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revision 1.403 by heimbach, Sat Dec 4 23:26:49 2004 UTC revision 1.1692 by jmc, Tue Jul 17 22:55:19 2012 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src: CG2D_NSA
8      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
9         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
10      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
11         change cg2d residual target to be expressed in Wunits (=> do not normalise
12         RHS ; this fix global_max Pb with TAF); update output.
13    o verification/tutorial_tracer_adjsens:
14       improve parameter consistency (and get rid of warnings):
15       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
16       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
17       - use staggerTimeStep (for stability) in som81; use default rotation period.
18    o pkg/exch2:
19      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
20        reset to 0 = 1 long line in X)
21    o pkg/mdsio:
22      - fix reading of dimensions from meta file for large-size domain
23    o model/src:
24      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
25      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
26        Cubed-Sphere Exch with CS-corners inside the domain;
27        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
28        globalArea and to set hasWetCSCorners.
29      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
30        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
31      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
32        useCDscheme and useCubedSphereExchange).
33    o pkg/seaice/seaice_growth.F :
34      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
35        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
36        when the previous code was not correct.
37      - in all cases diagnoze the boundary condition mismatch to SIaaflux
38      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
39        that term to QNET (essentially to set the melt/freeze water to 0degC).
40        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
41    o verification/global_ocean.cs32x15/input.seaice :
42      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
43      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
44      - update results (output.seaice.txt) accordingly.
45    o verification/lab_sea/input/data.seaice :
46      - remove SEAICEheatConsFix, which is now be tested
47        in global_ocean.cs32x15. The presently coded fix
48        is only consistent with real fresh water + nlfs.
49      - update results (output.txt) accordingly.
50    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
51    o AD_CONFIG.h file:
52      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
53      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
54        add it explicitly in each fortran src file where it is needed.
55        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
56        thus introducing potentially wrong dependency; therefore, better to include
57        it only where it's really needed, and after any other included OPTIONS file
58        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
59        or ALLOW_TANGENTLINEAR_RUN).
60    
61    checkpoint63p (2012/07/06)
62    o pkg/autodiff:
63      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
64      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
65        which are now read from new parameter file "data.autodiff" (inAdExact
66        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
67      - add file "data.autodiff" in all verification/*/input_ad/ directories.
68      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
69        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
70    o verification/tutorial_tracer_adjsens/
71      - add extra sub-verification which uses "SOM" advection scheme
72        (2nd Order-Moment Advection Scheme, Prather Limiter) with
73          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
74        and in data:
75          multiDimAdvection=.TRUE.,
76          tempAdvScheme=81,
77          saltAdvScheme=81,
78    o model/src:
79      - introduce ALLOW_BALANCE_RELAX which allow the removal
80       of the global mean of relaxation terms by setting
81       balanceThetaClimRelax and balanceSaltClimRelax
82      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
83       This case is now treated appropriately in seaice_growth.F
84    o pkg/seaice:
85      - do balanceEmPmR and balanceQnet based on the net fluxes
86        (SItflux) that enter the ocean+ice system rather than QNET
87        and EMPMR. Works best in real fresh water.
88      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
89        out of the diagnotics bloc, and stored in global arrays.
90    
91    checkpoint63o (2012/06/29)
92    o vertical mixing schemes:
93      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
94      - replace computation of density (in Function STATE1, opps_calc.F) by a call
95        to S/R FIND_RHO_SCALAR
96      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
97        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
98        affects output (vermix.ggl90) at truncation level.
99    o testreport:
100      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
101        (nSx,nSy) for the number of threads (from eedata.mth)
102    o model/src:
103      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
104        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
105    o verification/tutorial_tracer_adjsens/
106      - compile with ALLOW_CG2D_NSA
107      - run with nonlinFreeSurf=3
108      - update reference output_adm.txt
109    o tools/genmake2:
110      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
111        refine usePROFILES switching off (only when NetCDF is not available).
112    o verification (atmospheric set-up):
113      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
114    o pkg/profiles : refine profiles and files handling.
115    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
116    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
117      - changes to use model/src/the_main_loop.F rather than the ecco version
118        in ecco type adjoint runs.
119    o model/src:
120      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
121      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
122      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
123    o model/src:
124      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
125        update output of test experiment bottom_ctrl_5x5.
126    o pkg/generic_advdiff:
127      - implement vertical bi-harmonic diffusion (for now, only for T & S and
128        only explicitly).
129    o verification/bottom_ctrl_5x5/
130      update reference output (results changed quite some time ago,
131      not sure when; but new reference results look ok in terms of grdchk)
132    o verification/1D_ocean_ice_column/
133      For verification purposes, the exact adjoint rather than an approx.
134      should be used (e.g., to comare against F.D. or TLM).
135      removed autodiff_inadmode*_ad.F routines in code_ad/
136      Update results/ accordingly.
137    o pkg/cal:
138      - change cal_getdate.F so that output date is function of input time only
139        (less ambiguous, not mixed up with input iteration number).
140      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
141    o pkg/diagnostics:
142      - implement calendarDumps also for stats-diags
143      - implement calendarDumps also for snap-shot output (negative freq)
144      - for now, ignores calendarDumps if non-zero phase-lag.
145    
146    checkpoint63n (2012/06/04)
147    o model/src:
148      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
149        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
150      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
151        similar to calc_r_star.F); update results of experiment internal_wave and
152        tutorial_global_oce_in_p (affected @ truncation level).
153    o pkg/shelfice:
154      - add parameterisation of advective-diffusive flux into the ice shelf
155        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
156      - simply eps3/3a computation
157    o eesupp:
158     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
159       between tiles, just fill-in edges assuming locally periodic subdomain) and
160       add corresponding exchange subroutines (EXCH0);
161     - new CG-solver version (_EX0) for disconnected-tiles special case.
162    o model/src (CG-solvers):
163     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
164       (similar final residual output and max-Iter number as with standard version);
165     - allows to store and use lowest-residual solution (standard & _SR versions);
166     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
167     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
168    o eesup/src:
169     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
170       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
171    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
172    
173    checkpoint63m (2012/04/27)
174    o pkg/shelfice:
175     - account for partical cells in surface level below ice-shelf for hydrostatic
176       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
177    o ad test experiments:
178     - update and rename to "ad_optfile.local" local AD-optfile specific to a
179       particular adjoint verification experiment (in verification/*/code_ad/)
180    o pkg/seaice & pkg/exf:
181     - Part two of ECCO-CLIVAR code merges.
182       Completes merge of seaice area relax. code.
183       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
184       to be set in EXF_OPTIONS.h since this pkg controls its I/O
185       (and avoids second CPP option in SEAICE_OPTIONS.h)
186     - change default value of costIceStart & costIceEnd to a valid date.
187     - add snowPrecip to HSNOW in seaice_growth
188    o pkg/ptracers:
189     - move ptracers summary and setup check into separated S/R ; add a check for
190       valid PTRACERS_Iter0 value (error+stop or just warning).
191    o pkg/cal (+ pkg/ecco):
192     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
193       as input; and for AD, unless both are not differentiable (e.g., k index)).
194    o model/src:
195     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
196       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
197       temporary set to usingZCoords value (to be changed to F when using shelfice).
198     - hydrostatic pressure: implement partial cell near the surface also for
199       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
200       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
201    o pkg/ctrl/ctrl_init.F:
202     - add a formal parameter to s/r ctrl_init_rec to print
203       xx_$(ctrl_valiable)_file for easier debugging
204     - move call of cal_* routines into the if-block where they are really
205       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
206       to specify a startdate
207    o pkg/seaice:
208     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
209       global_ocean.cs32x15/code versions).
210     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
211       verification experiment global_ocean.cs32x15.seaice and update results.
212    o pkg/exf:
213     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
214       (according to useExfYearlyFields).
215    o pkg/cal:
216     - move calendar setting & summary (previously in cal_readparams.F) into new
217       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
218       length of the simulation is set (after SET_PARMS call); This is an attempt
219       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
220     - For safety: keep a record of pkg/cal parameter settings status
221               to allow to STOP if one pkg/cal S/R is called too early.
222     - add a stop in all basic pkg/cal subroutines if called before setting is done.
223     - modify cal_getdate.F: stop when nothing was returned;
224       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
225       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
226    
227    checkpoint63l (2012/04/04)
228    o pkg/bbl:
229      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
230        update global_with_exf output.yearly.txt file.
231    o pkg/cal:
232      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
233      - remove 2 unsused and very short (1 line only) functions ;
234      - remove unsused subroutines from AD-Diff list.
235    o model/src:
236      - start to implement clean wait to stop in initialization S/R (config_check.F,
237         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
238    o folowing PRINT_MESSAGE changes:
239      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
240    o pkg/bbl:
241      - modification so it can work with z*
242      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
243      - global_with_exf/input.yearly verification; changes output.yearly.txt
244    o eesupp/src:
245      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
246        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
247      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
248        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
249      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
250      - when using MPI, always set usingMPI=T ; set default accordingly and stop
251        if not consistent.
252      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
253        argument is zero (in case called within single-thread section).
254    o pkg/fizhi:
255        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
256        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
257    o pkg/exch2:
258      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
259        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
260      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
261        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
262        with bad ones coming from a not-yet-updated halo.
263        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
264    o pkg/frazil:
265        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
266        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
267    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
268    o verification/lab_sea
269      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
270      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
271      * nTimeSteps 3 -> 4
272      * changed reference output accordingly
273    o pkg/ctrl:
274      * fix ctrl_get_gen for xx_sst, xx_sss
275    o pkg/fizhi:
276      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
277        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
278      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
279        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
280        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
281    o pkg/gmredi:
282      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
283    o pkg/fizhi:
284      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
285        (old)aces open64 tuv test.
286    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
287    o pkg/mom_vecinv:
288      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
289        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
290        with non-lin free-surf).
291    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
292      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
293      some compilers (gfortran 4.6.0 on MacOS)
294    o momentum:
295      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
296        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
297        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
298    
299    checkpoint63k (2012/03/17)
300    o model/src:
301       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
302         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
303       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
304         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
305    o model/src: solve_*diagonal.F
306       - replace division with multiplication by inverse (similar to original version)
307         update output of AD exp. global_ocean.90x40x15.
308       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
309         to enable the use of the vectorized & differentiable solve_tridiagonal.F
310       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
311         vertical advection (to get solve_tridiagonal tested in AD mode).
312    o pkg/seaice: ECCO-CLIVAR merge:
313      1. seaice AREA relaxation
314         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
315         * runtime flag: SEAICE_tauAreaObsRelax
316      2. modified global mean cost imbalance code: CPP option
317          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
318    o another iteration on solve_*diagonal.F
319       Make choices independent of AUTODIFF
320       Default will be the adjoinable vectorized version.
321       Alternative choices are:
322       * non-adjoinable original version with low memory footprint:
323         #define SOLVE_DIAGONAL_LOWMEMORY
324       * still adjoinable but does not vectorize (k as inner-most loop):
325         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
326    o testreport
327     - add option to use a home made wrapper around "make"
328     - remove MITGCM_IEEE env. variable (no longer active)
329    o pkg/shelfice
330     - improve computation of friction velocity for velocity dependent
331       exchange coefficients: include velocities into SHELFICEBoundaryLayer
332       block to average velocities vertically
333     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
334    o Modify diagonal solvers, now three versions (upon request):
335      #ifndef SOLVE_DIAGONAL_AUTODIFF
336        1. default version (dating back a while ago)
337      #else /* def SOLVE_DIAGONAL_AUTODIFF */
338      # ifdef SOLVE_DIAGONAL_KINNER
339        2. adjoinable version with k-innermost loop (G. Forget)
340      # else
341        3. adjoinable vectorized version of 2.
342      # endif
343      #endif /* SOLVE_DIAGONAL_AUTODIFF */
344      All flags are currently set within routines, but could/should be moved to CPP-options.
345      Array bounds for 1. are as before, for 2.,3. cover the entire domain
346      (could be changed for 1. too).
347    o verification/lab_sea (fwd):
348      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
349        use 7 categories (except hb87), new solve4temp params (except salt_plume),
350        constant salinity (=4) or variable salinity (salt_plume) done through
351        SItracer.
352    o pkg/seaice:
353      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
354      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
355         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
356        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
357        SEAICE_freeze got retired) but already better than previously with
358        SEAICE_freeze=123456.7 deg.C;
359      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
360        (safer multi-threaded setting); always set SEAICEuseEVP;
361      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
362        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
363        stop if multiple specifications for the same coeff; make sure default
364        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
365    o pkg/obcs:
366      - allow to switch to upwind 1rst order advection scheme for the advective
367        flux computation at the open-boundary; disabled for adjoint built.
368    o pkg/ptracers:
369      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
370      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
371      - add parameter to decide when to start a tracer; use internal flag to
372        know which tracer to step-forward; switch this internal flag at the top
373        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
374        for adjoint built.
375    o pkg/seaice:
376      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
377      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
378      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
379    o pkg/ecco:
380      - fix writing of output file DiagnosCost_ClimSalt/Theta
381        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
382    o pkg/seaice:
383      - add missing initialisation of COR_ICE array in dynsolver.F
384      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
385        compiled either way, and is tested in all exps (multidim was only tested
386        in lab_sea ad before).
387      - cosmetic change to prepare for future addition of ITD. no change to results.
388        no defaults change.
389      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
390      - by lack of adequate verification experiments, I further used custom versions
391        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
392        should be correct.
393      - avoid recomputations in ad.
394    o array initialisation in adjoint mode:
395      1) pkg/mom_common/mom_calc_ke.F:
396        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
397        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
398        part this initialisation is gone, resulting in Floating Point Exception
399        (caught by open64 compiler with debug option).
400      2) model/src/convective_weights.F
401        set output convectCount over the full array range (instead of doing
402        an update): this fix a similar issue when called within recomputation (adjoint)
403        which could by-pass the initialisation (normally done in the caller S/R).
