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revision 1.1469 by ifenty, Wed Jun 29 21:44:26 2011 UTC revision 1.1680 by heimbach, Tue Jul 3 20:20:51 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 verification/tutorial_tracer_adjsens/
8      - add extra sub-verification which uses "SOM" advection scheme
9        (2nd Order-Moment Advection Scheme, Prather Limiter) with
10        #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
11        and in data:
12        multiDimAdvection=.TRUE.,
13        tempAdvScheme=81,
14        saltAdvScheme=81,
15    
16    checkpoint63o (2012/06/29)
17    o vertical mixing schemes:
18      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
19      - replace computation of density (in Function STATE1, opps_calc.F) by a call
20        to S/R FIND_RHO_SCALAR
21      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
22        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
23        affects output (vermix.ggl90) at truncation level.
24    o testreport:
25      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
26        (nSx,nSy) for the number of threads (from eedata.mth)
27    o model/src:
28      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
29        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
30    o verification/tutorial_tracer_adjsens/
31      - compile with ALLOW_CG2D_NSA
32      - run with nonlinFreeSurf=3
33      - update reference output_adm.txt
34    o tools/genmake2:
35      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
36        refine usePROFILES switching off (only when NetCDF is not available).
37    o verification (atmospheric set-up):
38      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
39    o pkg/profiles : refine profiles and files handling.
40    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
41    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
42      - changes to use model/src/the_main_loop.F rather than the ecco version
43        in ecco type adjoint runs.
44    o model/src:
45      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
46      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
47      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
48    o model/src:
49      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
50        update output of test experiment bottom_ctrl_5x5.
51    o pkg/generic_advdiff:
52      - implement vertical bi-harmonic diffusion (for now, only for T & S and
53        only explicitly).
54    o verification/bottom_ctrl_5x5/
55      update reference output (results changed quite some time ago,
56      not sure when; but new reference results look ok in terms of grdchk)
57    o verification/1D_ocean_ice_column/
58      For verification purposes, the exact adjoint rather than an approx.
59      should be used (e.g., to comare against F.D. or TLM).
60      removed autodiff_inadmode*_ad.F routines in code_ad/
61      Update results/ accordingly.
62    o pkg/cal:
63      - change cal_getdate.F so that output date is function of input time only
64        (less ambiguous, not mixed up with input iteration number).
65      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
66    o pkg/diagnostics:
67      - implement calendarDumps also for stats-diags
68      - implement calendarDumps also for snap-shot output (negative freq)
69      - for now, ignores calendarDumps if non-zero phase-lag.
70    
71    checkpoint63n (2012/06/04)
72    o model/src:
73      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
74        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
75      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
76        similar to calc_r_star.F); update results of experiment internal_wave and
77        tutorial_global_oce_in_p (affected @ truncation level).
78    o pkg/shelfice:
79      - add parameterisation of advective-diffusive flux into the ice shelf
80        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
81      - simply eps3/3a computation
82    o eesupp:
83     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
84       between tiles, just fill-in edges assuming locally periodic subdomain) and
85       add corresponding exchange subroutines (EXCH0);
86     - new CG-solver version (_EX0) for disconnected-tiles special case.
87    o model/src (CG-solvers):
88     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
89       (similar final residual output and max-Iter number as with standard version);
90     - allows to store and use lowest-residual solution (standard & _SR versions);
91     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
92     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
93    o eesup/src:
94     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
95       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
96    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
97    
98    checkpoint63m (2012/04/27)
99    o pkg/shelfice:
100     - account for partical cells in surface level below ice-shelf for hydrostatic
101       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
102    o ad test experiments:
103     - update and rename to "ad_optfile.local" local AD-optfile specific to a
104       particular adjoint verification experiment (in verification/*/code_ad/)
105    o pkg/seaice & pkg/exf:
106     - Part two of ECCO-CLIVAR code merges.
107       Completes merge of seaice area relax. code.
108       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
109       to be set in EXF_OPTIONS.h since this pkg controls its I/O
110       (and avoids second CPP option in SEAICE_OPTIONS.h)
111     - change default value of costIceStart & costIceEnd to a valid date.
112     - add snowPrecip to HSNOW in seaice_growth
113    o pkg/ptracers:
114     - move ptracers summary and setup check into separated S/R ; add a check for
115       valid PTRACERS_Iter0 value (error+stop or just warning).
116    o pkg/cal (+ pkg/ecco):
117     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
118       as input; and for AD, unless both are not differentiable (e.g., k index)).
119    o model/src:
120     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
121       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
122       temporary set to usingZCoords value (to be changed to F when using shelfice).
123     - hydrostatic pressure: implement partial cell near the surface also for
124       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
125       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
126    o pkg/ctrl/ctrl_init.F:
127     - add a formal parameter to s/r ctrl_init_rec to print
128       xx_$(ctrl_valiable)_file for easier debugging
129     - move call of cal_* routines into the if-block where they are really
130       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
131       to specify a startdate
132    o pkg/seaice:
133     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
134       global_ocean.cs32x15/code versions).
