    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
362      over land (non-legacy code)
363    o vectorize salt_plume package:
364      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
365      - this code computes plumebk everywhere (also over land), thus requires
366        code to avoid divisions by zero and catch the case of kLev=Nr.
367      - efficiency of salt_plume_frac is still sub-optimal
368    o tools (genmake2):
369      - fix makefile NAME specification (option: -makefile NAME) by adding
370        "-f $MAKEFILE" in few places where it was missing including makedepend
371        command (contribution from Paul).
372    
373    checkpoint63i (2012/01/24)
374    o model/src:
375      - add factorized versions of some EOS code to find_rho.F,
376        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
377    o model/src:
378      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
379      - change default celsius2K from 273.16 to 273.15
380      - to keep results unchanged, add back old value of celsius2K in verification
381        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
382         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
383    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
384      to make TAF generate vectorizable code
385    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
386       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
387       have flags that do this more efficiently.
388    o pkg/diagnostics/diagstats_calc.F
389      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
390    o pkg/obcs (with exch2):
391      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
392        and remove code (in obcs_readparms.F) which was based on EXCH of indices
393        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
394    o pkg/exf and seaice exp:
395      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
396        so that switching off area & heff advection flags does not affect results.
397      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
398      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
399        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
400        results of verification experiments: 1D_ocean_ice_column(fwd),
401        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
402        and offline_exf_seaice (all 4).
403    o pkg/seaice:
404      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
405        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
406      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
407        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
408        not multi-dim advection;
409      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
410        SHORTWAVE_HEATING #undef.
411    o optim: make Makefile more robust (?)
412    o pkg/obcs:
413      * fix treatment of obcs_read_pickup for TAF
414    o pkg/shelfice:
415      * add missing initialisation of num_shifwflx
416      * new adjoint verification exp. for isomip
417      * change Prandtl and Schmidt numbers from generic formulations
418        (in terms of model diffus. and visc.) to separate runtime
419        parameters, with Holland and Jenkins (1999) default values.
420    o pkg/exf (interpolation):
421      - extended input field (2 rows) near the N & S poles:
422        * fill in with the symetric value (when even Nb of data in longitude)
423        * add average value at the poles only for scalar quantities ; for vector
424          component interpolation, skip the averaging and keep duplicated values,
425          unless the 2 components have same location (uvInterp=T) in which case
426          interpolate the 2 components together using S/R EXF_INTERP_UV.
427      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
428        together: this allows to account properly for local orientation when
429        averaging at N & S pole.
430      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
431        exf-interpolation near N & S poles. Undef by default.
432      - add debug check/print on 1rst iter if debugLevel >=2.
433    o pkg/exf:
434      - change masking flags definition (no longer "parameter"), put them in
435        common block and set them in S/R EXF_INIT_FIXED.
436      - change recognized masking flag from s,u,v to c,w,s since the mask
437        to use (maskC,W,S) depends on position on model grid and has little to
438        do with scalar/vector difference; fix masking if using P-coordinates.
439      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
440        and update results of exp. global_with_exf (x2).
441      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
442    o pkg/obcs
443      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
444    o pkg/exf (interpolation):
445      - assume periodicity in X only if input field cover full longitude range.
446      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
447        and should vectorise).
448      - fix input lat of the 2 added row (in case we provide N.pole data).
449    
450    checkpoint63h (2011/12/30)
451    o pkg/seaice:
452      - change declaration of UVM from _RL to _RS in order to get B-grid
453        uIce,vIce monitor when _RS = real*4
454    o pkg/offline:
455      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
456      - compute vertical velocity if not read from file (switch on exactConserv
457        & staggerTimeStep);
458      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
459    o verification:
460      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
461        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
462        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
463      - update output of exp. global_ocean.cs32x15.viscA4 after changing
464        grid-file angles (used here for coriolis-3d);
465      - remove (or gzip) few files not needed to run fizhi-cs experiments.