404    o pkg/seaice:
405      - final version of turbulent flux params, as agreed at MIT ice meet:
406           SEAICE_mcPheePiston (default is ~ 0.000875)
407           SEAICE_mcPheeTaper (default is 0.)
408           SEAICE_frazilFrac (defualt is 1.)
409           SEAICE_mcPheeStepFunc (default is false)
410      - changes results at trunction error level
411      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
412    o added pkg/frazil:
413      - see frazil_description.tex for details
414      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
415    o pkg/shelfice/shelfice_thermodynamics.F
416      - fix exponents for velocity dependent exchange coefficients: change
417        from 2/3(=0) to 0.66666666666666667
418      - move computation of velocity dependent exchange coefficients into
419        separate loop, so that it applies to both thermodynamics
420      - move some divisions by constants out of loops
421    
422    checkpoint63j (2012/02/16)
423    o pkg/seaice:
424      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
425      - SItracer:  added run time params, and allow coupling to ocn salinity.
426    o pkg/seaice: remove (almost) all divisions by constants within loops
427      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
428      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
429      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
430      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
431    o pkg/seaice :
432      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
433        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
434      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
435      - add permanent SItflux diag that corresponds to TFLUX but includes
436        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
437      - allow activation/testing of a fix for suspected missing term in
438        ocn-ice heat budget (to be confirmed). To test this, you want to
439        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
440        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
441      - no change in results, fwd or ad.
442    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
443      - switch to variable freezing point.
444           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
445      - bug fix : the sublimation term that was missing is now activated.
446           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
447      - bug fix : flooding sign term for SIsal0.NE.0.
448           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
449    o pkg/seaice:
450      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
451        is now the default, and the old default constant freezing point is recovered
452        with SEAICE_tempFrz0    = -1.96,
453             SEAICE_dTempFrz_dS = 0.,
454      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
455      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
456      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
457        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
458      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
459        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
460      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
461        seaice_growth r149 for legacy branch (no results change).
462      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
463        from I. Fenty).
464      - results did not change except for global_ocean.cs32x15, mostly due to the
465        switch to variable freezing point (see above item for detail).
466    o pkg/thsice:
467      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
468        seawater freezing in thsice_calc_thickn (not used).
469    o pkg/seaice: turbulent flux term specification via run time params.
470      - replace CPP switches with run time switches to facilitate testing
471      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
472                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
473      - added runtime parameter : SEAICEturbFluxFormula
474      - move Mcphee constants to SEAICE_PARAMS.h
475      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
476                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
477                 remove seaice_summary call (moved to seaice_init_fixed)
478      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
479        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
480      - seaice_summary.F : add missing report of read turbulent flux term set up
481                           and SITRACER.
482      - seaice_check.F : check range; inform and stop if retired CPPs are used
483                         (incl. SEAICE_AGE).
484      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
485             CPP switch, same computation as before for the different options.
486      - change results at the truncation level.
487    o pkg/seaice:
488      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
489        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
490        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
491      - update verification/*/input*/data.seaice:
492        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
493        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
494        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
495        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
496    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
497      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
498        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
499        difference in results only due to machine truncation.
500      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
501        MaykutPolySatVap; keep MIN_LWDOWN.
502      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
503      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
504        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
505    o pkg/salt_plume:
506      - isolate saltPlumeFlux array exch into a specific S/R called from
507        do_oceanic_phys.F
508      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
509    o verification:
510      - move untested set-up to MITgcm_contrib/verification_other.
511    o pkg/seaice:
512      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
513    o pkg/seaice:
514      - seaice_solve4temp.F (keeping results unchanged):
515        * add 2 future run-time params to select which saturation vapor pressure
516          formula is used and how post-iteration fluxes are set.
517          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
518        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
519          the linearized expression to stay consistent with tsurf finding.
520      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
521        can be < 0.
522    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
523      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
524        conductive heat flux F_c , and add it explicitly when updating tsurf as
525        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
526        so that now F_ia has a consistent meaning through the entire routine.
527        This causes differences at truncation level: update output of fwd exp.
528        global_ocean.cs32x15.seaice.
529    o pkg/seaice:
530      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
531        of arrays, sign/direction of fluxes; no effect on results.
532      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
533        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
534        note: this should have been done before changing celsius2K default.
535      - to keep results unchanged, add back old value of celsius2K in verification
536        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
537      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
538        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
539        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
540        freezing temp is consistent with value in seaice_growth.F ; this causes
541        differences at machine truncation level: update lab_sea AD output (3/4).
542    o pkg/seaice:
543      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
544        and climsst/sss even when using seaice (to prevent calculation that might
545        use SST on land); does not affect any verification exp.
546      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
547        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
548    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
549      over land (non-legacy code)
550    o vectorize salt_plume package:
551      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
552      - this code computes plumebk everywhere (also over land), thus requires
553        code to avoid divisions by zero and catch the case of kLev=Nr.
554      - efficiency of salt_plume_frac is still sub-optimal
555    o tools (genmake2):
556      - fix makefile NAME specification (option: -makefile NAME) by adding
557        "-f $MAKEFILE" in few places where it was missing including makedepend
558        command (contribution from Paul).
559    
560    checkpoint63i (2012/01/24)
561    o model/src:
562      - add factorized versions of some EOS code to find_rho.F,
563        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
564    o model/src:
565      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
566      - change default celsius2K from 273.16 to 273.15
567      - to keep results unchanged, add back old value of celsius2K in verification
568        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
569         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
570    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
571      to make TAF generate vectorizable code
572    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
573       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
574       have flags that do this more efficiently.
575    o pkg/diagnostics/diagstats_calc.F
576      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
577    o pkg/obcs (with exch2):
578      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
579        and remove code (in obcs_readparms.F) which was based on EXCH of indices
580        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
581    o pkg/exf and seaice exp:
582      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
583        so that switching off area & heff advection flags does not affect results.
584      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
585      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
586        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
587        results of verification experiments: 1D_ocean_ice_column(fwd),
588        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
589        and offline_exf_seaice (all 4).
590    o pkg/seaice:
591      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
592        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
593      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
594        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
595        not multi-dim advection;
596      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
597        SHORTWAVE_HEATING #undef.
598    o optim: make Makefile more robust (?)
599    o pkg/obcs:
600      * fix treatment of obcs_read_pickup for TAF
601    o pkg/shelfice:
602      * add missing initialisation of num_shifwflx
603      * new adjoint verification exp. for isomip
604      * change Prandtl and Schmidt numbers from generic formulations
605        (in terms of model diffus. and visc.) to separate runtime
606        parameters, with Holland and Jenkins (1999) default values.
607    o pkg/exf (interpolation):
608      - extended input field (2 rows) near the N & S poles:
609        * fill in with the symetric value (when even Nb of data in longitude)
610        * add average value at the poles only for scalar quantities ; for vector
611          component interpolation, skip the averaging and keep duplicated values,
612          unless the 2 components have same location (uvInterp=T) in which case
613          interpolate the 2 components together using S/R EXF_INTERP_UV.
614      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
615        together: this allows to account properly for local orientation when
616        averaging at N & S pole.
617      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
618        exf-interpolation near N & S poles. Undef by default.
619      - add debug check/print on 1rst iter if debugLevel >=2.
620    o pkg/exf:
621      - change masking flags definition (no longer "parameter"), put them in
622        common block and set them in S/R EXF_INIT_FIXED.
623      - change recognized masking flag from s,u,v to c,w,s since the mask
624        to use (maskC,W,S) depends on position on model grid and has little to
625        do with scalar/vector difference; fix masking if using P-coordinates.
626      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
627        and update results of exp. global_with_exf (x2).
628      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
629    o pkg/obcs
630      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
631    o pkg/exf (interpolation):
632      - assume periodicity in X only if input field cover full longitude range.
633      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
634        and should vectorise).
635      - fix input lat of the 2 added row (in case we provide N.pole data).
636    
637    checkpoint63h (2011/12/30)
638    o pkg/seaice:
639      - change declaration of UVM from _RL to _RS in order to get B-grid
640        uIce,vIce monitor when _RS = real*4
641    o pkg/offline:
642      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
643      - compute vertical velocity if not read from file (switch on exactConserv
644        & staggerTimeStep);
645      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
646    o verification:
647      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
648        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
649        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
650      - update output of exp. global_ocean.cs32x15.viscA4 after changing
651        grid-file angles (used here for coriolis-3d);
652      - remove (or gzip) few files not needed to run fizhi-cs experiments.
653    o pkg/exf (vector interpolation):
654      - rotate vector component toward local grid-axis orientation using grid-angles
655        (stored in GRID.h) instead of locally computed rotation angle; keep old code
656        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
657    o pkg/seaice:
658      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
659        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
660    o pkg/PKG_OPTIONS.h files:
661      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
662        outside of the #ifdef ALLOW_THISPKG / #endif block.
663      - update verification/*/code/PKG_OPTIONS.h files.
664    o add a verification experiment (offline_exf_seaice/input.seaice) that test
665      the B-grid LSOR solver
666    o pkg/seaice: sort out emissivity and long wave radiation step 2:
667      - add emissivity for snow and ice as new run-time parameters
668        (unfortunately) that default to the corresponding exf values; this
669        changes results in most verification experiments so that for backward
670        compatibility these parameter have to be set explicitly to inconsistent
671        values (ugly);
672      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
673        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
674        until we agree how to handle this bug properly
675    o pkg/exf (interpolation):
676      - add a set of run-time param ({inputfield}_interpMethod), one for
677        each interpolated input field, to select the interpolation method
678        with a value of zero switching off the interpolation;
679      - print interpolation parameters to standard output;
680      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
681        (to use instead runoff_interpMethod=0 in data.exf).
682      - simplify default setting of interpolation parameters (for all fields,
683        set position to match model grid cell-center position, leading to trivial
684        interpolation in case of regular Lat-Lon grid) and fix for the case of
685        non-uniform delY.
686    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
687       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
688       this factor is absolutely required, because the lw exitance (= out-going
689       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
690       where the reflectivity rho = 1-emissivity for conservation reasons. Once
691       this is established, we can remove the CPP-Flag (if we want to).
692    o pkg/seaice:
693      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
694        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
695      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
696        what the name implies (and not emissivity*BoltzmannConstant), this means
697        the old default value of 5.5e-8 now means
698        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
699        S/R exf_readparms
700      - FV-discretization of the B-grid LSOR solver, turn on with
701        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
702        of the calling routine dynsolver, so that B and C-grid code look a
703        little more alike.
704      - fix index bugs in ostres.F (B-grid code)
705    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
706    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
707      default for SEAICE_emissivity, if useEXF; requires setting a wrong
708      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
709      backward compatiblity
710    o model/src: use sigmaR in calc_ivdc
711    
712    checkpoint63g (2011/12/16)
713    o pkg/seaice/seaice_growth.F:
714      fix heat conservation of the coupled ocean-seaice system.
715      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
716      solid vs liquid water treatment is resolved via QNET.
717    o pkg/seaice/seaice_growth.F:
718      add missing term for sublimation in saltFlux, which was breaking conservation.
719    o pkg/seaice/seaice_model.F:
720      Remove this patholigical case treatment in evolution branch,
721      where it is un-necessary and breaks conservation.
722      Update global_ocean.cs32x15/results accordingly for
723      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
724    o model/src:
725      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
726      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
727    o pkg/obcs:
728      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
729      tendency for temperature and salinity that is then applied to update
730      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
731      horizontal advection and diffusion contributions on the boundary (in
732      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
733      removing the mask in S/R timestep_tracer. The advantage of this approach is
734      that the updated tracer values include contributions from the surface
735      forcing and vertical diffusion.
736      This modification changes exp4.stevens because of vertical diffusion.
737    o model/src:
738      change non-curvilinear grid setting to also work with exch2 + blank tiles:
739      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
740        face dimensions.
741      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
742        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
743        and INI_SPHERICAL_POLAR_GRID.
744      change test-experiment global_ocean.90x40x15:
745      - split the domain in many more tiles (9x4 tiles of 10x10 each);
746      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
747      - update results of both test (std & dwnslp).
748    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
749       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
750    o model/src:
751      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
752        and fix initialisation when using sigma-coords.
753    o model/src:
754     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
755       to their current value at the beginning of forward_step.F": add a new run-time
756       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
757     - set doResetHFactors=T in the following test exp:
758        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
759        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
760        and tutorial_global_oce_in_p (nonLinFS in p)
761    o pkg/ecco
762      - added IES cost term
763    o verification/advect_xz
764      - scale down the depth by 1/100 (from 200 km to just 2.km)
765      - add secondary test using divergent flow, r-star and implicit vertical advection.
766      - add note (check_conserve_TS.txt) and matlab script to check global
767        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
768    o pkg/rbcs:
769      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
770    o pkg/obcs (Stevens BCs):
771      - fix various problems in the phase speed computations of the Stevens
772        boundary conditions:
773        - sign error for western and southern boundaries,
774        - time tendencies were underestimated by factor of dTracerLev and some just
775          zero (for multidim advection schemes) -> now estimate time tendencies
776          from difference between previous (n) time level and the one before (n-1);
777          this requires storing a field per tracer per boundary, also in the pickup
778          files.
779        - replace deltaTmom in cflMer/Zon computation with dTracerLev
780        - set default phase velocity to cflMer/Zon
781      - update verification experiment exp4.stevens
782    o pkg/generic_advdiff (implicit_r):
783      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
784        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
785      - fix implicit vertical diffusion or advection with NonLin FreeSurf
786        (was using current recip_hFacC instead of future recip_hFacC): set future
787        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
788        solver S/R ;
789      - fill diagnostics of vertical advective fluxes (computed from tendency)
790        when using implicit vert. advection;
791      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
792         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
793         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
794         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
795    o pkg/diagnostics:
796      - add diags for T & S tendency which goes through Adams-Bashforth.
797    
798    checkpoint63f (2011/11/30)
799    o pkg/obcs/obcs_calc_stevens.F:
800      - join some loops to reduce number of if-statements
801      - fix a bug in code for northern and southern boundaries.
802    o pkg/seaice/seaice_init_varia.F
803      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
804        caused zero ice-velocities for the B-grid code
805    o pkg/seaice/seaice_init_fixed.F
806      - fix a bug in the initialisation of the second metric terms
807        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
808      - this affects all seaice configurations with useCurviLinearGrid = .true.