135     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
136       verification experiment global_ocean.cs32x15.seaice and update results.
137    o pkg/exf:
138     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
139       (according to useExfYearlyFields).
140    o pkg/cal:
141     - move calendar setting & summary (previously in cal_readparams.F) into new
142       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
143       length of the simulation is set (after SET_PARMS call); This is an attempt
144       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
145     - For safety: keep a record of pkg/cal parameter settings status
146               to allow to STOP if one pkg/cal S/R is called too early.
147     - add a stop in all basic pkg/cal subroutines if called before setting is done.
148     - modify cal_getdate.F: stop when nothing was returned;
149       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
150       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
151    
152    checkpoint63l (2012/04/04)
153    o pkg/bbl:
154      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
155        update global_with_exf output.yearly.txt file.
156    o pkg/cal:
157      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
158      - remove 2 unsused and very short (1 line only) functions ;
159      - remove unsused subroutines from AD-Diff list.
160    o model/src:
161      - start to implement clean wait to stop in initialization S/R (config_check.F,
162         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
163    o folowing PRINT_MESSAGE changes:
164      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
165    o pkg/bbl:
166      - modification so it can work with z*
167      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
168      - global_with_exf/input.yearly verification; changes output.yearly.txt
169    o eesupp/src:
170      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
171        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
172      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
173        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
174      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
175      - when using MPI, always set usingMPI=T ; set default accordingly and stop
176        if not consistent.
177      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
178        argument is zero (in case called within single-thread section).
179    o pkg/fizhi:
180        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
181        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
182    o pkg/exch2:
183      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
184        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
185      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
186        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
187        with bad ones coming from a not-yet-updated halo.
188        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
189    o pkg/frazil:
190        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
191        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
192    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
193    o verification/lab_sea
194      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
195      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
196      * nTimeSteps 3 -> 4
197      * changed reference output accordingly
198    o pkg/ctrl:
199      * fix ctrl_get_gen for xx_sst, xx_sss
200    o pkg/fizhi:
201      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
202        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
203      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
204        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
205        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
206    o pkg/gmredi:
207      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
208    o pkg/fizhi:
209      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
210        (old)aces open64 tuv test.
211    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
212    o pkg/mom_vecinv:
213      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
214        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
215        with non-lin free-surf).
216    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
217      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
218      some compilers (gfortran 4.6.0 on MacOS)
219    o momentum:
220      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
221        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
222        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
223    
224    checkpoint63k (2012/03/17)
225    o model/src:
226       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
227         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
228       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
229         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
230    o model/src: solve_*diagonal.F
231       - replace division with multiplication by inverse (similar to original version)
232         update output of AD exp. global_ocean.90x40x15.
233       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
234         to enable the use of the vectorized & differentiable solve_tridiagonal.F
235       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
236         vertical advection (to get solve_tridiagonal tested in AD mode).
237    o pkg/seaice: ECCO-CLIVAR merge:
238      1. seaice AREA relaxation
239         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
240         * runtime flag: SEAICE_tauAreaObsRelax
241      2. modified global mean cost imbalance code: CPP option
242          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
243    o another iteration on solve_*diagonal.F
244       Make choices independent of AUTODIFF
245       Default will be the adjoinable vectorized version.
246       Alternative choices are:
247       * non-adjoinable original version with low memory footprint:
248         #define SOLVE_DIAGONAL_LOWMEMORY
249       * still adjoinable but does not vectorize (k as inner-most loop):
250         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
251    o testreport
252     - add option to use a home made wrapper around "make"
253     - remove MITGCM_IEEE env. variable (no longer active)
254    o pkg/shelfice
255     - improve computation of friction velocity for velocity dependent
256       exchange coefficients: include velocities into SHELFICEBoundaryLayer
257       block to average velocities vertically
258     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
259    o Modify diagonal solvers, now three versions (upon request):
260      #ifndef SOLVE_DIAGONAL_AUTODIFF
261        1. default version (dating back a while ago)
262      #else /* def SOLVE_DIAGONAL_AUTODIFF */
263      # ifdef SOLVE_DIAGONAL_KINNER
264        2. adjoinable version with k-innermost loop (G. Forget)
265      # else
266        3. adjoinable vectorized version of 2.
267      # endif
268      #endif /* SOLVE_DIAGONAL_AUTODIFF */
269      All flags are currently set within routines, but could/should be moved to CPP-options.
270      Array bounds for 1. are as before, for 2.,3. cover the entire domain
271      (could be changed for 1. too).
272    o verification/lab_sea (fwd):
273      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
274        use 7 categories (except hb87), new solve4temp params (except salt_plume),
275        constant salinity (=4) or variable salinity (salt_plume) done through
276        SItracer.
277    o pkg/seaice:
278      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
279      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
280         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
281        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
282        SEAICE_freeze got retired) but already better than previously with
283        SEAICE_freeze=123456.7 deg.C;
284      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
285        (safer multi-threaded setting); always set SEAICEuseEVP;
286      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
287        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
288        stop if multiple specifications for the same coeff; make sure default
289        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
290    o pkg/obcs:
291      - allow to switch to upwind 1rst order advection scheme for the advective
292        flux computation at the open-boundary; disabled for adjoint built.