466    o pkg/exf (vector interpolation):
467      - rotate vector component toward local grid-axis orientation using grid-angles
468        (stored in GRID.h) instead of locally computed rotation angle; keep old code
469        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
470    o pkg/seaice:
471      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
472        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
473    o pkg/PKG_OPTIONS.h files:
474      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
475        outside of the #ifdef ALLOW_THISPKG / #endif block.
476      - update verification/*/code/PKG_OPTIONS.h files.
477    o add a verification experiment (offline_exf_seaice/input.seaice) that test
478      the B-grid LSOR solver
479    o pkg/seaice: sort out emissivity and long wave radiation step 2:
480      - add emissivity for snow and ice as new run-time parameters
481        (unfortunately) that default to the corresponding exf values; this
482        changes results in most verification experiments so that for backward
483        compatibility these parameter have to be set explicitly to inconsistent
484        values (ugly);
485      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
486        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
487        until we agree how to handle this bug properly
488    o pkg/exf (interpolation):
489      - add a set of run-time param ({inputfield}_interpMethod), one for
490        each interpolated input field, to select the interpolation method
491        with a value of zero switching off the interpolation;
492      - print interpolation parameters to standard output;
493      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
494        (to use instead runoff_interpMethod=0 in data.exf).
495      - simplify default setting of interpolation parameters (for all fields,
496        set position to match model grid cell-center position, leading to trivial
497        interpolation in case of regular Lat-Lon grid) and fix for the case of
498        non-uniform delY.
499    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
500       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
501       this factor is absolutely required, because the lw exitance (= out-going
502       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
503       where the reflectivity rho = 1-emissivity for conservation reasons. Once
504       this is established, we can remove the CPP-Flag (if we want to).
505    o pkg/seaice:
506      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
507        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
508      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
509        what the name implies (and not emissivity*BoltzmannConstant), this means
510        the old default value of 5.5e-8 now means
511        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
512        S/R exf_readparms
513      - FV-discretization of the B-grid LSOR solver, turn on with
514        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
515        of the calling routine dynsolver, so that B and C-grid code look a
516        little more alike.
517      - fix index bugs in ostres.F (B-grid code)
518    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
519    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
520      default for SEAICE_emissivity, if useEXF; requires setting a wrong
521      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
522      backward compatiblity
523    o model/src: use sigmaR in calc_ivdc
524    
525    checkpoint63g (2011/12/16)
526    o pkg/seaice/seaice_growth.F:
527      fix heat conservation of the coupled ocean-seaice system.
528      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
529      solid vs liquid water treatment is resolved via QNET.
530    o pkg/seaice/seaice_growth.F:
531      add missing term for sublimation in saltFlux, which was breaking conservation.
532    o pkg/seaice/seaice_model.F:
533      Remove this patholigical case treatment in evolution branch,
534      where it is un-necessary and breaks conservation.
535      Update global_ocean.cs32x15/results accordingly for
536      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
537    o model/src:
538      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
539      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
540    o pkg/obcs:
541      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
542      tendency for temperature and salinity that is then applied to update
543      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
544      horizontal advection and diffusion contributions on the boundary (in
545      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
546      removing the mask in S/R timestep_tracer. The advantage of this approach is
547      that the updated tracer values include contributions from the surface
548      forcing and vertical diffusion.
549      This modification changes exp4.stevens because of vertical diffusion.
550    o model/src:
551      change non-curvilinear grid setting to also work with exch2 + blank tiles:
552      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
553        face dimensions.
554      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
555        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
556        and INI_SPHERICAL_POLAR_GRID.
557      change test-experiment global_ocean.90x40x15:
558      - split the domain in many more tiles (9x4 tiles of 10x10 each);
559      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
560      - update results of both test (std & dwnslp).
561    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
562       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
563    o model/src:
564      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
565        and fix initialisation when using sigma-coords.