809        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
810        = .true. (default)
811      - the only verification experiment affected is global_ocean.cs32x15:
812        icedyn, seaice, and seaice_dynmix (AD)
813    o pkg/thsice/thsice_diagnostics_state.F
814      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
815        not contain garbage that can lead to surprises in diagstats_calc.F
816    o model/src:
817      - move bi,bj loops inside INTEGR_CONTINUITY ;
818      - call INTEGR_CONTINUITY directly from forward_step.F
819        (previously called from momentum_correction_step.F)
820      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
821        forward_step.F and pkg/ecco/the_main_loop.F
822    o model/src/do_oceanic_phys.F:
823      - reset addMass to zero only if useICEFRONT ;
824      - separated k-loop for rhoInSitu calculation ;
825      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
826        and at constant T,S (= WdRHOdP);
827      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
828        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
829        transport of locally-referenced potential density);
830        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
831    o gluemnc:
832      - replace ncrcat with ncks when adding variables to *.glob.nc
833      - change the way variables without record dimensions are handled so that
834        files that have variables with and without record variables can be glued:
835        add a record dimension with a new unique name to be able to differentiate
836        between variable with and without a-prior record dimensions. Remove
837        this record dimension before adding the variable to the *.glob.nc file.
838        This procedure automatically works also for grid.*.nc files that do not
839        have any record dimension.
840    o verification/cpl_aim+ocn:
841      - generate new reference output on baudelaire (gfortran, mpich2) (previously
842        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
843    o pkg/obcs/obcs_calc_stevens.F:
844      - add code for northern and southern boundaries.
845      - reorder some loops to save some operations and so that drFBar can be scalar
846    o model/src:
847      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
848        truncation) and add diagnostics for Adams-Bashforth tendency increment.
849      - update test-exp. AD output:
850        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
851      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
852        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
853        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
854        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
855        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
856        tutorial_plume_on_slope.
857    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
858      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
859      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
860      does not even come with an F77 compiler anymore, this should not be
861      a limitation
862    
863    checkpoint63e (2011/11/06)
864    o pkg/seaice adjoint of LSR:
865      - substantially rework STORE dirs.
866      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
867        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
868        and only perform SOLV_MAX_FIXED adjoint iters.
869        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
870        always goes to same record, meaning that the last forward field will be
871        the one used in the adjoint - an approximation.
872      - now produces non-zero LSR-related gradients, and acceptable gradients for
873        An's zonal (x-z) test case (to be checked in)
874      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
875        (but these are screwed up by the thermodynamics in the first place);
876        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
877        output_adm.txt also reflects changes to seaice_lsr
878      - global_ocean.cs32x15:
879        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
880          (output_adm.seaice.txt was updated)
881        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
882          (output_adm.seaice_dynmix.txt)
883    o test-exp. exp4+stevens:
884      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
885    o pkg/seaice (lsr solver):
886      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
887        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
888      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
889      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
890        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
891      - compute (with new S/R) and print initial (+ free-driff sol. if available)
892        and final residual of linearised system.
893    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
894      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
895    o pkg/obcs: Stevens BCs (still only for east and west)
896      - fix Stevens BCs by using intermediate velocities of previous
897        time step as "baroclinic" contribution rather velocity of one grid cell
898        inside the boundaries; more consistent but makes the entire treatment
899        more complicated, requires new pickup files and two new S/Rs:
900        obcs_copy_uv_n and obcs_save_uv_n
901        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
902        (undefined by default)
903      - silently move computation of some grid factors into separate loops to
904        save some recomputations
905      - add a hack for non-linear free surface
906      - add a verification experiment to exp4 that tests this code
907    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
908    
909    checkpoint63d (2011/10/25)
910    o pkg/obcs + seaice-dynamics:
911      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
912        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
913        values (consistent with an implicit method).
914      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
915        return to older implementation (same results as before); note that none of
916        the "experimental" OBCS_SEAICE options are implemented in the new version.
917      - switch test exp. seaice_obcs to use new version (update output).
918    o pkg/seaice:
919      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
920      - add parenthesis in Water-Ice drag calculations (evp & lsr);
921      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
922        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
923      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
924        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
925    o pkg/layers:
926      - Include potential density as new coordinate (Thanks to David Munday)
927    o pkg/dic:
928      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
929        carbonate computation/output to CALC_PCO2_APPROX
930    o pkg/generic_advdiff
931      - make TAF generate code that vectorizes:
932        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
933    o model/src:
934      - improve vectorization also for adjoint code of
935        solve_tridiagonal and solve_pentadiagonal. As this requires up to
936        5 new 3D-fields, this code is only turned on for the combination of
937        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
938        for singular matrix check (only for TARGET_NEC_SX).
939      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
940        ALLOW_AUTODIFF. This flag now needs to be set outside of
941        solve_tri/pentadiagonal.F
942    o pkg/exf:
943      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
944        optional namelist EXF_NML_OBCS).
945      - add many debug-print (to trace down where pkg/cal error msg comes from)
946    o pkg/mom_vecinv/mom_vi_hdissip.F
947      - rearrange loops so that vectorization is improved and in particular
948        the adjoint routine vectorizes. The code is a little longer now, but I
949        think easier to read.
950        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
951    o pkg/seaice:
952      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
953    o pkg/exch2:
954      - alternative code (without tile x tile matrix) for cumulated (global) sum;
955        used as default; keep using matrix version in adjustment.cs-32x32x1.
956    o tools/build_options:
957      - after merging some MPI and/or multi-threads specific optfiles so that
958        the modified default optfile support both built (using genmake2 -mpi
959        for the MPI built, using genmake2 -omp for OpenMP built),
960        move now obsolete optfiles to tools/build_options/unsupported/
961       (add copy of email sent to support list in doc/optfiles_changes.txt)
962    
963    checkpoint63c (2011/09/28)
964    o pkg/ebm:
965      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
966        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
967    o pkg/seaice (SItracer pickup)
968    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
969      To be done:
970      - thorough testing of missing fields in S/R seaice_read_pickup
971      - thorough matching between generic tracers and specific fields used
972        (e.g. volume-weighted age, area-weighted age, salinity, ...)
973    o pkg/grdchk:
974      - all procs calculate and print finite-difference gradient (for testreport)
975      - change description output used by testreport;
976      - AD testing: also compare and report Finite-difference gradient;
977        => update all output_adm*.txt
978    o test exp. global_ocean_ebm:
979      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
980        and turn on exactConserve; update (fwd) output.
981    o pkg/seaice (LSR):
982      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
983      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
984        * identical results with non-CS topology (but save up to half of EXCH calls)
985        * no much changes in cs-32 verification tests since no ice at face edges
986         (differences due to convergence criteria, since nb of iterations changed)
987        * expect some differences on lat-lon-cap grid.
988        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
989    o pkg/exch2:
990      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
991        many tiles); until alternative coding is added, just add a stop.
992    o pkg/kpp:
993      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
994        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
995    o optfiles:
996      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
997        into corresponding standard one, which now support different build:
998        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
999      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1000    o pkg/obcs (seaice):
1001      - add missing EXCH for uIce,vIce after applying OBCS;
1002      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1003        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1004        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1005      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1006      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1007        and eedata.mth for MPI and mutlti-threaded testing.
1008    o pkg/flt:
1009      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1010      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1011      - fix pickup and trajectories + profiles output with multi-threads;
1012      - add parameter to select group of fields to write along trajectory and
1013        profile (default unchanged);
1014      - only call PORT_RAND* function when flt_noise <> 0;
1015      - add multi-threaded test for verification exp. flt_example.
1016    o eesupp/src:
1017      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1018      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1019        actual number (from env.var. setting).
1020    o pkg/ebm:
1021      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1022      - add multi-threaded test for verification exp. global_ocean_ebm
1023    
1024    checkpoint63b (2011/08/29)
1025    o pkg/ebm:
1026      - fix sign of runoff;
1027      - update directly forcing fields (Qnet,EmPmR) to use standard
1028        external_forcing_surf.F (remove ebm_forcing_surf.F);
1029      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1030      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1031        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1032      - update global_ocean_ebm parameters file data and update output (fwd+ad).
1033    o verification/matrix_example:
1034      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1035        MPI and mutlti-threaded testing.
1036    o pkg/matrix:
1037      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1038      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1039      - fix for multi-threaded (remove DATA statement);
1040      - use standard DIFFERENT_MULTIPLE function;
1041      - add MATRIX_OPTIONS.h
1042    o verification/matrix_example:
1043       To allow to split the domain in several tiles, change the domain size
1044        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1045        Western side) of land points.
1046    o (*_)write_pickup:
1047      - fix few bugs in mypackage_read/write_pickup.F
1048      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1049        array of length 1 (was caught by compiler syntax-check).
1050    o pkg/diagnostics (velocity potential solver):
1051      - fix initialisation of main diagonal matrix (for overlap values)
1052    o tools/build_options:
1053      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1054        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1055      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1056        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1057        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1058        and use "-devel" testreport option for standard testing on baudelaire.
1059    o pkg/grdchk:
1060      - Assume that all gradient-check position are within the same tile
1061        corresponding to global indices (iGloTile,jGloTile) and that
1062        positions (i,j indices or nbeg) are local to this tile;
1063      - set tile local-indices and proc. number according to tile global-indices;
1064      - remove grdchkwhichproc from namelist (retired param);
1065      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1066      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1067    o adding package bbl (Bottom Boundary Layer)
1068      description in MITgcm/pkg/bbl/bbl_description.tex
1069      example/test experiment in MITgcm_contrib/bbl
1070    o adjoint verifications
1071      - changed 5 experiments to multi-tiles
1072        * global_ocean.90x40x15
1073        * obcs_ctrl
1074        * offline_exf_seaice
1075        * tutorial_dic_adjoffline
1076        * tutorial_tracer_adjsens
1077        changed reference output for those that crossed tile boundaries
1078        (changed choices of gradient check positions)
1079      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1080      - temporary bug fix in grdchk_loc.F for obcs
1081    o genmake2 & testreport
1082      - add target "obj" (just for OBJFILES files) to Makefile;
1083      - add option to specify FEXTRAFLAGS on command line.
1084    o pkg/mypackage:
1085      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1086    
1087    checkpoint63a (2011/08/02)
1088    o pkg/diagnostics (velocity potential):
1089      - fix velocity-potential calculation when using OBCS: balance net inflow
1090        at each level (new S/R OBCS_DIAG_BALANCE).
1091      - fix some of the problems with OBCS in stream-function calculation.
1092    o pkg/exf/exf_readparms.F
1093      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1094        EXF_NML_OBCS) more consistent, so that you need not have these lists
1095        in data.exf when they are not used.
1096    o optim/optim_readdata.F:
1097      - add some output about obcs variables that might help debugging
1098      - add a check about nvarlength
1099    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1100    o pkg/diagnostics (velocity potential):
1101      - fix mask for OBCS (still problems in stream-function with OBCS);
1102      - add specific parameter (default = main code CG2D params) for solver;
1103      - in case of poor convergence, use solution corresponding to lowest residual.
1104    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1105      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1106      and should be avoided where possible.
1107    o model/src (rStar):
1108      - include r* effect on reference-state (PhiRef) in totPhiHyd
1109        (so that it's really the potential anomaly at the cell center);
1110        affect solution only if z* with full pressure in EOS.
1111      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1112        update output (because of z* in totPhiHyd and viscA4 changes);
1113      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1114        @ constant r) until interpolation at constant r is implemented.
1115    o pkg/diagnostics
1116      - fix RCENTER diagnostics in case cell center is not at interface middle
1117    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1118      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1119      that THETA and SALT are "conservative temperature" and "absolute
1120      salinity"
1121    o pkg/ctrl
1122      - fix computation of endrec in s/r ctrl_init_rec
1123      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1124    o pkg/seaice/seaice_growth.F
1125      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1126        remove then obsolete STORE directives
1127      - fix STORE directives for tice and tices, so that only the
1128        appropriate part of the fields are stored (and not the entire
1129        field); update global_ocean.cs32x15.seaice AD output.
1130      - cosmetic changes: adjust CPP flags and indentation for better
1131        legibilty
1132    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1133      Chris Wilson)
1134    o pkg/gmredi:
1135       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1136       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1137    
1138    checkpoint63  (2011/07/11)
1139    o pkg/exch2:
1140     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1141     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1142       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1143       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1144    o pkg/diagnostics:
1145     - deal with pairs of post-processed diags which are computed together; in
1146       particular, re-order list of diags within 1 file to save 2nd computation.
1147     - add S/R to compute velocity stream-function (called after velocity-potential
1148       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1149     - add parameter to select grid-point location where PsiVEL == 0.
1150    o eesupp/src:
1151       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1152       (specific S/R needed with exch2 topology - for now, just print an error msg)
1153    o pkg/shelfice
1154     - Implement friction velocity-dependent transfer coefficients following
1155       Holland and Jenkins, JPO, 1999
1156       Original code by M. Losch with small modifs.
1157       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1158       and runtime flag SHELFICEuseGammaFrict
1159    o verification lab_sea & global_ocean.cs32x15:
1160     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1161       does not miss some dependencies (but is slower) and also works with many files
1162       (default makedepend limitation for AD built).
1163     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1164    o pkg/diagnostics:
1165     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1166        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1167       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1168     - Extend the use of "missing_value" setting from data.diagnostics for the case
1169       of counter-diagnostics (where fraction-weight is zero). This applies both to
1170       MNC and MDS output files.
1171    o pkg/seaice/seaice_growth.F:
1172      - add 'a priori' cap of latent heat flux based on actual mass considerations
1173        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1174        non-legacy seaice_solve4temp.
1175      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1176        flux taken from the ocean if the total actual latent heat fluxes exceed
1177        the maximum)
1178      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1179       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1180      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1181       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1182      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1183      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1184    o verification 1D_ocean_ice_column:
1185       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1186       update results
1187    o pkg/diagnostics:
1188     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1189       which are not filled-up but computed from other diags ; In this case, the mate
1190       diag points to the primary (filled-up) diag to used for post processing.
1191     - Update Velocity-potential computation using post-processed diag framework.
1192     ==> Change the ordering of fields and time-periods in MDS output file
1193       when using periodic averaging: now writes one time record with the full set
1194       of fields for this time period, then the next time reccord (it used to be
1195       one field with the full set of time records then the next field).
1196         Note: this is now similar to NetCDF (MNC) output file. <==
1197    
1198    checkpoint62z (2011/06/21)
1199    o adjoint monitor:
1200     - Add adjoint monitor output for packages exf, seaice
1201       and update relevant testreport output
1202    o pkg/seaice:
1203     - re-order diags inits so that they appear in order in available_diagnostics.log
1204     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1205       area/heff/hsnow preceeding thermodynamic growth/melt.