293    o pkg/ptracers:
294      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
295      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
296      - add parameter to decide when to start a tracer; use internal flag to
297        know which tracer to step-forward; switch this internal flag at the top
298        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
299        for adjoint built.
300    o pkg/seaice:
301      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
302      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
303      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
304    o pkg/ecco:
305      - fix writing of output file DiagnosCost_ClimSalt/Theta
306        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
307    o pkg/seaice:
308      - add missing initialisation of COR_ICE array in dynsolver.F
309      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
310        compiled either way, and is tested in all exps (multidim was only tested
311        in lab_sea ad before).
312      - cosmetic change to prepare for future addition of ITD. no change to results.
313        no defaults change.
314      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
315      - by lack of adequate verification experiments, I further used custom versions
316        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
317        should be correct.
318      - avoid recomputations in ad.
319    o array initialisation in adjoint mode:
320      1) pkg/mom_common/mom_calc_ke.F:
321        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
322        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
323        part this initialisation is gone, resulting in Floating Point Exception
324        (caught by open64 compiler with debug option).
325      2) model/src/convective_weights.F
326        set output convectCount over the full array range (instead of doing
327        an update): this fix a similar issue when called within recomputation (adjoint)
328        which could by-pass the initialisation (normally done in the caller S/R).
329    o pkg/seaice:
330      - final version of turbulent flux params, as agreed at MIT ice meet:
331           SEAICE_mcPheePiston (default is ~ 0.000875)
332           SEAICE_mcPheeTaper (default is 0.)
333           SEAICE_frazilFrac (defualt is 1.)
334           SEAICE_mcPheeStepFunc (default is false)
335      - changes results at trunction error level
336      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
337    o added pkg/frazil:
338      - see frazil_description.tex for details
339      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
340    o pkg/shelfice/shelfice_thermodynamics.F
341      - fix exponents for velocity dependent exchange coefficients: change
342        from 2/3(=0) to 0.66666666666666667
343      - move computation of velocity dependent exchange coefficients into
344        separate loop, so that it applies to both thermodynamics
345      - move some divisions by constants out of loops
346    
347    checkpoint63j (2012/02/16)
348    o pkg/seaice:
349      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
350      - SItracer:  added run time params, and allow coupling to ocn salinity.
351    o pkg/seaice: remove (almost) all divisions by constants within loops
352      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
353      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
354      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
355      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
356    o pkg/seaice :
357      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
358        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
359      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
360      - add permanent SItflux diag that corresponds to TFLUX but includes
361        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
362      - allow activation/testing of a fix for suspected missing term in
363        ocn-ice heat budget (to be confirmed). To test this, you want to
364        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
365        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
366      - no change in results, fwd or ad.
367    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
368      - switch to variable freezing point.
369           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
370      - bug fix : the sublimation term that was missing is now activated.
371           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
372      - bug fix : flooding sign term for SIsal0.NE.0.
373           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
374    o pkg/seaice:
375      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
376        is now the default, and the old default constant freezing point is recovered
377        with SEAICE_tempFrz0    = -1.96,
378             SEAICE_dTempFrz_dS = 0.,
379      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
380      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
381      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
382        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
383      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
384        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
385      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
386        seaice_growth r149 for legacy branch (no results change).
387      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
388        from I. Fenty).
389      - results did not change except for global_ocean.cs32x15, mostly due to the
390        switch to variable freezing point (see above item for detail).
391    o pkg/thsice:
392      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
393        seawater freezing in thsice_calc_thickn (not used).
394    o pkg/seaice: turbulent flux term specification via run time params.
395      - replace CPP switches with run time switches to facilitate testing
396      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
397                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
398      - added runtime parameter : SEAICEturbFluxFormula
399      - move Mcphee constants to SEAICE_PARAMS.h
400      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
401                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
402                 remove seaice_summary call (moved to seaice_init_fixed)
403      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
404        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
405      - seaice_summary.F : add missing report of read turbulent flux term set up
406                           and SITRACER.
407      - seaice_check.F : check range; inform and stop if retired CPPs are used
408                         (incl. SEAICE_AGE).
409      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
410             CPP switch, same computation as before for the different options.
411      - change results at the truncation level.
412    o pkg/seaice:
413      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
414        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
415        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
416      - update verification/*/input*/data.seaice:
417        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
418        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
419        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
420        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
421    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
422      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
423        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
424        difference in results only due to machine truncation.
425      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
426        MaykutPolySatVap; keep MIN_LWDOWN.
427      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
428      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
429        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
430    o pkg/salt_plume:
431      - isolate saltPlumeFlux array exch into a specific S/R called from
432        do_oceanic_phys.F
433      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
434    o verification:
435      - move untested set-up to MITgcm_contrib/verification_other.