566    o model/src:
567     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
568       to their current value at the beginning of forward_step.F": add a new run-time
569       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
570     - set doResetHFactors=T in the following test exp:
571        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
572        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
573        and tutorial_global_oce_in_p (nonLinFS in p)
574    o pkg/ecco
575      - added IES cost term
576    o verification/advect_xz
577      - scale down the depth by 1/100 (from 200 km to just 2.km)
578      - add secondary test using divergent flow, r-star and implicit vertical advection.
579      - add note (check_conserve_TS.txt) and matlab script to check global
580        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
581    o pkg/rbcs:
582      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
583    o pkg/obcs (Stevens BCs):
584      - fix various problems in the phase speed computations of the Stevens
585        boundary conditions:
586        - sign error for western and southern boundaries,
587        - time tendencies were underestimated by factor of dTracerLev and some just
588          zero (for multidim advection schemes) -> now estimate time tendencies
589          from difference between previous (n) time level and the one before (n-1);
590          this requires storing a field per tracer per boundary, also in the pickup
591          files.
592        - replace deltaTmom in cflMer/Zon computation with dTracerLev
593        - set default phase velocity to cflMer/Zon
594      - update verification experiment exp4.stevens
595    o pkg/generic_advdiff (implicit_r):
596      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
597        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
598      - fix implicit vertical diffusion or advection with NonLin FreeSurf
599        (was using current recip_hFacC instead of future recip_hFacC): set future
600        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
601        solver S/R ;
602      - fill diagnostics of vertical advective fluxes (computed from tendency)
603        when using implicit vert. advection;
604      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
605         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
606         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
607         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
608    o pkg/diagnostics:
609      - add diags for T & S tendency which goes through Adams-Bashforth.
610    
611    checkpoint63f (2011/11/30)
612    o pkg/obcs/obcs_calc_stevens.F:
613      - join some loops to reduce number of if-statements
614      - fix a bug in code for northern and southern boundaries.
615    o pkg/seaice/seaice_init_varia.F
616      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
617        caused zero ice-velocities for the B-grid code
618    o pkg/seaice/seaice_init_fixed.F
619      - fix a bug in the initialisation of the second metric terms
620        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
621      - this affects all seaice configurations with useCurviLinearGrid = .true.
622        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
623        = .true. (default)
624      - the only verification experiment affected is global_ocean.cs32x15:
625        icedyn, seaice, and seaice_dynmix (AD)
626    o pkg/thsice/thsice_diagnostics_state.F
627      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
628        not contain garbage that can lead to surprises in diagstats_calc.F
629    o model/src:
630      - move bi,bj loops inside INTEGR_CONTINUITY ;
631      - call INTEGR_CONTINUITY directly from forward_step.F
632        (previously called from momentum_correction_step.F)
633      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
634        forward_step.F and pkg/ecco/the_main_loop.F
635    o model/src/do_oceanic_phys.F:
636      - reset addMass to zero only if useICEFRONT ;
637      - separated k-loop for rhoInSitu calculation ;
638      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
639        and at constant T,S (= WdRHOdP);
640      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
641        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
642        transport of locally-referenced potential density);
643        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
644    o gluemnc:
645      - replace ncrcat with ncks when adding variables to *.glob.nc
646      - change the way variables without record dimensions are handled so that
647        files that have variables with and without record variables can be glued:
648        add a record dimension with a new unique name to be able to differentiate
649        between variable with and without a-prior record dimensions. Remove
650        this record dimension before adding the variable to the *.glob.nc file.
651        This procedure automatically works also for grid.*.nc files that do not
652        have any record dimension.
653    o verification/cpl_aim+ocn:
654      - generate new reference output on baudelaire (gfortran, mpich2) (previously
655        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
656    o pkg/obcs/obcs_calc_stevens.F:
657      - add code for northern and southern boundaries.