1206     - modified diag: SIdA; output actual effect, as the description states.
1207     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1208     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1209       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1210        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1211     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1212     - added diagnostics for seaice generic tracers (SItr*).
1213     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1214     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1215     I. Fenty: 18-Jun-2011:
1216     Minor changes to seaice package:
1217     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1218        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1219       - Differentiated "regularization variables" from "floor variables"
1220        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1221        * hiceMin became SEAICE_hice_reg (old hiceMin)
1222          (with _reg meaning regularization variable)
1223       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1224        so as to ensure energy conservation when going between phases
1225      - A22 was not used anywhere
1226     2) Changed regularization procedure for heffActual and hsnowActual to ensure
1227        well-boundedness and smooth adjoint in seaice_growth.F
1228     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1229        because the old regularization always set heffActual >= 0.05 cm
1230     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1231        on AREA when HEFF > 0.
1232      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1233        requiring that DISABLE_AREA_FLOOR *not* be defined
1234     Affected verifications:
1235      - 1D_ocean_ice_column (output.txt output_adm.txt)
1236      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1237    o pkg/diagnostics:
1238      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1239      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1240        (was _RL, now integer) with option = 0 to retrieve all levels.
1241      - add pieces of code to compute velocity potential at each level (new diagnostics
1242        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1243        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1244      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1245        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1246        and in diagnostics_fract_fill.F (do not need a valid pointer for the
1247        diagnostics counter-mate); check that definition of counter-diagnostic
1248        includes a valid counter-mate (in diagnostics_set_levels.F).
1249    o model/src (rStar):
1250      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1251        affect solution only if z* with full pressure in EOS;
1252        update output of test-exp global_ocean.90x40x15.
1253    o pkg/seaice:
1254      - introduce siEps=1e-5 parameter
1255      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
1256      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
1257      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
1258        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
1259        as well as ice cover age and ridging index (attached to AREA).
1260        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1261        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1262        Up to SItrMaxNum=3 tracers can be used simultaneously.
1263    o pkg/salt_plume:
1264      -introduce SPsalFRAC run time parameter that sets the fraction of the
1265       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1266       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1267    o model debug options:
1268      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1269        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1270      - Refine debug-msg printing selection (3 new levels):
1271        debugMode  : controls printing of debug messages (sequence of S/R calls).
1272        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1273         debLevZero =  0 ; /* level of disabled aux. msg printing */
1274         debLevA =  1 ; /* level of minimum  aux. msg printing */
1275         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
1276         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
1277         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1278         debLevE =  5 ; /* level of extensive debug printing */
1279        New debugLevel default: with default debugMode value (=F),
1280          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1281          and if debugMode=T, default debugLevel = 4 (debLevD).
1282        Relation with previous settings:
1283         debLevB (=2) corresponds to former debLevA (=1)
1284         debLevD (=4) corresponds to former debLevB (=2)
1285        Note:
1286         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1287         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1288            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1289      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1290        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1291    o pkg/obcs:
1292      - change OBCSfixTopo default from True to False (should not change the results);
1293        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1294    o pkg/thsice:
1295      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1296        2nd layer seaice sublimation (unlikely to happen)
1297      - use Interior mask for OBCS in thsice_advection.F (similar to what is
1298        done in gad_advection & seaice_advection).
1299    o adjoint:
1300      bug fix spotted by Gael Forget:
1301      seaice_advection and thsice_advection still had
1302      legacy CPP options to avoid CS corner updates for adjoint
1303    o pkg/seaice:
1304      => Change some of the defaults (2011/05/29):
1305         - change SEAICEuseFluxForm default (from False to True)
1306         - change DIFF1 default (from 0.004 m/s to 0. m/s)
1307         And print warnings if DIFF1 is not set in data.seaice and centered
1308          avection scheme is used without any diffusion.
1309      also:
1310      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1311      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1312      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1313        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1314        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1315      update results of test exp.:
1316         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1317             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1318             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1319         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1320         seaice_obcs: output (SEAICEuseFluxForm=T)
1321      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1322          for standard fwd & AD lab_sea tests (to keep the same output).
1323    o pkg/seaice/seaice_growth.F:
1324      - use Ian Fenty's capping formulas for actual ice
1325      thickness thoughout EVOLUTION branch.
1326      - put treatment pathological case #2) in CPP brackets
1327      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1328      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1329    o pkg/seaice:
1330      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1331      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1332      also pass fac as a param, which can be 1. (to update the tendency
1333      field) or the time step (to update the field itself).
1334      - seaice_advdiff.F: for multidim, call seaice_diffusion with
1335      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1336      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1337      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1338      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1339    o pkg/seaice:
1340      diffusion with centered advection scheme (diffus.F & advect.F):
1341      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1342        to just compute the laplacian of input-field.
1343      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1344      - fix flux-form version in diffus.F to conserve tracer.
1345      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1346       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1347    
1348    checkpoint62y (2011/05/26)
1349    o pkg/seaice:
1350     - seaice_growth.F : in EVOLUTION branch, always include
1351       a_QSWbyATM_cover in qnet (as it should be).
1352     - verification/global_ocean.cs32x15 : update results accordingly
1353       (output.seaice.txt output_adm.seaice.txt).
1354    o pkg/seaice + obcs:
1355     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1356       equivalent of assuming no tracer gradient outside the OB region.
1357       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
1358     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
1359       after changes above);
1360     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
1361       only at OB location (instead of over a band of OLx width).
1362    o pkg/seaice:
1363     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
1364       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
1365    o pkg/obcs:
1366      - split header file "OBCS.h" into 4 separated files:
1367        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
1368       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
1369         (contain no conditional statement which depends on OBCS options).
1370      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
1371        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
1372    o ctrl, cost, grdchk & autodiff pkgs:
1373      - make options file more standard (like other {PKG}_OPTIONS.h file but
1374        with AD_CONFIG.h); clean-up some of the included header files.
1375    o pkg/obcs:
1376      - do not mask tracer when applying OB (tracer == 0 could generate problems)
1377      - apply tracer OB values to tracer field only at OB location (instead of
1378        over a band of OLx width)
1379      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1380      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1381        obcs_apply_tloc.F & obcs_apply_sloc.F
1382    o obcs in model/src:
1383      - call OBCS_APPLY_W only if NonHydrostatic.
1384      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1385      - reset dEtaHdt and wVel to zero outside OB interior region ;
1386      - leave tracer unchanged outside OB interior region: This has no effect
1387        on the solution but just to prevent unrealistic tracer value outside OB.
1388      - zero out velocity outside OB interior region: This has no effect on
1389        the solution but just to prevent unrealistic velocity outside OB.
1390    o obcs and non-lin free-surf:
1391       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1392       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1393       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1394       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1395       update results of test-exp. exp4(nlfs).
1396    o exp4 (nlfs) test-exp:
1397       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1398       with NonLin-FreeSurf); update output.nlfs.txt
1399    o obcs and 2d/3d solver norm:
1400       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1401       and outside OB interior region (will allow to place OB further inside the
1402       domain). Depending on the domain, can affects cg2d-Norm (previous
1403       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1404       and cg3d-Norm (previous Norm was computed before canceling OB terms),
1405       e.g. in tutorial_plume_on_slope.
1406      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1407    o pkg rbcs:
1408      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1409      - add capability to apply relaxation to horizontal velocity uVel & vVel.
1410    o pkg/grdchk: add gradient check for control variable xx_shifwflx
1411    o pkg/shelfice/shelfice_init_fixed.F
1412      fix CPP-flag combinations
1413    o pkg/seaice: Merge iceage code of Pierre Rampal
1414      * update/change/correct ice age calculations
1415      * add age updates for pathological cases
1416      Probably needs more testing...
1417    
1418    checkpoint62x (2011/05/13)
1419    o pkg/mom_vecinv:
1420       high-order vorticity scheme: use interior masks (maskInW & S)
1421       to zero-out (outside OB) gradient of vorticity.
1422    o verification exp.:
1423       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1424       hs94.128x64x5 and seaice_obcs ; update results.
1425    o pkg/obcs:
1426      fix bug in OBeta for YZ sections in obcs_exf_load.F
1427    o pkg/ctrl, pkg/shelfice, and optim:
1428      - add new control variable xx_shifwflx (fresh water flux underneath ice
1429        shelves). This is almost as tedious as obcs-ctrl, because the
1430        variables needs its own mask.
1431      - add a cost function term that penalizes the deviation of xx_shifwflx
1432        from the first guess (zero) in analogy to other control variables
1433    o pkg/shelfice:
1434      - start basic adjoint
1435    o pkg/ctrl:
1436      - remove extra 2D field "for good measure" when initializing in
1437        ctrl_set_globfld_[xy/xz/yz].F
1438      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1439      - improve error messages in ctrl_set_unpack_*
1440    o OBC implementation in momentum:
1441       use interior masks (maskInC,W & S) in momentum S/R:
1442       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1443       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1444       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1445       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1446       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1447        (and also with Leith/Smagorinsky harmonic-viscosity).
1448       Update output of experiment dome and exp4 (+nlfs).
1449    o exp4 test-exp:
1450      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1451        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1452        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1453        time-varying OB at Western-side for wVel (NonHyd); update output.
1454      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1455        and biharmonic-viscosity ; also use prescribed time varying OB.
1456    o pkg/obcs:
1457      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1458    o model/src:
1459      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1460      - initialise startTime & nIter0 with unlikely values: allows to set one
1461        from the other without ambiguity.
1462    o seaice_obcs test-exp.:
1463      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1464    o pkg/obcs:
1465      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1466        no longer needed with maskInC,W,S in pkg/generic_advdiff.
1467    o pkg/seaice:
1468      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1469        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1470      - fixed bug in the initialization of sea ice salinity variable HSALT
1471        in seaice_init_varia.F  (removed dependence on ICE2WATR)
1472    o fizhi-cs test exp.:
1473       switch reference output convention for these 2 non-standard test-exp,
1474        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1475          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1476       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1477    o model/inc:
1478      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1479        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1480    o pkg/seaice:
1481      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1482    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1483      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1484        and initial HSALT
1485    
1486    checkpoint62w (2011/04/26)
1487    o pkg/mom_fluxform:
1488      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1489      - use parameter "sideDragFactor" in no-slip BC side-drag part.
1490      - update output of exp. global_ocean.90x40x15
1491    o pkg/mom_vecinv:
1492      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1493    o update seaice exp.:
1494      use more consistent parameter values (remove "backward compatability only":
1495       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1496      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1497       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1498    o update test-exp global_ocean.90x40x15:
1499      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1500      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1501      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1502      o turn on zStar & viscA4 in standard set-up (dir input/)
1503        and update output files: output.txt & output.dwnslp.txt
1504    o new AD-test experiment: obcs_ctrl
1505      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1506    o pkg/dic:
1507      fix two bugs in handling water vapour pressure in carbonate chemistry
1508      and air-sea fluxes. Found by Val Bennington and Galen McKinley
1509      (add DIC Option = WATERVAP_BUG to recover old results)
1510      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1511    o adding allowInteriorFreezing option to check for water below freezing point
1512      at depth and bring the negative heat anomaly to the surface level
1513    o pkgs _fields_load:
1514      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1515      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1516        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1517        rbcs to get interpolation weights and time reccord number.
1518      - fix multi-threading in aim_fields_load.F
1519      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1520    o external_fields_load:
1521      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1522       interpolation weights) to use in a periodic time-series ; do not divide by
1523       time-step to convert to integer:
1524       - this fixes case where externForcingPeriod is not multiple of time-step
1525          (Thanks to Christopher L. Wolfe)
1526       - this fixes case where externForcingPeriod is an odd multiple of time-step
1527         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1528      store index of time-record which is currently loaded:
1529       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1530       - needed for the adjoint but not yet used because of extensive recomputations;
1531         (to be fixed soon)
1532    
1533    checkpoint62v (2011/04/02)
1534    o verification/1D_ocean_ice_column added to test Ian Fenty's
1535      pkg/seaice_growth.F modifications for improving sea ice code differentiability
1536    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1537      (new velocity statistics after changing maskInW & maskInS definition)
1538    o pkg/generic_advdiff with OBCS:
1539      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1540      equivalent to assumption of no tracer gradient outside the OB region.
1541      This will affect the results if using obcs+biharmonic diffusion.
1542      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1543    o pkg/obcs:
1544      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1545      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1546      in Interior region. No impact on solution but affects Velocity monitor stats.
1547    o pkg/ptracers (adjoint)
1548      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1549      tape file for each tracer
1550    o model/inc/src and pkg/autodiff: add parameters that allow to turn
1551      of parts of the adjoint code at run time. For now, there are only
1552      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1553      parameters are set in data.pkg.
1554      This is the lazy coward's version of doing this, but still useful for
1555      debugging. In order to do it right, everything needs to be moved to
1556      pkg/autodiff.
1557    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1558      the end; this fixes the adjoint balancing code for open boundaries.
1559    o pkg/ctrl:
1560      - change behavior of xx_${varname}period to be analogous to exf-conventions:
1561        xx_${varname}period =   0.,  means time-independent control part
1562        xx_${varname}period = -12., means one-year-periodic monthly control part
1563      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1564        clean up ctrl_init a little, remove unused variables
1565      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1566      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1567    
1568    checkpoint62u (2011/03/15)
1569    o model/src:
1570      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1571        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1572      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1573        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1574    o pkg/ctrl/obcs/ecco:
1575      - remove obsolete, unused, and partially broken code:
1576        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1577        ALLOW_CTRL_OBCS_BALANCE
1578      - put a stop statement into ecco/cost_obcsvol.F, but also add
1579        cost_obcsvol to ecco_ad_diff.list
1580    o pkg/ecco: fix counting cost function contributions for obcs (code
1581      by Matt M.) and diffkr for diagnostics
1582    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1583      add cost penalty terms for initial uvel, vvel, eta controls
1584      and I/O for prior error files
1585    o pkg/mdsio:
1586       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1587       (new argument) to check for tiled file in mdsioLocalDir : this fix the
1588       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1589    o pkg/ctrl:
1590     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1591       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1592       unused and superfluous variables
1593     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1594    o pkg/ecco
1595     - enable adjoint of Stevens OB
1596    o pkg/ctrl/ecco/grdchk:
1597      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1598        Fortunately, we do not have any tests for the numerous cpp-flagged
1599        option of "obcs as control parameters" so we will never know
1600        if this is an improvement (but at least now things compile).