436    o pkg/seaice:
437      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
438    o pkg/seaice:
439      - seaice_solve4temp.F (keeping results unchanged):
440        * add 2 future run-time params to select which saturation vapor pressure
441          formula is used and how post-iteration fluxes are set.
442          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
443        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
444          the linearized expression to stay consistent with tsurf finding.
445      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
446        can be < 0.
447    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
448      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
449        conductive heat flux F_c , and add it explicitly when updating tsurf as
450        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
451        so that now F_ia has a consistent meaning through the entire routine.
452        This causes differences at truncation level: update output of fwd exp.
453        global_ocean.cs32x15.seaice.
454    o pkg/seaice:
455      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
456        of arrays, sign/direction of fluxes; no effect on results.
457      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
458        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
459        note: this should have been done before changing celsius2K default.
460      - to keep results unchanged, add back old value of celsius2K in verification
461        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
462      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
463        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
464        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
465        freezing temp is consistent with value in seaice_growth.F ; this causes
466        differences at machine truncation level: update lab_sea AD output (3/4).
467    o pkg/seaice:
468      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
469        and climsst/sss even when using seaice (to prevent calculation that might
470        use SST on land); does not affect any verification exp.
471      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
472        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
473    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
474      over land (non-legacy code)
475    o vectorize salt_plume package:
476      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
477      - this code computes plumebk everywhere (also over land), thus requires
478        code to avoid divisions by zero and catch the case of kLev=Nr.
479      - efficiency of salt_plume_frac is still sub-optimal
480    o tools (genmake2):
481      - fix makefile NAME specification (option: -makefile NAME) by adding
482        "-f $MAKEFILE" in few places where it was missing including makedepend
483        command (contribution from Paul).
484    
485    checkpoint63i (2012/01/24)
486    o model/src:
487      - add factorized versions of some EOS code to find_rho.F,
488        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
489    o model/src:
490      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
491      - change default celsius2K from 273.16 to 273.15
492      - to keep results unchanged, add back old value of celsius2K in verification
493        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
494         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
495    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
496      to make TAF generate vectorizable code
497    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
498       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
499       have flags that do this more efficiently.
500    o pkg/diagnostics/diagstats_calc.F
501      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
502    o pkg/obcs (with exch2):
503      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
504        and remove code (in obcs_readparms.F) which was based on EXCH of indices
505        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
506    o pkg/exf and seaice exp:
507      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
508        so that switching off area & heff advection flags does not affect results.
509      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
510      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
511        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
512        results of verification experiments: 1D_ocean_ice_column(fwd),
513        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
514        and offline_exf_seaice (all 4).
515    o pkg/seaice:
516      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
517        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
518      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
519        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
520        not multi-dim advection;
521      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
522        SHORTWAVE_HEATING #undef.
523    o optim: make Makefile more robust (?)
524    o pkg/obcs:
525      * fix treatment of obcs_read_pickup for TAF
526    o pkg/shelfice:
527      * add missing initialisation of num_shifwflx
528      * new adjoint verification exp. for isomip
529      * change Prandtl and Schmidt numbers from generic formulations
530        (in terms of model diffus. and visc.) to separate runtime
531        parameters, with Holland and Jenkins (1999) default values.
532    o pkg/exf (interpolation):
533      - extended input field (2 rows) near the N & S poles:
534        * fill in with the symetric value (when even Nb of data in longitude)
535        * add average value at the poles only for scalar quantities ; for vector
536          component interpolation, skip the averaging and keep duplicated values,
537          unless the 2 components have same location (uvInterp=T) in which case
538          interpolate the 2 components together using S/R EXF_INTERP_UV.
539      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
540        together: this allows to account properly for local orientation when
541        averaging at N & S pole.
542      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
543        exf-interpolation near N & S poles. Undef by default.
544      - add debug check/print on 1rst iter if debugLevel >=2.
545    o pkg/exf:
546      - change masking flags definition (no longer "parameter"), put them in
547        common block and set them in S/R EXF_INIT_FIXED.
548      - change recognized masking flag from s,u,v to c,w,s since the mask
549        to use (maskC,W,S) depends on position on model grid and has little to
550        do with scalar/vector difference; fix masking if using P-coordinates.
551      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
552        and update results of exp. global_with_exf (x2).
553      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
554    o pkg/obcs
555      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
556    o pkg/exf (interpolation):
557      - assume periodicity in X only if input field cover full longitude range.
558      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
559        and should vectorise).
560      - fix input lat of the 2 added row (in case we provide N.pole data).
561    
562    checkpoint63h (2011/12/30)
563    o pkg/seaice:
564      - change declaration of UVM from _RL to _RS in order to get B-grid
565        uIce,vIce monitor when _RS = real*4
566    o pkg/offline:
567      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
568      - compute vertical velocity if not read from file (switch on exactConserv
569        & staggerTimeStep);
570      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
571    o verification:
572      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
573        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
574        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
575      - update output of exp. global_ocean.cs32x15.viscA4 after changing
576        grid-file angles (used here for coriolis-3d);
577      - remove (or gzip) few files not needed to run fizhi-cs experiments.