658      - reorder some loops to save some operations and so that drFBar can be scalar
659    o model/src:
660      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
661        truncation) and add diagnostics for Adams-Bashforth tendency increment.
662      - update test-exp. AD output:
663        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
664      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
665        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
666        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
667        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
668        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
669        tutorial_plume_on_slope.
670    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
671      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
672      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
673      does not even come with an F77 compiler anymore, this should not be
674      a limitation
675    
676    checkpoint63e (2011/11/06)
677    o pkg/seaice adjoint of LSR:
678      - substantially rework STORE dirs.
679      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
680        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
681        and only perform SOLV_MAX_FIXED adjoint iters.
682        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
683        always goes to same record, meaning that the last forward field will be
684        the one used in the adjoint - an approximation.
685      - now produces non-zero LSR-related gradients, and acceptable gradients for
686        An's zonal (x-z) test case (to be checked in)
687      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
688        (but these are screwed up by the thermodynamics in the first place);
689        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
690        output_adm.txt also reflects changes to seaice_lsr
691      - global_ocean.cs32x15:
692        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
693          (output_adm.seaice.txt was updated)
694        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
695          (output_adm.seaice_dynmix.txt)
696    o test-exp. exp4+stevens:
697      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
698    o pkg/seaice (lsr solver):
699      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
700        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
701      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
702      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
703        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
704      - compute (with new S/R) and print initial (+ free-driff sol. if available)
705        and final residual of linearised system.
706    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
707      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
708    o pkg/obcs: Stevens BCs (still only for east and west)
709      - fix Stevens BCs by using intermediate velocities of previous
710        time step as "baroclinic" contribution rather velocity of one grid cell
711        inside the boundaries; more consistent but makes the entire treatment
712        more complicated, requires new pickup files and two new S/Rs:
713        obcs_copy_uv_n and obcs_save_uv_n
714        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
715        (undefined by default)
716      - silently move computation of some grid factors into separate loops to
717        save some recomputations
718      - add a hack for non-linear free surface
719      - add a verification experiment to exp4 that tests this code
720    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
721    
722    checkpoint63d (2011/10/25)
723    o pkg/obcs + seaice-dynamics:
724      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
725        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
726        values (consistent with an implicit method).
727      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
728        return to older implementation (same results as before); note that none of
729        the "experimental" OBCS_SEAICE options are implemented in the new version.
730      - switch test exp. seaice_obcs to use new version (update output).
731    o pkg/seaice:
732      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
733      - add parenthesis in Water-Ice drag calculations (evp & lsr);
734      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
735        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
736      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
737        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
738    o pkg/layers:
739      - Include potential density as new coordinate (Thanks to David Munday)
740    o pkg/dic:
741      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
742        carbonate computation/output to CALC_PCO2_APPROX
743    o pkg/generic_advdiff
744      - make TAF generate code that vectorizes:
745        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
746    o model/src:
747      - improve vectorization also for adjoint code of
748        solve_tridiagonal and solve_pentadiagonal. As this requires up to
749        5 new 3D-fields, this code is only turned on for the combination of
750        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
751        for singular matrix check (only for TARGET_NEC_SX).
752      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
753        ALLOW_AUTODIFF. This flag now needs to be set outside of
754        solve_tri/pentadiagonal.F
755    o pkg/exf:
756      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
757        optional namelist EXF_NML_OBCS).
758      - add many debug-print (to trace down where pkg/cal error msg comes from)
759    o pkg/mom_vecinv/mom_vi_hdissip.F
760      - rearrange loops so that vectorization is improved and in particular
761        the adjoint routine vectorizes. The code is a little longer now, but I
762        think easier to read.
763        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
764    o pkg/seaice:
765      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
766    o pkg/exch2:
767      - alternative code (without tile x tile matrix) for cumulated (global) sum;
768        used as default; keep using matrix version in adjustment.cs-32x32x1.