1601      - remove an obsolete initialization from ecco_cost_init_barfiles.F
1602      - fix some problems within never used ifdefs to make the code compile
1603    o pkg/obcs:
1604     - Refine Interior mask definition to work with more complex OB (e.g.
1605       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1606       read in Interior mask from file. Check if Interior mask is consistent
1607       with OB list of indices.
1608    o pkg/seaice
1609     - beginning code for a seaice tracer package,
1610       but currently only used for seaice age: SEAICE_AGE
1611       SEAICE_num = 4
1612       iTracer = 1: area-weighted ice age
1613               = 2: volume-weighted ice age
1614               = 3, 4: template for one-year vs. multi-year ice
1615       data.seaice has new namelist SEAICE_PARM03 for arrays related to
1616       SEAICE_num
1617    
1618    checkpoint62t (2011/03/05)
1619    o pkg/obcs:
1620     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1621       then normal component. This ensures that the normal component is set
1622       correctly even when it conficts with tangential setting from an other OB.
1623       Affects results of test-experiment seaice_obcs: update the output.txt
1624    o pkg/obcs:
1625     - add code to monitor statistics of dynamical fields at OB.
1626     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1627       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1628       - change default: balance the Net inflow through all OB (instead of balancing
1629         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1630     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1631       to match Nortern OB inflow (OBCS_balanceFacN=0).
1632    o pkg/seaice:
1633     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1634    o pkg/seaice (seaice_growth v 1.113):
1635     - reverting seaice_growth to v 1.111 in order to have code with exact bit
1636       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1637       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1638       runtime flag SEAICEareaFormula is kept but is inactive
1639    o model/src:
1640     - add new param to scale curvilinear grid distance and area when using
1641       a different sphere radius from the grid-files.
1642     - test/check multi-threads EXCH applied to local variable (cg2d_x)
1643    o adjoint:
1644     - enable adjoint of Stevens OB
1645     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1646       (a bit delicate because of potentially modified adj. common block structure;
1647       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1648    
1649    checkpoint62s (2011/02/15)
1650    o pkg/seaice (seaice_growth v 1.112):
1651     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1652       computing the ice cover tendency from effective thickness tendencies. Include
1653       Ian Fenty's formula.
1654     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1655       SEAICEareaFormula.
1656     - simplify notations for the various d_HEFF/d_AREA terms.
1657    o pkg/gmredi:
1658     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1659       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1660       add a verification test-run (front_relax.bvp) to test GM_useBVP.
1661    o pkg/seaice (seaice_growth v 1.111):
1662     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1663     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1664       also melt ice.
1665    o pkg/seaice:
1666     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1667     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1668    o pkg/cheapaml:
1669     - from Nico Wienders: New version of this package.
1670    o pkg/flt:
1671     - add CPP options to prevent floats to re-enter the opposite side of
1672       a periodic domain (default: keep periodicity)
1673    o pkg/gmredi:
1674     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1675       (needed for multi-dim advection).
1676     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
1677    o model/src:
1678     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1679    o tutorial_tracer_adjsens
1680     - extend to NLFS and replace maskC by hFacC
1681       (change reference output accordingly)
1682    
1683    checkpoint62r (2011/01/24)
1684    o testreport:
1685     - add option -deloutp (-do) to remove output file after successful run
1686     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
1687       extract exact list of procs from this file ; adjust COMMAND by
1688       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
1689    o pkg/ecco: replace old ineffective way of penalizing deviations from
1690      first guess (of obcs) with code by Matt Mazloff
1691    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
1692      exf/cal
1693      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
1694        and handle case of obcs?period == 0
1695        Not affected by these changes: There is still an inconsistency in
1696        the computation of start/endrec for the obcs variables for ALLOW_CAL
1697        defined (see comment by Menemenlis, 7-Mar-2003)
1698      - make S/R ctrl_get_gen_rec return something meaningful even if
1699        ALLOW_CAL is not defined
1700      - ctrl_getobcs?: simplify code so that it does not need to use
1701                       S/R exf_swapfields
1702    o testreport:
1703       allow to test MPI with different number of processors for each experiment:
1704       create file "SIZE.h.mpi" in each build dir.
1705       Note: update of "-command" argument not yet implemented.
1706    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1707      alleviate the need for additional 3D tapes when using
1708      the non-inear free surface in the adjoint. This is done
1709      by adding an 'update' of hfacc etc. to their current
1710      value at the beginning of forward_step.F.
1711    o pkg/seaice
1712      seaice_lsr: move stress-divergence computations out of outer pseudo-
1713      timestepping loop
1714    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
1715      up, so that the calls of the ctrl_* subroutines are really at the end
1716      of the routine.
1717    o pkg/gmredi:
1718      allow to specify a 2-D horizontal map and a 1-D vertical profil
1719      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
1720    o pkg/seaice:
1721      move lsr iterations from seaice_dynsolver to seaice_lsr.
1722    o pkg/seaice:
1723      reduce memory footprint of seaice mutldim advection tapes,
1724      by using a 2D tape independent of the generic_advdiff ones,
1725      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
1726    
1727    checkpoint62q (2010/12/29)
1728    o model/src:
1729      - check horizontal grid-spacing for unset or zero/negative values.
1730      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
1731    o pkg/flt:
1732      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
1733      - precision of input and output files set according to readBinaryPrec
1734        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
1735      - initial float position from tiled file was not converted to index space
1736        (looks like a bug): fixed to make it similar to initial pos. global file.
1737    o global_ocean.cs32x15:
1738       change SIZE.h of AD set-up to get same tiling as with MPI.
1739       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
1740    o model/src:
1741       add flag to control printing of domain fields (bathymetry, hFac ...) in
1742       ini_mask_etc (call to plot_fieds_xy*).
1743    o pkg/thsice:
1744       if useEXF, some forcing fields are not valid in overlap: fixed by computing
1745       over the interior only + apply EXCH at the end (like with SEAICE advection).
1746    o pkg/mdsio:
1747      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
1748        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
1749      - change barrier call for safe multi-threads access to 3-D shared buffer.
1750      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
1751      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
1752        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1753    o pkg/flt:
1754      - add fourth-order Runge-Kutta integration
1755      - add basic exch2 support (only 1 facet supported so far!)
1756    o pkg/mdsio+rw:
1757      new S/R to read local (or tile independent) vector (read counterpart of
1758       mds_writevec_loc, and front-end write_glvec_rl/rs).
1759    o global_ocean.cs32x15: additional input_ad.seaice experiment
1760        that uses pkg/seaice rather than pkg/thsice.
1761        (using multidim advection for seaice)
1762    o towards more F95 syntax for array specification in namelist:
1763      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
1764        of all verification experiments.
1765           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
1766          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
1767      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
1768    o global_ocean.cs32x15: additional input.seaice experiment
1769        that uses pkg/seaice rather than pkg/thsice.
1770    
1771    checkpoint62p (2010/12/17)
1772    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
1773        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
1774    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
1775        allow for use of multim. advection in seaice adjoint.
1776    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
1777      - first attempt to close budgets by taking into account the freshwater
1778        flux implied by the sublimation of snow and ice. So far only the
1779        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
1780        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
1781    o eesupp/src:
1782      new S/R with new option (NML_EXTENDED_F77) to change array specification
1783      from F95 standard to commonly accepted extended F77 form.
1784      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
1785      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
1786      for less tolerant f77 compiler (e.g., pgf77, g77).
1787    o globalFiles:
1788      commented out in parameter file "data" since it's not safe with MPI
1789      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
1790      in this case); no longer commented out in restart test (tst_2+2).
1791    o add adTapeDir to specify a special directory where adjoint tapes are
1792      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
1793      and cannot be used together with mdsioLocalDir.
1794    o nesting pkgs:
1795      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
1796      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1797      - add parameter files + utils dir + output from short run on beagle.
1798    o pkg/seaice:
1799        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
1800    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
1801      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
1802    
1803    checkpoint62o (2010/11/25)
1804    o pkg/exf:
1805      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
1806    o pkg/seaice:
1807      - seaice_ocean_stress: split a loop for better vectorization of the
1808        adjoint code
1809      - seaice_growth.F: fix bug in conservation of freshwater connected to
1810        capping of heff, put contribution into d_HEFFbyNEG
1811      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
1812        by something more sensible (parameters that are what their name implies)
1813      - change some defaults, so that by default exf-parameters are used for
1814        things like rhoAir, cpAir,latent/sensible heat parameters, in order
1815        to reproduce the old results, many data.seaice now contain funny values
1816        for cpAir and latent heat of sublimation
1817    o packages_readparms.F: move exf_readparms up in line so that
1818        exf-parameters are visible for other packages (e.g. seaice)
1819    o debugMode & debugLevel=2:
1820      - differentiate between debugMode & debugLevel=2:
1821        debugMode: controls printing of debug messages (sequence of S/R calls).
1822        debugLevel: controls printing of algorithm intermediate results and stats.
1823      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
1824        => allows to print debug-stats without all sequence of call messages.
1825      - switch control of debug print from debugLevel to debugMode in many S/R.
1826    o pkg/obcs (obcs-sponge):
1827        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
1828        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
1829    o pkg/generic_advdiff:
1830      - record overlap minimum size for each advection scheme;
1831      - refine criteria on overlap minimum size;
1832      - check and stop (in gad_check) if overlap size is too small.
1833    o pkg/obcs:
1834      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
1835        once, in ptracers_implicit.F)
1836      - with seaice: remove test on empty file name in obcs_apply_seaice (always
1837        apply OB values when tile has OB)
1838    o model/src, coriolis setting:
1839      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
1840        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
1841        files (selectCoriMap=3) with any grid.
1842      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
1843    o pkg/seaice/seaice_growth.F:
1844        a few cosmetic changes that reduce the number of lines of code
1845    o pkg/obcs: add boundary conditions following Stevens (1990)
1846      - the code follows old MOM/NAOSIM code
1847      - so far it is only implemented for the eastern and western boundaries
1848        and NOT for pTracers
1849    o pkg/rbcs:
1850      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
1851        beginning of the first rbcs forcing period.
1852      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
1853        offline package, i.e., one file per time, labeled by iteration number;
1854        deltaTrbcs sets the timestep with which the data was generated;
1855        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
1856      - rbcsForcingCycle=0 makes forcing non-cyclic.
1857      - make arithmetic safe for negative times and odd forcing periods.
1858    
1859    checkpoint62n (2010/11/09)
1860    o pkg/seaice:
1861        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
1862    o pkg/obcs:
1863       New S/R to copy tracer value from the OB location to narrow band region
1864        (width = same as overlap) beyond the OB: preserve OB value (needed for
1865        high-order scheme) which were overwritten by EXCH call if in overlap
1866        region. Applied to theta, salt, ptracer and advected seaice variables.
1867       With seaice: use maskInC in similar way as in gad_advection.F,
1868        in seaice_advection.F and advect.F.
1869       Update output of experiment seaice_obcs and change exp4 to test OBCS with
1870        4th order Adv.Scheme. for pasive salt and ptracer.
1871    o tools/genmake2:
1872      - when looking for an optfile (not specified), only search for Fortran compiler
1873        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
1874      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
1875        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1876      - set default for CPP to "cpp -traditional -P" (was the case without specifying
1877        an optfile, but otherwise default was just "cpp".
1878      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1879      - when "CC" is not set in the optfile, look for possible C compiler
1880        (instead of just setting CC=cc)
1881      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1882        => add a ".F" to ".o" rule for source files with no "#include" (such as
1883           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1884      - move gfortran before g77 in list of possible Fortran compiler (consistent
1885        with reference compiler switch from g77 to gfortran)
1886    o pkg/seaice:
1887      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1888        seaice_check that stops the model, when the CPP flag is used.
1889      o seaice_growth.F: make capping of ice volume conserving by returning the
1890        capped ice as freshwater to EmPmR. This does not change the verification
1891        experiments but will change runs where the capping is acutally active
1892    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1893      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1894         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1895         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1896    o tools/genmake2:
1897      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1898      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1899      - clean previous genmake log files before anything else.
1900      - change Makefile to remove testreport log files (*.tr_log) and genmake log
1901        files only with "CLEAN" target (instead of "Clean");
1902    o pkg/generic_advdiff:
1903      Change OBCS in multiDim advection (gad_advection.F):
1904       Use maskInC to prevent intermediate update of tracer-field in OB regions,
1905       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1906       which were applying future time-step OB values.
1907      This way, all explicit calculations use current-time-step OB values
1908       (simpler and more consistent).
1909      Affects results when set-up uses time-varying OBC and multi-dim advection;
1910       update output of experiment seaice_obcs.
1911    o pkg/seaice:
1912      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1913       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1914         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1915      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1916       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1917       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1918    o pkg aim (2010/10/26):
1919      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1920        formulation with obliquity, eccentricity, ... as run-time parameters,
1921      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1922        upward shortwave radition at the surface (all-sky and clear-sky).
1923    o pkg/obcs:
1924      - writing sections with globalFiles=T does not work: switch to tiled-files
1925        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1926      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1927      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1928    
1929    checkpoint62m (2010/10/21)
1930    o pkg/seaice: vectorize seaice_solve4temp.F
1931      - move iterations loops outside of i/j-loops
1932      - requires 2D arrays for TB and effConduct
1933      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1934        modified in this routine
1935      - a little bit of clean up, adjusting indentation, etc.
1936      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1937        performance and '**TWO' by '**2' (because TWO is a float),
1938        replaced ONE, ZERO
1939    o eesupp/src:
1940       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1941    o pkg/seaice/seaice_growth.F
1942      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
1943      merging process. The merged routine has two branches, and one activates the 'evolution'
1944      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
1945      In summary, here is what the '10/10 revision' did consist of
1946        part 1: seaice_growth.F revisions 1.71 to 1.75
1947          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
1948            The emphasis here was on improving readability (e.g. by trying to use meaningful
1949            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
1950        part 1.5:
1951          - revising the lab_sea experiment to make it a more useful (i.e. stable
1952            and representative of an actual model run). This was done by generating a
1953            (winter) pickup to start from, switching back the main experiment dynamic
1954            solver from evp to lsr, having one of the experiments use the free drift solution.
1955        part 2: seaice_growth.F revisions 1.76 to 1.85
1956          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
1957          - Sorting out the various fields units and sign (set early on and reset at the end)
1958            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
1959            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
1960          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
1961            and simplifying logical expressions to further improve readibility.