578    o pkg/exf (vector interpolation):
579      - rotate vector component toward local grid-axis orientation using grid-angles
580        (stored in GRID.h) instead of locally computed rotation angle; keep old code
581        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
582    o pkg/seaice:
583      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
584        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
585    o pkg/PKG_OPTIONS.h files:
586      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
587        outside of the #ifdef ALLOW_THISPKG / #endif block.
588      - update verification/*/code/PKG_OPTIONS.h files.
589    o add a verification experiment (offline_exf_seaice/input.seaice) that test
590      the B-grid LSOR solver
591    o pkg/seaice: sort out emissivity and long wave radiation step 2:
592      - add emissivity for snow and ice as new run-time parameters
593        (unfortunately) that default to the corresponding exf values; this
594        changes results in most verification experiments so that for backward
595        compatibility these parameter have to be set explicitly to inconsistent
596        values (ugly);
597      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
598        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
599        until we agree how to handle this bug properly
600    o pkg/exf (interpolation):
601      - add a set of run-time param ({inputfield}_interpMethod), one for
602        each interpolated input field, to select the interpolation method
603        with a value of zero switching off the interpolation;
604      - print interpolation parameters to standard output;
605      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
606        (to use instead runoff_interpMethod=0 in data.exf).
607      - simplify default setting of interpolation parameters (for all fields,
608        set position to match model grid cell-center position, leading to trivial
609        interpolation in case of regular Lat-Lon grid) and fix for the case of
610        non-uniform delY.
611    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
612       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
613       this factor is absolutely required, because the lw exitance (= out-going
614       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
615       where the reflectivity rho = 1-emissivity for conservation reasons. Once
616       this is established, we can remove the CPP-Flag (if we want to).
617    o pkg/seaice:
618      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
619        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
620      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
621        what the name implies (and not emissivity*BoltzmannConstant), this means
622        the old default value of 5.5e-8 now means
623        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
624        S/R exf_readparms
625      - FV-discretization of the B-grid LSOR solver, turn on with
626        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
627        of the calling routine dynsolver, so that B and C-grid code look a
628        little more alike.
629      - fix index bugs in ostres.F (B-grid code)
630    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
631    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
632      default for SEAICE_emissivity, if useEXF; requires setting a wrong
633      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
634      backward compatiblity
635    o model/src: use sigmaR in calc_ivdc
636    
637    checkpoint63g (2011/12/16)
638    o pkg/seaice/seaice_growth.F:
639      fix heat conservation of the coupled ocean-seaice system.
640      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
641      solid vs liquid water treatment is resolved via QNET.
642    o pkg/seaice/seaice_growth.F:
643      add missing term for sublimation in saltFlux, which was breaking conservation.
644    o pkg/seaice/seaice_model.F:
645      Remove this patholigical case treatment in evolution branch,
646      where it is un-necessary and breaks conservation.
647      Update global_ocean.cs32x15/results accordingly for
648      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
649    o model/src:
650      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
651      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
652    o pkg/obcs:
653      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
654      tendency for temperature and salinity that is then applied to update
655      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
656      horizontal advection and diffusion contributions on the boundary (in
657      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
658      removing the mask in S/R timestep_tracer. The advantage of this approach is
659      that the updated tracer values include contributions from the surface
660      forcing and vertical diffusion.
661      This modification changes exp4.stevens because of vertical diffusion.
662    o model/src:
663      change non-curvilinear grid setting to also work with exch2 + blank tiles:
664      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
665        face dimensions.
666      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
667        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
668        and INI_SPHERICAL_POLAR_GRID.
669      change test-experiment global_ocean.90x40x15:
670      - split the domain in many more tiles (9x4 tiles of 10x10 each);
671      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
672      - update results of both test (std & dwnslp).
673    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
674       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
675    o model/src:
676      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
677        and fix initialisation when using sigma-coords.
678    o model/src:
679     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
680       to their current value at the beginning of forward_step.F": add a new run-time
681       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
682     - set doResetHFactors=T in the following test exp:
683        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
684        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
685        and tutorial_global_oce_in_p (nonLinFS in p)
686    o pkg/ecco
687      - added IES cost term
688    o verification/advect_xz
689      - scale down the depth by 1/100 (from 200 km to just 2.km)
690      - add secondary test using divergent flow, r-star and implicit vertical advection.
691      - add note (check_conserve_TS.txt) and matlab script to check global
692        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
693    o pkg/rbcs:
694      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
695    o pkg/obcs (Stevens BCs):
696      - fix various problems in the phase speed computations of the Stevens
697        boundary conditions:
698        - sign error for western and southern boundaries,
699        - time tendencies were underestimated by factor of dTracerLev and some just
700          zero (for multidim advection schemes) -> now estimate time tendencies
701          from difference between previous (n) time level and the one before (n-1);
702          this requires storing a field per tracer per boundary, also in the pickup
703          files.