769    o tools/build_options:
770      - after merging some MPI and/or multi-threads specific optfiles so that
771        the modified default optfile support both built (using genmake2 -mpi
772        for the MPI built, using genmake2 -omp for OpenMP built),
773        move now obsolete optfiles to tools/build_options/unsupported/
774       (add copy of email sent to support list in doc/optfiles_changes.txt)
775    
776    checkpoint63c (2011/09/28)
777    o pkg/ebm:
778      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
779        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
780    o pkg/seaice (SItracer pickup)
781    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
782      To be done:
783      - thorough testing of missing fields in S/R seaice_read_pickup
784      - thorough matching between generic tracers and specific fields used
785        (e.g. volume-weighted age, area-weighted age, salinity, ...)
786    o pkg/grdchk:
787      - all procs calculate and print finite-difference gradient (for testreport)
788      - change description output used by testreport;
789      - AD testing: also compare and report Finite-difference gradient;
790        => update all output_adm*.txt
791    o test exp. global_ocean_ebm:
792      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
793        and turn on exactConserve; update (fwd) output.
794    o pkg/seaice (LSR):
795      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
796      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
797        * identical results with non-CS topology (but save up to half of EXCH calls)
798        * no much changes in cs-32 verification tests since no ice at face edges
799         (differences due to convergence criteria, since nb of iterations changed)
800        * expect some differences on lat-lon-cap grid.
801        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
802    o pkg/exch2:
803      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
804        many tiles); until alternative coding is added, just add a stop.
805    o pkg/kpp:
806      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
807        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
808    o optfiles:
809      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
810        into corresponding standard one, which now support different build:
811        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
812      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
813    o pkg/obcs (seaice):
814      - add missing EXCH for uIce,vIce after applying OBCS;
815      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
816        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
817        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
818      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
819      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
820        and eedata.mth for MPI and mutlti-threaded testing.
821    o pkg/flt:
822      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
823      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
824      - fix pickup and trajectories + profiles output with multi-threads;
825      - add parameter to select group of fields to write along trajectory and
826        profile (default unchanged);
827      - only call PORT_RAND* function when flt_noise <> 0;
828      - add multi-threaded test for verification exp. flt_example.
829    o eesupp/src:
830      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
831      - USE_OMP_THREADING: check that number of threads (from eedata) matches
832        actual number (from env.var. setting).
833    o pkg/ebm:
834      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
835      - add multi-threaded test for verification exp. global_ocean_ebm
836    
837    checkpoint63b (2011/08/29)
838    o pkg/ebm:
839      - fix sign of runoff;
840      - update directly forcing fields (Qnet,EmPmR) to use standard
841        external_forcing_surf.F (remove ebm_forcing_surf.F);
842      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
843      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
844        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
845      - update global_ocean_ebm parameters file data and update output (fwd+ad).
846    o verification/matrix_example:
847      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
848        MPI and mutlti-threaded testing.
849    o pkg/matrix:
850      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
851      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
852      - fix for multi-threaded (remove DATA statement);
853      - use standard DIFFERENT_MULTIPLE function;
854      - add MATRIX_OPTIONS.h
855    o verification/matrix_example:
856       To allow to split the domain in several tiles, change the domain size
857        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
858        Western side) of land points.
859    o (*_)write_pickup:
860      - fix few bugs in mypackage_read/write_pickup.F
861      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
862        array of length 1 (was caught by compiler syntax-check).
863    o pkg/diagnostics (velocity potential solver):
864      - fix initialisation of main diagonal matrix (for overlap values)
865    o tools/build_options:
866      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
867        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
868      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
869        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
870        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
871        and use "-devel" testreport option for standard testing on baudelaire.