1962        part 3: seaice_growth.F revisions 1.86 to 1.89
1963          - Re-organize the blocks of code more logically.
1964          - Merging the '_if.F' pieces that add something new.
1965    o pkg/thsice:
1966      - vectorize thsice_solve4temp and thsice_get_exf.
1967        Problem: thsice_solve4temp has an unvectorizable statement that
1968        might also be problematic for TAF
1969      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
1970        does not change the verifcation experiment, but will change all
1971        experiments that have this flag undefined (not tested in verification);
1972        a little reorganization to save a few 2D fields and recomputations
1973      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1974      - 2nd step:  fix some store dirs
1975        o seems to work somewhat, i.e. using ifort but not g77
1976        o likely cause are incomplete init. or recomputation
1977        o start verification/global_ocean.cs32x15/input_ad.thsice
1978    o pkg/obcs: add support for exch2
1979      - the position of the boundary and prescribed values are specified using
1980        a global domain with exch2 facets stacked
1981        - in x for N,S boundaries (like W2_mapIO=-1)
1982        - in y for E,W boundaries (so E,W boundaries do not overlap)
1983    o pkg/mdsio: add support for writing global sections with exch2
1984        file layout is as for obcs described above:
1985        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1986        - for y-z sections, facets are stacked in y
1987    o pkg/thsice:
1988       - change a few routines for better vectorization: thsice_albedo.F,
1989         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1990         not affected, but in particular the latter routine has changed
1991         dramatically (not necessarily easier to read now).
1992       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1993       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1994    o verification/lab_sea:
1995      - overhaul of the forward model experiments. The main motivation
1996        for this revision is that lab_sea has proven quite fragile (when
1997        changing the sea-ice code, and switching platforms) to a point
1998        when failures were very hard to attribute to specific code problems.
1999      - the suspected reason for this fragility is noise amplification by evp so,
2000        to start with, we decided to replace evp with lsr in the main experiment.
2001      - the input.lsr experiment thus became obsolete and was removed.
2002      - it was replaced with the input.fd experiment that uses an
2003        analytical "free drift" solution as the ice velocity field.
2004      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2005        will hopefully allow us to discriminate problems due to dynamic solvers
2006        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2007        us to test additional options, along with the salt plume package.
2008      - Finally a pickup was generated (at the end of a one year run) to
2009        make the tests more representative of an actual model run. Previously
2010        the tests starting point was a 1m thickness of ice everywhere.
2011    o pkg/seaice:
2012      - introducing S\R seaice_freedrift.F that compute the
2013        analytical solution to an approximate ice momentum
2014        equation (i.e. the simple stress/coriolis balance).
2015      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2016        of the free drift velocity field, and enable its use.
2017        To actually use the free drift solution as the model ice
2018        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2019    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2020    
2021    checkpoint62l (2010/10/04)
2022    o pkg/seaice:
2023      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2024      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2025       version (with USE_ORIGINAL_SBI undef);
2026    o add hooks for new packages OASIS, the package will follow
2027      (hooks exclude the seaice pkg for now)
2028    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2029      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2030      rather than mdsio_readvector.F/mdsio_writevector.F, within
2031      adread_adwrite.F to read/write adjoint-related tapes to disk.
2032    o eesupp and pkg/mdsio: ALLOW_WHIO
2033      Option to write/read 2D fields to files including tiles halos.
2034      The main purpose is for adjoint related "tape I/O".
2035      The secondary purpose is for debugging phases.
2036      A word on those rather specifically intended purposes.
2037      The code was meant to be stripped down to the bare minimum.
2038      Typically, there is a unique and basic mapping to the global
2039      buffer (tile by tile, then proc by proc, then level by level), and
2040      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2041      meant to generate user friendly outputs of various shapes and forms.
2042      Rather it is intended, for the knowledgeabale developers,
2043      to be largely independent of the many mdsio options, to allow
2044      outputs of tiles+halos in debugging phases and in adjoint runs,
2045      and to allow some flexibility in tuning (adoint) I/O depending on each
2046      file system behavior. With regard to tuning, most of the potential knobs
2047      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2048      to specify directories, to specify the typical size of I/O calls, etc.)
2049      are not yet included, and will be added if they prove useful.
2050    o pkg/seaice:
2051       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2052    o pkg/seaice:
2053       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2054       code (seaice_budget_ice_if.F) which enable to recover old standard
2055       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2056       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2057    o model/src (rStar):
2058       use simple average (not area weighted) of rStarFac at U,V point when using
2059       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2060       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2061    
2062    checkpoint62k (2010/09/17)
2063    o adjoint
2064       * changed verification/global_ocean.cs32x15 ; adjoint now tests
2065         Adams-Bashforth 3 + NLFS + RSTAR
2066       * some more modifs required for ECCO-GODAE v4
2067    o pkg/seaice
2068       add SEAICE_AGE_VOL option to use volume instead of area for
2069       integrating SEAICE_AGE
2070    o model/src:
2071       first check-in of sigma & hybrid-sigma coordinate code ; also includes
2072       non-linear free-surface parts ; but pressure-gradient not yet coded.
2073    o pkg/ptracers:
2074       option for ptracer to convert Salt Relax into additional EmP.
2075        tested in exp. global_ocean.90x40x15.dwnslp (update output)
2076    
2077    checkpoint62j (2010/08/25)
2078    o pkg/ggl90:
2079       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
2080    o pkg/dic: car_flux.F, phos_flux.F
2081      - reduce number of exp-calls in order to improve performance
2082      - clean up a little (replace fields by their macros, etc., fix
2083        typo in CPP-flag)
2084    o pkg/ggl90: minor changes
2085      - GGL90diffKrS was removed --> always use GGL90diffKr
2086      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
2087      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
2088        (commented out for now)
2089      - change in max/min operations to ensure that smoothing is ok
2090      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
2091      - always use diffKrNrT as background profile (i.e. never use diffKr field)
2092    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
2093    o pkg/dic:
2094      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
2095        vectorization
2096      - small bug fix in insol for the unlikely case of a cartesian grid
2097      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
2098        + now vectorize, which also removes adjoint recomputations;
2099        + replace integer maksp1 by _RL maskp1
2100        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
2101    
2102    checkpoint62i (2010/07/21)
2103    o pkg/flt:
2104      - with OBCS: stop floats which enter the OB region
2105    o model/src:
2106      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
2107        for implicit vertical advection.
2108    o pkg/seaice:
2109     - account for melting in seaice age evolution.
2110     - remove double counting of seaice ridging effect on seaice age.
2111    
2112    checkpoint62h (2010/06/18)
2113    o pkg/exch2:
2114     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
2115    o tools/genmake2
2116      - remove "-pdefault" option: redundant with the use of "packages.conf";
2117      - remove file pkg/pkg_default : set the default as a pkg group
2118        ("default_pkg_list") defined in pkg/pkg_groups;
2119      - fix for case pkg/pkg_depend is missing (was hanging before);
2120      - add option "-pgroups" to specify a different pkg_groups than the default.
2121    o verification/adjustment.cs-32x32x1:
2122       add a "minimal" set-up test (code_min & input_min) which only compiles
2123       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
2124    o tools/genmake2
2125      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
2126      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
2127    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
2128      files are nearly the same anyway.
2129      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
2130       - redefinition of tau(i,i) (by a factor of ustar)
2131       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
2132       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
2133       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
2134       - replace
2135         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
2136         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
2137         by
2138         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
2139         (changes results)
2140       -> exf_bulkformulae v1.22,
2141          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
2142          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
2143                    output.txt 1.63
2144           offline_exf_seaice: output.seaicetd.txt 1.7
2145           seaice_obcs: output.txt 1.10)
2146      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
2147       -> exf_bulkformulae v1.23,
2148          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
2149          and global_ocean.cs32x15.icedyn (only 11 matching digits)
2150      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
2151    o adjoint of exch-1:
2152     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
2153       (note: was already like this when using EXCH-2) and remove flow dir
2154       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
2155     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
2156     - update pkg/exch2 diff list.
2157    
2158    checkpoint62g (2010/05/19)
2159    o eesupp/src (exch-1):
2160     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
2161       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
2162       (renamed to exch1_*rx_cube.F).
2163     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
2164       to call new exch1 S/R ; update Makefile and .cvsignore.
2165     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
2166       exch2_xy_rx later)
2167      Note: after updating your code, need to run "make clean" in eesupp/src
2168    o test experiment bottom_ctrl_5x5:
2169       new output_adm.txt with fewer grdchk & less monitor output.
2170    o model/src:
2171      remove the call to ini_cori in initialise_varia.F (just keep the usual one
2172       in initialise_fixed.F). More consistent with coriolis & horizontal grid
2173       beeing treated in the same way (ini_grid is not called a 2nd time).
2174    o pkg/exf:
2175      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
2176      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
2177      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
2178      - cosmetic changes to exf_bulkformulae.F to make it look more like
2179        exf_bulk_largeyeager04.F
2180    o eesupp/src (exch-1):
2181      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
2182      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
2183        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
2184        (even without using MPI).
2185      - Message mode: move RecvAck setting (indicator of buffer being ready)
2186        from send_put to recv_get S/R (was useless before, but not sure if
2187        it's much more useful now);
2188      - Switch the order of sync: MPI-proc 1rst and then threads;
2189      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
2190      - fix AD code for communication mode ='get' (but not used).
2191    o model/src:
2192      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
2193      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
2194    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
2195    o pkg/ctrl: require a specific set of control variables and exf-flags for
2196      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
2197    o model/src:
2198     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
2199       1rst forward sweep, to avoid over-writing output files during recomputations
2200       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
2201     b) 2nd version:
2202      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
2203      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
2204         writePickupAtEnd) + seaice & ptracers output;
2205      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
2206    o model/src:
2207      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
2208    o pkg/exch2:
2209      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
2210      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
2211    o pkg/autodiff & exch2:
2212      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
2213      (for now, only if ALLOW_EXCH2 is defined).
2214    o pkg/autodiff:
2215      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
2216        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
2217       + clean-up comments (_RS is not always real*4)
2218      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
2219      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
2220        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
2221    o testreport (AD-tests):
2222      no longer link files from dir "../input" (1rst link files from
2223      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
2224    
2225    checkpoint62f (2010/04/29)
2226    o model/src/the_main_loop.F:
2227      adjust store directives for seaice evp and multicategory according to
2228      pkg/ecco/the_main_loop.F
2229    o adjoint:
2230      global_sum_ad was incomplete (noted many times by many people ;)
2231      nice description by Jean U. as follows:
2232      * allreduce(var) in global_sum.F can be interpreted as
2233        reduce(sum) followed by broadcast of sum.
2234      * The adjoint of that is
2235        sum(adjoint) followed by broadcast(summed adjoint value)
2236        or in other words, allreduce(sum, adjoint vars)
2237      We were missing the sum(adjoint)!
2238      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
2239      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
2240      The fix should produce 16-digit accuracy between
2241      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
2242      multi-CPU single-tile (e.g. nSx=1, nPx-2)
2243      We'll probably change this yet again shortly
2244    o eesupp/src:
2245      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
2246    o pkg/icefront
2247      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
2248        specification of addmass array based on a 2D field, which is added
2249        at bottommost wet level at each horizontal location.
2250    o model/src:
2251     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
2252     layout; (not always compatible with delX,delY setting; commented out for now).
2253    o pkg/exch2:
2254     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
2255     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
2256    
2257    checkpoint62e (2010/04/15)
2258    o pkg/obcs:
2259      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
2260    o pkg/dic:
2261      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
2262        (note: not presently tested in any forward verification exp.)
2263       update tutorial_global_oce_biogeo AD output file.
2264    o pkg/exf:
2265      - account for the variation of albedo as a function of zenith angle
2266        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
2267    o build_options:
2268     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
2269    o pkg/dic:
2270      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
2271      - use binary pickup file for restart;
2272      - initialise atmos-CO2 box from dic_pCO2 parameter;
2273      - fix multi-threaded.
2274    o pkg/rbcs:
2275     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
2276       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
2277     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
2278       and update output.txt
2279    o pkg/kpp:
2280     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
2281     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
2282       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
2283       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
2284     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
2285       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
2286    o pkg/offline:
2287      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
2288      (bug was added in version 1.10 on 2007-08-23).
2289    o pkg/offline:
2290      - no need to specify periodicExternalForcing, etc ... to use offline pack
2291      - offline input files no longer just single prec --> parameter offlineLoadPrec
2292    o verification/lab_sea:
2293      change AD test to multi-tile setup and update all 4 AD output.
2294      NOTE: while cost function values remain very similar,
2295      gradients are very different, although gradient checks are self-consistent
2296      Should try to get to the bottom of this (cost function summation order?)
2297    o pkg/dic:
2298      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
2299      a weakness of TAF that drops part of double precision in log10 derivative.
2300      <= changes removed since problem has been fixed in current TAF version 1.9.71
2301      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
2302    o pkg/ecco:
2303      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
2304      update all 4 lab_sea AD output.
2305    
2306    checkpoint62d (2010/03/22)
2307    o build_options:
2308      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
2309    o remove unbalanced quote (single or double) in commented line of source code
2310      (may cause some warning with some preprocessor/makedepend versions).
2311    o pkg/seaice:
2312      fix seaice_model.F for adjoint (gael) and update AD results of experiments
2313       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
2314    o testreport:
2315      add option '-runonly' (short: '-ro') to just do the run part (without make).
2316    o eesupp: remove JAM communication code (obsolete).
2317    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
2318      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
2319      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
2320      (update also the output).
2321    
2322    checkpoint62c (2010/03/02)
2323    o tools/build_options :
2324       move (some) old optfiles from build_options/ to build_options/unsupported/
2325    o model/src and pkg/exf
2326       surface relaxation -- separating data and data.exf options
2327       The point is to ensure that we specify the surface relaxation
2328       either in data or in data.exf (but not half and half) and to
2329       avoid an accidental relaxation to 0 (which happened if a time
2330       scale was specified but the file name was left empty)
2331    o model/src model/inc and pkg/mom_common
2332       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
2333       => addition to the viscosity field as computed by others schemes
2334    o tools/build_options:
2335      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
2336        but keep the former optfile for few weeks for smooth transition
2337    o pkg/ecco
2338      - allow user defined cost function contributions
2339         CPP: ALLOW_USERCOST_CONTRIBUTION
2340         USAGE: compute contributions in cost_usercost_all.F
2341      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
2342          the two options are complementary.