704        - replace deltaTmom in cflMer/Zon computation with dTracerLev
705        - set default phase velocity to cflMer/Zon
706      - update verification experiment exp4.stevens
707    o pkg/generic_advdiff (implicit_r):
708      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
709        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
710      - fix implicit vertical diffusion or advection with NonLin FreeSurf
711        (was using current recip_hFacC instead of future recip_hFacC): set future
712        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
713        solver S/R ;
714      - fill diagnostics of vertical advective fluxes (computed from tendency)
715        when using implicit vert. advection;
716      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
717         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
718         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
719         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
720    o pkg/diagnostics:
721      - add diags for T & S tendency which goes through Adams-Bashforth.
722    
723    checkpoint63f (2011/11/30)
724    o pkg/obcs/obcs_calc_stevens.F:
725      - join some loops to reduce number of if-statements
726      - fix a bug in code for northern and southern boundaries.
727    o pkg/seaice/seaice_init_varia.F
728      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
729        caused zero ice-velocities for the B-grid code
730    o pkg/seaice/seaice_init_fixed.F
731      - fix a bug in the initialisation of the second metric terms
732        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
733      - this affects all seaice configurations with useCurviLinearGrid = .true.
734        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
735        = .true. (default)
736      - the only verification experiment affected is global_ocean.cs32x15:
737        icedyn, seaice, and seaice_dynmix (AD)
738    o pkg/thsice/thsice_diagnostics_state.F
739      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
740        not contain garbage that can lead to surprises in diagstats_calc.F
741    o model/src:
742      - move bi,bj loops inside INTEGR_CONTINUITY ;
743      - call INTEGR_CONTINUITY directly from forward_step.F
744        (previously called from momentum_correction_step.F)
745      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
746        forward_step.F and pkg/ecco/the_main_loop.F
747    o model/src/do_oceanic_phys.F:
748      - reset addMass to zero only if useICEFRONT ;
749      - separated k-loop for rhoInSitu calculation ;
750      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
751        and at constant T,S (= WdRHOdP);
752      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
753        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
754        transport of locally-referenced potential density);
755        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
756    o gluemnc:
757      - replace ncrcat with ncks when adding variables to *.glob.nc
758      - change the way variables without record dimensions are handled so that
759        files that have variables with and without record variables can be glued:
760        add a record dimension with a new unique name to be able to differentiate
761        between variable with and without a-prior record dimensions. Remove
762        this record dimension before adding the variable to the *.glob.nc file.
763        This procedure automatically works also for grid.*.nc files that do not
764        have any record dimension.
765    o verification/cpl_aim+ocn:
766      - generate new reference output on baudelaire (gfortran, mpich2) (previously
767        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
768    o pkg/obcs/obcs_calc_stevens.F:
769      - add code for northern and southern boundaries.
770      - reorder some loops to save some operations and so that drFBar can be scalar
771    o model/src:
772      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
773        truncation) and add diagnostics for Adams-Bashforth tendency increment.
774      - update test-exp. AD output:
775        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
776      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
777        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
778        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
779        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
780        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
781        tutorial_plume_on_slope.
782    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
783      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
784      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
785      does not even come with an F77 compiler anymore, this should not be
786      a limitation
787    
788    checkpoint63e (2011/11/06)
789    o pkg/seaice adjoint of LSR:
790      - substantially rework STORE dirs.
791      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
792        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
793        and only perform SOLV_MAX_FIXED adjoint iters.
794        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
795        always goes to same record, meaning that the last forward field will be
796        the one used in the adjoint - an approximation.
797      - now produces non-zero LSR-related gradients, and acceptable gradients for
798        An's zonal (x-z) test case (to be checked in)
799      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
800        (but these are screwed up by the thermodynamics in the first place);
801        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
802        output_adm.txt also reflects changes to seaice_lsr
803      - global_ocean.cs32x15:
804        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
805          (output_adm.seaice.txt was updated)
806        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
807          (output_adm.seaice_dynmix.txt)
808    o test-exp. exp4+stevens:
809      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
810    o pkg/seaice (lsr solver):
811      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
812        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
813      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
814      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
815        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
816      - compute (with new S/R) and print initial (+ free-driff sol. if available)
817        and final residual of linearised system.
818    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
819      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
820    o pkg/obcs: Stevens BCs (still only for east and west)
821      - fix Stevens BCs by using intermediate velocities of previous
822        time step as "baroclinic" contribution rather velocity of one grid cell
823        inside the boundaries; more consistent but makes the entire treatment
824        more complicated, requires new pickup files and two new S/Rs:
825        obcs_copy_uv_n and obcs_save_uv_n
826        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
827        (undefined by default)
828      - silently move computation of some grid factors into separate loops to
829        save some recomputations
830      - add a hack for non-linear free surface
831      - add a verification experiment to exp4 that tests this code
832    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
833    
834    checkpoint63d (2011/10/25)
835    o pkg/obcs + seaice-dynamics:
836      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
837        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
838        values (consistent with an implicit method).