872    o pkg/grdchk:
873      - Assume that all gradient-check position are within the same tile
874        corresponding to global indices (iGloTile,jGloTile) and that
875        positions (i,j indices or nbeg) are local to this tile;
876      - set tile local-indices and proc. number according to tile global-indices;
877      - remove grdchkwhichproc from namelist (retired param);
878      - send adjoint gradient to all procs so that all procs print it to STDOUT;
879      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
880    o adding package bbl (Bottom Boundary Layer)
881      description in MITgcm/pkg/bbl/bbl_description.tex
882      example/test experiment in MITgcm_contrib/bbl
883    o adjoint verifications
884      - changed 5 experiments to multi-tiles
885        * global_ocean.90x40x15
886        * obcs_ctrl
887        * offline_exf_seaice
888        * tutorial_dic_adjoffline
889        * tutorial_tracer_adjsens
890        changed reference output for those that crossed tile boundaries
891        (changed choices of gradient check positions)
892      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
893      - temporary bug fix in grdchk_loc.F for obcs
894    o genmake2 & testreport
895      - add target "obj" (just for OBJFILES files) to Makefile;
896      - add option to specify FEXTRAFLAGS on command line.
897    o pkg/mypackage:
898      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
899    
900    checkpoint63a (2011/08/02)
901    o pkg/diagnostics (velocity potential):
902      - fix velocity-potential calculation when using OBCS: balance net inflow
903        at each level (new S/R OBCS_DIAG_BALANCE).
904      - fix some of the problems with OBCS in stream-function calculation.
905    o pkg/exf/exf_readparms.F
906      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
907        EXF_NML_OBCS) more consistent, so that you need not have these lists
908        in data.exf when they are not used.
909    o optim/optim_readdata.F:
910      - add some output about obcs variables that might help debugging
911      - add a check about nvarlength
912    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
913    o pkg/diagnostics (velocity potential):
914      - fix mask for OBCS (still problems in stream-function with OBCS);
915      - add specific parameter (default = main code CG2D params) for solver;
916      - in case of poor convergence, use solution corresponding to lowest residual.
917    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
918      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
919      and should be avoided where possible.
920    o model/src (rStar):
921      - include r* effect on reference-state (PhiRef) in totPhiHyd
922        (so that it's really the potential anomaly at the cell center);
923        affect solution only if z* with full pressure in EOS.
924      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
925        update output (because of z* in totPhiHyd and viscA4 changes);
926      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
927        @ constant r) until interpolation at constant r is implemented.
928    o pkg/diagnostics
929      - fix RCENTER diagnostics in case cell center is not at interface middle
930    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
931      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
932      that THETA and SALT are "conservative temperature" and "absolute
933      salinity"
934    o pkg/ctrl
935      - fix computation of endrec in s/r ctrl_init_rec
936      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
937    o pkg/seaice/seaice_growth.F
938      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
939        remove then obsolete STORE directives
940      - fix STORE directives for tice and tices, so that only the
941        appropriate part of the fields are stored (and not the entire
942        field); update global_ocean.cs32x15.seaice AD output.
943      - cosmetic changes: adjust CPP flags and indentation for better
944        legibilty
945    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
946      Chris Wilson)
947    o pkg/gmredi:
948       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
949       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
950    
951    checkpoint63  (2011/07/11)
952    o pkg/exch2:
953     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
954     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
955       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
956       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
957    o pkg/diagnostics:
958     - deal with pairs of post-processed diags which are computed together; in
959       particular, re-order list of diags within 1 file to save 2nd computation.
960     - add S/R to compute velocity stream-function (called after velocity-potential
961       calculation) from divergence free transport -> new diagnostics "PsiVEL".
962     - add parameter to select grid-point location where PsiVEL == 0.
963    o eesupp/src:
964       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
965       (specific S/R needed with exch2 topology - for now, just print an error msg)
966    o pkg/shelfice
967     - Implement friction velocity-dependent transfer coefficients following
968       Holland and Jenkins, JPO, 1999
969       Original code by M. Losch with small modifs.
970       Enable with CPP option SHI_ALLOW_GAMMAFRICT
971       and runtime flag SHELFICEuseGammaFrict
972    o verification lab_sea & global_ocean.cs32x15:
973     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
974       does not miss some dependencies (but is slower) and also works with many files
975       (default makedepend limitation for AD built).