2343    o pkg/smooth
2344      - migration from contrib to the main repository
2345    
2346    checkpoint62b (2010/01/26)
2347    o pkg/monitor:
2348      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
2349        (in case someone forgot to update customized pieces of code)
2350    o nonHydrostatic:
2351      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
2352      - add a simple 2-D experiment (short_surf_wave) to test it.
2353    o pkg/icefront:
2354       adding the shell of, and the hooks to, a new package that
2355       will model melting and freezing of vertical glacier ice fronts
2356    o momentum:
2357      add diagnostics of momentum tendency from Hydrostatic pressure gradient
2358       (without surf.pressure term: would need a 2nd filling since implicit term).
2359    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
2360      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
2361      cannot deal with the former
2362    o cleaning:
2363      - remove all (except OpenAD) old TLM output from results_ad dirs.
2364      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
2365      - comment out maskH definition (replaced by maskInC)
2366    o pkg/monitor:
2367      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
2368        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
2369    
2370    checkpoint62a (2010/01/15)
2371    o model/src:
2372      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
2373    o pkg/diagnostics:
2374      - add optional level number diagnostics (i.e., level number to be define
2375        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
2376      - strictly check for valid parser-code(10) ;
2377      - check if adding diag to the list from the right place.
2378    o pkg/longstep:
2379      - change parameters and fix tracer conservation with rstar/nonlinear free surface
2380    o diagnostics:
2381     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
2382       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
2383    o pkg/diagnostics:
2384     - Add option for writing vertical integral (sum of selected levels) of an output
2385        field instead of writing output field levels. Activate this option on a per
2386        output-file basis, by setting the 2nd character of fileflag to 'I'.
2387     - Add field-specific information relative to level integral in 3rd postion
2388        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
2389        vertically (x level-thickness x hFac), "r"=same but without hFac.
2390    o do_the_model_io:
2391      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
2392        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
2393        writing pickups and stopping.
2394    o pkg/diagnostics (for now, only with mdsio):
2395      - write time information to meta file (and modify accordingly rdmds.m) :
2396        time-averaged diagnostics output: write starting and ending time of the
2397        time-averaging interval ; snap-shot diagnostics output remains unchanged;
2398    o pkg/timeave:
2399      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
2400        always Nr), now assumed to be equal to number of levels of averaged field;
2401        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
2402    o pkg/sbo:
2403      - fix ocean bottom pressure global-average & 2-D time-ave output (was
2404        neither initialised nor filled).
2405      - add starting iteration in suffix of global-average output file
2406        (to avoid over-writing the file after a restart)
2407      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
2408    o time-average:
2409      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
2410        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
2411         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
2412        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
2413      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
2414      - fix missing accumulation for pkg/opps.
2415      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
2416         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
2417      - fix initialisation of time-ave vars and do only full time-step increment
2418        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
2419    o pkg/layers:
2420      - use standard RW pkg S/R to write the output
2421        and remove local write_fld version (which had a problem).
2422      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
2423      - fix LAYERS_CALC argument list.
2424    o pkg/timeave:
2425      - store cumulative-time in a simple tiled array (drop the level index)
2426      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
2427    o pkg/ocn,aim_compon_interf
2428      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
2429    
2430    checkpoint62  (2009/12/23)
2431    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
2432        (was not previously tested in any other exp.)
2433    o pkg/monitor:
2434      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
2435        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
2436        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
2437      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
2438      - change del2 calculation.
2439      - use interior masks (instead of maskH, <- to be remove).
2440      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
2441    o mask & obcs:
2442      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
2443      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
2444        (called after packages_init_fixed)
2445    o pkg/obcs:
2446      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
2447        Fixes bug in obcs+exf with nSx*nSy.GT.1
2448      - fix multi-tile handling in obcs balance code
2449    o nonHydrostatic:
2450      - Implement AB-3 for non-hydrostatic vertical momentum ;
2451        (change ordering of var. stored in pickup file when using NH)
2452      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
2453      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
2454        (in prep. for new NH free surface form).
2455    o pkg/obcs:
2456      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
2457    o model/src:
2458      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
2459    
2460    checkpoint61z (2009/12/01)
2461    o nonHydrostatic:
2462      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
2463        a spurious source of energy in simple baroclinic adjusment test case.
2464      Update all non-hydrostatic exp output.
2465    o model/src (3-d solver):
2466      Change again 3-D solver free-surface RHS term when exactConserv=T:
2467        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
2468        (which was not the case with previous formulation).
2469      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
2470      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
2471    o nonHydrostatic:
2472      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
2473        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
2474      - change 3-D solver to work with r* (for now, only with linear free-surf.)
2475      - add few debug diagnostics (cg3d_x, residual)
2476    o model/src:
2477      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
2478        update output of exp. global_ocean.cs32x15.viscA4
2479    o update output of exp. global_ocean.cs32x15.icedyn after removing
2480      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
2481    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2482    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
2483      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
2484    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
2485      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
2486      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
2487      to test this code
2488    o pkg/cd_code:
2489      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
2490       C-grid momentum. D-grid velocity used to be stepped forward in time with
2491       Adams-Bashforth only on surface pressure term. Tests show that using AB on
2492       D-grid coriolis term improves stability (as expected from CD-scheme paper).
2493      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
2494      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
2495       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
2496       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
2497      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
2498           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
2499    o pkg/obcs:
2500     - fix bug in initialisation (broken since Oct 1rst modification)
2501       for useOBCSprescribe without useEXF.
2502    
2503    checkpoint61y (2009/11/15)
2504    o pkg/seaice
2505     - change (once again) the discretization for the evp solver: rather than
2506       squaring the averages of strain rates, average the squares to give
2507       a better approximation to VP behavior (in simple test); this breaks
2508       verification experiments that use EVP (lab_sea and lab_sea.hb87)
2509        --> update outputs
2510    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
2511      to improve vectorization of adjoint code on TARGET_NEC_SX
2512    o verification/vermix:
2513      - change vermix to a more "classical" 1d column with high vertical
2514        resolution, seasonal heat flux forcing and constant wind forcing
2515        --> update outputs
2516    o pkg/seaice
2517     - fix diagnostics of principal stress components for EVP
2518     - add optional diagnostics of non-linear convergence for LSOR solver
2519     - make maximum zeta a runtime parameter
2520    o model/src (3-d solver):
2521      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
2522       which consisted in removing the Surf. Non-Hydrostatic pressure from the
2523       whole column and adding it to Eta (inspired from Casualli, 1999):
2524       Only affects 3-D solver initial guess and only if using ExactConserv,
2525       but tests did show a degradation of solver convergence. For this reason,
2526       decide to disable this piece of code.
2527       to recover previous version, just set zeroPsNH = exactConserv (line 78).
2528      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
2529    o pkg/ggl90:
2530     - fix previous modif (unfortunatly has not been documented here).
2531    o pkg/seaice/autodiff:
2532     - add CPP flag to include clipping of zeta in EVP code;
2533       although clipping of zeta is not necessary for EVP and not recommended
2534       it was done by default, now clipping is disabled by default
2535     - modify computation and store zetaC/Z in seaice_evp for TAF
2536     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
2537     - change seaice_calc_viscosities/strainrates for better
2538       vectorization after AD by TAF
2539     - rearrange common blocks in SEAICE.h once again for easier dumps of
2540       adjoint output, adjust adcommon.h and g_common.h
2541     - change flux form of default advection scheme for better vectorization
2542       of adjoint code
2543     - modify lab_sea/input.lsr to test the flux form of default advection
2544       scheme
2545    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
2546      transition in checkpoint61r)
2547    
2548    checkpoint61x (2009/10/19)
2549    o adjoint: adding two new verification experiments
2550      * tutorial_global_biogeo: an online dic sensitivity experiment
2551        (work with G. Forget)
2552      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
2553        (an update of the Dutkiewicz et al., 2006 paper)
2554      Both use the same CO2FLUX cost function, but different controls
2555      Gradient checks look good, but some recomp. could still be traightened out
2556      Should add xx_dic control variable to test at some point
2557    o model/src:
2558      add run-time parameters to check and/or mask initial Temp & Salt
2559    o pkg/ptracers:
2560      apply zonal filter (if used) to all passive tracers
2561    
2562    checkpoint61w (2009/10/12)
2563    o adjoint:
2564      * update and finish work on adjoint of dic package (G. Forget)
2565      * start adjoint of offline package
2566      * bug fix for cube-sphere TLM code (active_file_g.F)
2567    o tutorial_global_oce_optim:
2568      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
2569      and add SIZE.h_mpi for MPI testing
2570    o pkg autodiff
2571     - fix bug in autodiff_restore
2572     - make genmake2 remove comments and empty lines from ad_input_code.f in
2573       order to reduce file size (new script file remove_comments_sed)
2574    o allows to specify vertical profile of vertical viscosity (viscArNr)
2575    o pkg autodiff
2576      autodiff_ini_model_io: comment out writing of grid information to netcdf
2577      files, because at this time the grid fields are a bunch of zeros
2578      (this is analogous to ini_mnc_vars.F)
2579    o pkg seaice/autodiff:
2580     left-over from removing the 3-time-level fields:
2581     - small rearrangement of common blocks (SEAICE.h)
2582     - fix field declaration in order to get meaningful output in
2583       adseaice.*.nc (adcommon.h)
2584    o pkg obcs:
2585     - go through NH code only if nonHydrostatic=T
2586     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
2587     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
2588       => Update output of experiment seaice_obcs
2589     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
2590     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
2591     - fix restart for useOBCSprescribe + useEXF
2592    o pkg ctrl
2593     - make obcs as control parameter work also with useSingleCPUio
2594     - replace a few sny and snx by Ny and Nx to be consistent with
2595       ctrl_set_globfld_x/yz.F
2596    o pkg seaice
2597     - re-introduce global field frWtrAtm for the case of
2598       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
2599     - catch the case of an empty filename in seaice_cost_init_fixed.F
2600    o pkg ecco:
2601     - small bug fixes in the_main_loop
2602      . fix order of monitor arguments
2603      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
2604      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
2605        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
2606     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
2607       imbalance diagnostics for wmean_h/sflux = 0
2608     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
2609     - catch the case of empty filenames in ecco_cost_init_fixed.F
2610       and ecco_readparms.F
2611     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
2612       to make this statement meaningfull in ecco_cost_weights.F
2613    o pkg zonal_filt:
2614      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
2615      - when using rStar, filter uVel*hFacW instead of uVel
2616       (tested without topography: fix a Pb of growing instability with NLFS)
2617    o pkg/aim/thsice:
2618     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
2619      (works as SST restoring)
2620    o pkg/thsice:
2621     -add specific parameter for salt restoring in slab mixed-layer
2622       (by default equal to the temperature restoring)
2623    
2624    checkpoint61v (2009/09/21)
2625    o pkg/kpp:
2626     -add double diffusive contributions as a hack, turned off by default
2627      for now, and the code can be excluded with a CPP-flag
2628      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
2629     -add a verification experiments to "vermix" to test this code
2630    o pkg/mom_common:
2631      Move computation of length scales to mom_init_fixed.F (avoid recomputation
2632      at each time-steps*levels).
2633    o pkg/layers:
2634      Created a new package for computing volume fluxes in temperature or
2635      [not yet implemented] density layers, e.g. for calculating residual
2636      overturning circulations.
2637    o pkg/diagnostics:
2638      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
2639    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
2640    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
2641      To avoid mixing type (RS/RL) of input/output array argument,
2642      replace single mixed-type array with a pair from each type (RS/RL).
2643    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
2644      is now implemented for all pkgs (previously only done for the main pickup)
2645    
2646    checkpoint61u (2009/08/25)
2647    o pkg/obcs:
2648      - change OB?eta from _RS to _RL and put them into a separate commen block
2649      - add code to read OB?eta from a file via obcs_prescribe_read: the code
2650        compiles and does not destroy any other experiments, the data is read
2651        properly, but the code is not tested in actual applications
2652    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
2653      create a meaningful unit attribute for the time coordinate variable
2654    o pkg/ebm: add plenty of missing "_d 0" ;
2655       update results of experiment global_ocean_ebm (fwd + adjoint tests)
2656      Notes: several pieces of code only works for (very) specific set up
2657       (domain size, lat range, etc ...); should be documented & stop if one
2658       of those assumptions is not meet.
2659    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
2660       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
2661          and offline_exf_seaice (seaicetd + adjoint).
2662    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
2663       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
2664        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
2665    o few changes to pass when compiling with strick checking of arguments
2666       across S/R (allow to find few bugs in S/R calls).
2667    o pkg/seaice:
2668     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
2669       2d-fields, for slightly better performance
2670    
2671    checkpoint61t (2009/07/22)
2672    o pkg/seaice:
2673     - remove unused variables in seaice_evp
2674     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
2675    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
2676       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
2677       each processor opens a different file (a fix from Matt).
2678    o cg2d:
2679       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
2680       this reduces number of EXCH calls by 2 when using exch2.
2681       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
2682       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
2683    o pkg/thsice:
2684       add code for Near Infra-Red albedo (from Jeff)
2685       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
2686    o ini_model_io:
2687       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
2688       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
2689       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
2690    
2691    checkpoint61s (2009/06/30)
2692    o pkg/exch2 (exch2_rxN_cube*):
2693       remove last BARRIER (no need to synchronise after getting data from shared
2694       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
2695    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
2696      and generate new output (for the 2 tests) using default rotationPeriod.
2697    o pkg/exch2:
2698      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
2699        (was already the case with AUTODIFF_EXCH2 defined)
2700      - add bj in exch2 arrays and S/R.
2701      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
2702        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
2703    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
2704      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
2705        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
2706      - verification experiment natl_box.longstep
2707    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
2708      allow different versions of ifort (8 or 9) and different versions
2709       of mpi (mpich or mpich2) to be used with the same optfile.
2710      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
2711       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
2712    o pkg/seaice:
2713      fix previous modif (3-level field removed) for old-pickup reading
2714    
2715    checkpoint61r (2009/06/25)
2716    o pkg/seaice:
2717     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
2718      1. introduce fields for time step (N-1)
2719      2. do not use levels 2 and 3 anymore (but keep them)
2720      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
2721         includes changes to pkg/thsice/thsice_get_velocity.F,
2722         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
2723         pkg/obcs/obcs_apply_uvice.F.