839      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
840        return to older implementation (same results as before); note that none of
841        the "experimental" OBCS_SEAICE options are implemented in the new version.
842      - switch test exp. seaice_obcs to use new version (update output).
843    o pkg/seaice:
844      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
845      - add parenthesis in Water-Ice drag calculations (evp & lsr);
846      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
847        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
848      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
849        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
850    o pkg/layers:
851      - Include potential density as new coordinate (Thanks to David Munday)
852    o pkg/dic:
853      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
854        carbonate computation/output to CALC_PCO2_APPROX
855    o pkg/generic_advdiff
856      - make TAF generate code that vectorizes:
857        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
858    o model/src:
859      - improve vectorization also for adjoint code of
860        solve_tridiagonal and solve_pentadiagonal. As this requires up to
861        5 new 3D-fields, this code is only turned on for the combination of
862        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
863        for singular matrix check (only for TARGET_NEC_SX).
864      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
865        ALLOW_AUTODIFF. This flag now needs to be set outside of
866        solve_tri/pentadiagonal.F
867    o pkg/exf:
868      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
869        optional namelist EXF_NML_OBCS).
870      - add many debug-print (to trace down where pkg/cal error msg comes from)
871    o pkg/mom_vecinv/mom_vi_hdissip.F
872      - rearrange loops so that vectorization is improved and in particular
873        the adjoint routine vectorizes. The code is a little longer now, but I
874        think easier to read.
875        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
876    o pkg/seaice:
877      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
878    o pkg/exch2:
879      - alternative code (without tile x tile matrix) for cumulated (global) sum;
880        used as default; keep using matrix version in adjustment.cs-32x32x1.
881    o tools/build_options:
882      - after merging some MPI and/or multi-threads specific optfiles so that
883        the modified default optfile support both built (using genmake2 -mpi
884        for the MPI built, using genmake2 -omp for OpenMP built),
885        move now obsolete optfiles to tools/build_options/unsupported/
886       (add copy of email sent to support list in doc/optfiles_changes.txt)
887    
888    checkpoint63c (2011/09/28)
889    o pkg/ebm:
890      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
891        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
892    o pkg/seaice (SItracer pickup)
893    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
894      To be done:
895      - thorough testing of missing fields in S/R seaice_read_pickup
896      - thorough matching between generic tracers and specific fields used
897        (e.g. volume-weighted age, area-weighted age, salinity, ...)
898    o pkg/grdchk:
899      - all procs calculate and print finite-difference gradient (for testreport)
900      - change description output used by testreport;
901      - AD testing: also compare and report Finite-difference gradient;
902        => update all output_adm*.txt
903    o test exp. global_ocean_ebm:
904      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
905        and turn on exactConserve; update (fwd) output.
906    o pkg/seaice (LSR):
907      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
908      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
909        * identical results with non-CS topology (but save up to half of EXCH calls)
910        * no much changes in cs-32 verification tests since no ice at face edges
911         (differences due to convergence criteria, since nb of iterations changed)
912        * expect some differences on lat-lon-cap grid.
913        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
914    o pkg/exch2:
915      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
916        many tiles); until alternative coding is added, just add a stop.
917    o pkg/kpp:
918      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
919        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
920    o optfiles:
921      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
922        into corresponding standard one, which now support different build:
923        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
924      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
925    o pkg/obcs (seaice):
926      - add missing EXCH for uIce,vIce after applying OBCS;
927      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
928        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
929        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
930      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
931      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
932        and eedata.mth for MPI and mutlti-threaded testing.
933    o pkg/flt:
934      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
935      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
936      - fix pickup and trajectories + profiles output with multi-threads;
937      - add parameter to select group of fields to write along trajectory and
938        profile (default unchanged);
939      - only call PORT_RAND* function when flt_noise <> 0;
940      - add multi-threaded test for verification exp. flt_example.
941    o eesupp/src:
942      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
943      - USE_OMP_THREADING: check that number of threads (from eedata) matches
944        actual number (from env.var. setting).
945    o pkg/ebm:
946      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
947      - add multi-threaded test for verification exp. global_ocean_ebm
948    
949    checkpoint63b (2011/08/29)
950    o pkg/ebm:
951      - fix sign of runoff;
952      - update directly forcing fields (Qnet,EmPmR) to use standard
953        external_forcing_surf.F (remove ebm_forcing_surf.F);
954      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
955      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
956        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
957      - update global_ocean_ebm parameters file data and update output (fwd+ad).
958    o verification/matrix_example:
959      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
960        MPI and mutlti-threaded testing.
961    o pkg/matrix:
962      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
963      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
964      - fix for multi-threaded (remove DATA statement);
965      - use standard DIFFERENT_MULTIPLE function;
966      - add MATRIX_OPTIONS.h
967    o verification/matrix_example:
968       To allow to split the domain in several tiles, change the domain size
969        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
970        Western side) of land points.
971    o (*_)write_pickup:
972      - fix few bugs in mypackage_read/write_pickup.F
973      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
974        array of length 1 (was caught by compiler syntax-check).