976     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
977    o pkg/diagnostics:
978     - add run-time parameter "useMissingValue" (def=False) to fill land-point
979        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
980       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
981     - Extend the use of "missing_value" setting from data.diagnostics for the case
982       of counter-diagnostics (where fraction-weight is zero). This applies both to
983       MNC and MDS output files.
984    o pkg/seaice/seaice_growth.F:
985      - add 'a priori' cap of latent heat flux based on actual mass considerations
986        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
987        non-legacy seaice_solve4temp.
988      - add diagnostic of the residual sublimation freshwater flux (the freshwater
989        flux taken from the ocean if the total actual latent heat fluxes exceed
990        the maximum)
991      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
992       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
993      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
994       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
995      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
996      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
997    o verification 1D_ocean_ice_column:
998       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
999       update results
1000    o pkg/diagnostics:
1001     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1002       which are not filled-up but computed from other diags ; In this case, the mate
1003       diag points to the primary (filled-up) diag to used for post processing.
1004     - Update Velocity-potential computation using post-processed diag framework.
1005     ==> Change the ordering of fields and time-periods in MDS output file
1006       when using periodic averaging: now writes one time record with the full set
1007       of fields for this time period, then the next time reccord (it used to be
1008       one field with the full set of time records then the next field).
1009         Note: this is now similar to NetCDF (MNC) output file. <==
1010    
1011    checkpoint62z (2011/06/21)
1012    o adjoint monitor:
1013     - Add adjoint monitor output for packages exf, seaice
1014       and update relevant testreport output
1015    o pkg/seaice:
1016     - re-order diags inits so that they appear in order in available_diagnostics.log
1017     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1018       area/heff/hsnow preceeding thermodynamic growth/melt.
1019     - modified diag: SIdA; output actual effect, as the description states.
1020     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1021     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1022       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1023        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1024     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1025     - added diagnostics for seaice generic tracers (SItr*).
1026     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1027     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1028     I. Fenty: 18-Jun-2011:
1029     Minor changes to seaice package:
1030     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1031        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1032       - Differentiated "regularization variables" from "floor variables"
1033        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1034        * hiceMin became SEAICE_hice_reg (old hiceMin)
1035          (with _reg meaning regularization variable)
1036       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1037        so as to ensure energy conservation when going between phases
1038      - A22 was not used anywhere
1039     2) Changed regularization procedure for heffActual and hsnowActual to ensure
1040        well-boundedness and smooth adjoint in seaice_growth.F
1041     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1042        because the old regularization always set heffActual >= 0.05 cm
1043     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1044        on AREA when HEFF > 0.
1045      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1046        requiring that DISABLE_AREA_FLOOR *not* be defined
1047     Affected verifications:
1048      - 1D_ocean_ice_column (output.txt output_adm.txt)
1049      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1050  o pkg/diagnostics:  o pkg/diagnostics:
1051    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1052    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
# Line 11  o pkg/diagnostics: Line 1054  o pkg/diagnostics:
1054    - add pieces of code to compute velocity potential at each level (new diagnostics    - add pieces of code to compute velocity potential at each level (new diagnostics
1055      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1056      for now, using same params as CG2D (target-resisual, max Nb of iter ...).      for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1057      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1058        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1059        and in diagnostics_fract_fill.F (do not need a valid pointer for the
1060        diagnostics counter-mate); check that definition of counter-diagnostic
1061        includes a valid counter-mate (in diagnostics_set_levels.F).
1062  o model/src (rStar):  o model/src (rStar):
1063    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1064      affect solution only if z* with full pressure in EOS;      affect solution only if z* with full pressure in EOS;
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