975    o pkg/diagnostics (velocity potential solver):
976      - fix initialisation of main diagonal matrix (for overlap values)
977    o tools/build_options:
978      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
979        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
980      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
981        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
982        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
983        and use "-devel" testreport option for standard testing on baudelaire.
984    o pkg/grdchk:
985      - Assume that all gradient-check position are within the same tile
986        corresponding to global indices (iGloTile,jGloTile) and that
987        positions (i,j indices or nbeg) are local to this tile;
988      - set tile local-indices and proc. number according to tile global-indices;
989      - remove grdchkwhichproc from namelist (retired param);
990      - send adjoint gradient to all procs so that all procs print it to STDOUT;
991      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
992    o adding package bbl (Bottom Boundary Layer)
993      description in MITgcm/pkg/bbl/bbl_description.tex
994      example/test experiment in MITgcm_contrib/bbl
995    o adjoint verifications
996      - changed 5 experiments to multi-tiles
997        * global_ocean.90x40x15
998        * obcs_ctrl
999        * offline_exf_seaice
1000        * tutorial_dic_adjoffline
1001        * tutorial_tracer_adjsens
1002        changed reference output for those that crossed tile boundaries
1003        (changed choices of gradient check positions)
1004      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1005      - temporary bug fix in grdchk_loc.F for obcs
1006    o genmake2 & testreport
1007      - add target "obj" (just for OBJFILES files) to Makefile;
1008      - add option to specify FEXTRAFLAGS on command line.
1009    o pkg/mypackage:
1010      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1011    
1012    checkpoint63a (2011/08/02)
1013    o pkg/diagnostics (velocity potential):
1014      - fix velocity-potential calculation when using OBCS: balance net inflow
1015        at each level (new S/R OBCS_DIAG_BALANCE).
1016      - fix some of the problems with OBCS in stream-function calculation.
1017    o pkg/exf/exf_readparms.F
1018      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1019        EXF_NML_OBCS) more consistent, so that you need not have these lists
1020        in data.exf when they are not used.
1021    o optim/optim_readdata.F:
1022      - add some output about obcs variables that might help debugging
1023      - add a check about nvarlength
1024    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1025    o pkg/diagnostics (velocity potential):
1026      - fix mask for OBCS (still problems in stream-function with OBCS);
1027      - add specific parameter (default = main code CG2D params) for solver;
1028      - in case of poor convergence, use solution corresponding to lowest residual.
1029    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1030      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1031      and should be avoided where possible.
1032    o model/src (rStar):
1033      - include r* effect on reference-state (PhiRef) in totPhiHyd
1034        (so that it's really the potential anomaly at the cell center);
1035        affect solution only if z* with full pressure in EOS.
1036      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1037        update output (because of z* in totPhiHyd and viscA4 changes);
1038      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1039        @ constant r) until interpolation at constant r is implemented.
1040    o pkg/diagnostics
1041      - fix RCENTER diagnostics in case cell center is not at interface middle
1042    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1043      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1044      that THETA and SALT are "conservative temperature" and "absolute
1045      salinity"
1046    o pkg/ctrl
1047      - fix computation of endrec in s/r ctrl_init_rec
1048      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1049    o pkg/seaice/seaice_growth.F
1050      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1051        remove then obsolete STORE directives
1052      - fix STORE directives for tice and tices, so that only the
1053        appropriate part of the fields are stored (and not the entire
1054        field); update global_ocean.cs32x15.seaice AD output.
1055      - cosmetic changes: adjust CPP flags and indentation for better
1056        legibilty
1057    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1058      Chris Wilson)
1059    o pkg/gmredi:
1060       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1061       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1062    
1063    checkpoint63  (2011/07/11)
1064    o pkg/exch2:
1065     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1066     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1067       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1068       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1069    o pkg/diagnostics:
1070     - deal with pairs of post-processed diags which are computed together; in
1071       particular, re-order list of diags within 1 file to save 2nd computation.
1072     - add S/R to compute velocity stream-function (called after velocity-potential
1073       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1074     - add parameter to select grid-point location where PsiVEL == 0.
1075    o eesupp/src:
1076       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1077       (specific S/R needed with exch2 topology - for now, just print an error msg)
1078  o pkg/shelfice  o pkg/shelfice
1079   - Implement friction velocity-dependent transfer coefficients following   - Implement friction velocity-dependent transfer coefficients following
1080     Holland and Jenkins, JPO, 1999     Holland and Jenkins, JPO, 1999
# Line 27  o pkg/seaice/seaice_growth.F: Line 1098  o pkg/seaice/seaice_growth.F:
1098      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1099      non-legacy seaice_solve4temp.      non-legacy seaice_solve4temp.
1100    - add diagnostic of the residual sublimation freshwater flux (the freshwater    - add diagnostic of the residual sublimation freshwater flux (the freshwater
1101      flux taken from the ocean if the total actual latent heat fluxes exceed      flux taken from the ocean if the total actual latent heat fluxes exceed
1102      the maximum)      the maximum)
1103    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1104     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
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