2724     - completely remove code for leap-frog time stepping for second order
2725       advection
2726     - adjusted adjoint accordingly;
2727       gradient checks have improved by an order of magnitude!
2728    
2729    checkpoint61q (2009/06/22)
2730    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
2731     - the boundary conditions along open boundaries are unclear, because the
2732       associated masks are set to zero and are thus treated as closed when
2733       applying the slip-boundary conditions.
2734     - move initialisation of grid variables from seaice_init_varia to _fixed
2735    o adding doc/diags_changes.txt
2736    o model/src:
2737      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
2738       to avoid "_diags" naming if no relation to pkg/diagnostics.
2739      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
2740       file and only call PLOT_FIELD_XYZ if debugMode=T.
2741      remove few PLOT_FIELD_XY calls outside initialisation.
2742      remove few unnecessary BARRIER.
2743    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
2744      of salt_plume package in Southern Ocean
2745    o pkg/thsice:
2746     - fix hOceMxL in overlap (needed for sea-ice advection);
2747       update output of experiment global_ocean.cs32x15.icedyn.
2748    o pkg/seaice:
2749     - make the (placeholder-)tracer IceAge a little more meaningful
2750      by avoiding ridging of age due to convergent ice flow
2751     - add diagnostics for surface temperature, atmospheric and oceanic
2752       heat flux, and atmospheric and oceanic ice growth
2753    
2754    checkpoint61p (2009/06/10)
2755    o eesupp (global_max & global_sum):
2756     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
2757     - remove starting & endding barrier (no longer needed)
2758    o pkg/mdsio, writelocal:
2759       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
2760       (remove the STOP): uses shared buffer IO to store data from all threads
2761       and then let master-thread write nThreads tiles.
2762    o pkg/mdsio (read/write field):
2763     - tiled IO done in 1 piece (all levels at a time);
2764     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
2765     - multi-threaded: allow to read/write local (non-shared) array
2766       (was already working with singleCpuIO ; now works also without);
2767       => no longer needs barrier call after reading a file (added inside
2768       mds_read/write field).
2769     - move barrier calls outside gather/scatter_2d to mds_read/write_field
2770    o pkg/obcs/exf
2771      - exf_getffieldrec.F: add a few ". _d 0" and
2772                            add code to catch the case fldperiod = 0.  
2773      - obcs_precribe_read.F: change if statements so that they match
2774                              the variable type (_RL)
2775      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
2776        exf_iprec) as part of namelist EXF_NML_01
2777    o pkg/mdsio:
2778      - read/write tiled (local) files: read/write 1-level tile chunk at a time
2779        (instead of segment of length sNx); expected to speed up tiled IO.
2780    o pkg/exch2:
2781      - take buffer copy from/to array out of S/R exch2_send/recv into new
2782        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
2783        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
2784      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
2785      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
2786        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
2787        including Topology header file (and common blocks).
2788      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
2789        remove 2nd exch call in exch2_s3d_rx (no longer needed).
2790      - document S/R arg. list (+ update some comments)
2791    o pkg/seaice:
2792      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
2793        temperature and humidity over sea ice based on climatological values.
2794      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
2795        of LSR (this change is expected to change the results slightly because now
2796        it uses slightly difference moduli from the second last LSR solution, but
2797        that is more consistent with the stress computations; this part of the code
2798        is not tested in the verification experiments)
2799      - fix diagnostics for flux of ice in case of B-grid
2800      - turn strain rates eij and press into global fields within global
2801        common block in SEAICE.h for more straighforward diagnostics
2802      - fix diagnostics for principal stress components, press, zeta, eta
2803        to give something meaning full
2804    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
2805      new output (all 4 tests) using default rotationPeriod.
2806    o pkg KPP:
2807      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
2808      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
2809        and normal grid from 1 to Nr)
2810    o Fix computations of L4rdt in mom_calc_visc.F
2811    o eesupp:
2812      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
2813      should be called before a "stop" if we know that all process are going
2814      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
2815    
2816    checkpoint61o (2009/05/26)
2817    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
2818    o model/src/ini_curvilinear_grid.F:
2819       compute angleSin/CosC when they are not read from a file
2820    o pkg/seaice:
2821       add pseudo time stepping for LSOR
2822    o pkg/exch2:
2823       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
2824    o pkg/seaice:
2825       Adding separate sea ice albedo, drag coefficients, and HO in Southern
2826       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
2827    o SingleCpuIO:
2828       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
2829    o pkg/seaice:
2830       put exchanged variable in (local) common block for MPI+Multi-Threads
2831       to work (necessary with exch1, and for now with exch2 too).
2832    o verification: to get more experiments tested with mpi, mth and mpi+mth,
2833      change tiling of:
2834       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
2835       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
2836      update output of exp:
2837       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
2838       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
2839      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
2840                       (note: output.txt generated on faulks using only 1 tile)
2841    o eesupp & mdsio (SingleCpuIO):
2842     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
2843       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
2844       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
2845     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
2846     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
2847       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
2848    o pkg/exch2:
2849     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
2850       read parameter file "data.exch2" if it exists; otherwise try default regular
2851       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
2852     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
2853       with new code (not to be used, just as a backup solution).
2854     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
2855       in utils/exch2/input.
2856    
2857    checkpoint61n (2009/05/12)
2858    o eesupp & mdsio (SingleCpuIO):
2859      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
2860        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
2861        receive real*4 array (instead of real*8) to read/write 32.bit files.
2862        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
2863         and remove new mapping S/R)
2864    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
2865      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
2866        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
2867        when using exch2. Add S/R to map global io-buffer to global model array.
2868      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
2869    
2870    checkpoint61m (2009/04/29)
2871    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
2872      and add 3 other S/R for other types (R4,R8,RS).
2873      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
2874    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
2875     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
2876     - reduce number of macro definitions (keep only those which are used);
2877       can always call directly the corrresponding S/R if needed.
2878     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
2879       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
2880     Fixed wrong type of arg in:
2881       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
2882       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
2883     To fix: global_sum of var in common block is wrong (multi-threaded) in:
2884       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
2885     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
2886    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
2887      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
2888    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
2889    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
2890      edges are closed (zero depth); might happen with "blank tiles";
2891      for now, disabled if using OBCS.
2892    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
2893      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
2894    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
2895      to reduce length of 1.D array print in STDOUT.
2896    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
2897      + use 48 tiles (16x8): this will allow to test "blank tiles".
2898    o start to test MPI + multi-threaded (change testreport to skip tests
2899      where number of tiles do not match).
2900    o genmake2: add option "-omp" to turn on Open-MP ;
2901      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
2902    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
2903      and keep the original tile numbering. Note: compatible with old
2904      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
2905    
2906    checkpoint61l (2009/04/07)
2907    o Overlaps had been forgotten in calculating ijk keys : fixed
2908    o fix cyrus makedepend for gcc 4.4
2909    o experiment fizhi-cs-aqualev20:
2910      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
2911      and generate new output. Note: new output is much closer to the old
2912      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
2913      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
2914    o pkg/fizhi:
2915     - change to avoid indices going deliberately over array-bounds
2916     - remove unnecessary MPI stuff
2917     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
2918     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
2919       does not go over array-bounds and therefore returns reliable output.
2920     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
2921       this S/R has 4 output arguments, which are used inside "get_alarm";
2922       when it is called with the same variable "ndum" in place of several
2923       output arguments, this produces weird side effect inside "get_alarm"
2924      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
2925       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
2926       address) and produces error.
2927    o tools/gemake2: (March 27-29 2009)
2928      with option "-mpi": link *_mpi files from "MODS" dir (this is what
2929      testreport does).
2930    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
2931    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
2932       update lab_sea.lsr & lab_sea.salt_plume results
2933    o pkg/seaice:
2934      Major overhaul of the LSOR solver: change discretization from original
2935      finite differences to finite volume. The old routine is still in the
2936      file seaice_lsr.F and can be turned on with the CPP-flag
2937      SEAICE_OLD_AND_BAD_DISCRETIZATION
2938      Along with this change, the discretization of the strain rates is changed.
2939      The same flag turns on the old discretization in seaice_calc_strainrates.F
2940      All verification experiments with seaice are affected (except for
2941      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
2942      results by setting the above flag.
2943      Further changes involve changes in defaults:
2944      - ALLOW_FLOODING is defined and turned on by default
2945      - SEAICEadvSnow = .true. is now the default
2946      - SEAICEadvSalt = .true. is now the default
2947      - SEAICEadvAge  = .true. is now the default
2948      - SEAICE_clipVelocities  = .false. is now the default
2949                                         (as per J. Zhang's recommendation)
2950      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
2951        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
2952      - seaice_growth: replace computation of UG by a simple copy from wspeed
2953    
2954    checkpoint61k (2009/03/18)
2955    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
2956      seaice_lsr: fixed a few metric terms,
2957                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
2958                  add more debugging diagnostics
2959      seaice_evp: removed superfluous many metric terms of FV discretization
2960                  of stress divergence
2961                  affects lab_sea, lab_sea.hb87
2962      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
2963                  of stress divergence for non-evp solver
2964                  (this part is not tested anywhere)
2965      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
2966                  they were effectively only half slip
2967                  affects lab_sea.hb87
2968      updated all relevant verification experiments (except lab_sea//output_adm.txt
2969        which was left over, but fails at level 7 & 6)
2970    
2971    checkpoint61j (2009/03/17)
2972    o pkg/seaice: turn a few hard wired parameters into run time parameters
2973    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
2974      time in seconds as promised by the usints in seaice_monitor and exf_monitor
2975    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
2976      that are not cubed-sphere grids
2977    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2978    o pkg/ctrl:
2979      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
2980    o non-hydrostatic (calc_gw.F):
2981      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
2982      update output of exp. global_ocean.cs32x15.viscA4
2983    o remove backward compatibility for thetaMin,phiMin
2984      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
2985    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
2986      interpolated wind field not only for curvilineargrid=.true., but also
2987      for a rotated grid (rotateGrid=.true.)
2988    o pkg/exf: add capability to bypass interpolation for runoff
2989      by setting yet another CPP-flag
2990    o eesupp/src, B-grid exchange:
2991      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
2992    o autodiff
2993      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
2994      allows to switch to single-prec common blocks;
2995      corresponding switch occurs in tamc.h, integer isbyte
2996      TAF store directivs "byte" and "kind" seem equivalent;
2997      Most tamc.h have been updated correspondingly.
2998    
2999    checkpoint61i (2009/02/13)
3000    o autodiff:
3001      fix autodiff_sore/_restore indices for obcs
3002      (spotted by I. Hoteit, M. Mazloff)
3003    o pkg/autodiff, pkg/ctrl:
3004      Add flag to reduce all tapelev I/O to single-prec.
3005      In data.ctrl set
3006        doSinglePrecTapelev = .TRUE.
3007    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
3008      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
3009    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
3010      real fresh water flux (not yet)
3011    o pkg/mdsio & rw:
3012     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
3013     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
3014    o pkg/flt:
3015     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
3016       init_fixed & ini_varia.
3017     - clean-up & simplify linear interpolation S/R:
3018       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
3019     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
3020     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
3021     - add vert. coordinate & horiz. indices to output files.
3022     - change vertical position in initial condition, from index to depth [m].
3023     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
3024       (easier to get to a curvilinear grid) ; delX,delY no longer used.
3025    o pkg/ggl90: a few modifications:
3026     - fix bottom boundary condition, and interpolation of KappaE
3027       near top and bottom
3028     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
3029     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
3030     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
3031    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
3032      (maintain temporary backward compatibility, until next checkpoint)
3033    
3034    checkpoint61h (2009/01/27)
3035    o pkg/diagnostics with "periodic averaging diagnostics":
3036      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
3037    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
3038    o pkg/obcs: fix loop ranges for balancing code
3039    o pkg/flt:
3040     - improve criteria for finding which tile owns a float.
3041     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
3042    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
3043      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
3044      with ocean biogeo)
3045    o pkg/flt:
3046     - do some cleaning and fix the restart ;
3047     - add output.txt in flt_example/results to get this pkg tested.
3048    o genmake2: add an EXTENDED_SRC option and flag.
3049       for now, cannot be turned on on command line (only through genmake_local)
3050    o pkg/mdsio: read/write vector:
3051     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
3052     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
3053       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
3054     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
3055      (drop to 4 digits matching for grad). But this test does not look very
3056      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
3057    
3058    checkpoint61g (2008/12/29)
3059    o pkg/flt:
3060      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
3061       + make OPTIONS file more standard.
3062      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
3063      - fix _BYTESWAPIO CPP-Flag
3064      - standard reading of file-parameter "data.flt"
3065      - fix argument list of S/R FLT_RESTART
3066      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
3067    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
3068    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
3069      a still unfixed compiler/optimization bug
3070    
3071    checkpoint61f (2008/11/21)
3072    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
3073      update results of global_ocean.cs32x15.icedyn test.
3074    o move getcon.F from model/src to pkg/fizhi.
3075    o pkg/exf: add parameter for extrapolation of temp up to the surface
3076       and option to prevent negative evap (in bulk_largeyeager04 only).
3077    o Prather Advection scheme: fix tracer conservation for divergent flow
3078      (e.g., when using NonLin Free-Surface).
3079    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
3080    o gmredi (Visbeck-variable-K):
3081     - add more parameters to Visbeck-variable-K.
3082     - use a 5 points average for dSigmaR in Visbeck-K calculation
3083       (more "homogenous": same stencil and same weights as in dSigmaH)
3084     - update output of ideal_2D_oce experiment.
3085    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
3086      (#undef REAL4_IS_SLOW)
3087     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
3088       coordinate variable
3089     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
3090       (surface forcing fields), removes some of the functionality
3091     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
3092     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
3093       probably not all: copy _RS surface flux fields to RL field before
3094       calling DIAGNOSTICS_FILL
3095     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
3096       real*4 (CALL EXCH_*_RS) versions.
3097     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
3098       (generate new output).
3099    
3100    checkpoint61e (2008/10/23)
3101    o gmredi (Visbeck-variable-K):
3102      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
3103      - change computation of Visbeck-K where Slope > Smax :        
3104        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
3105        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
3106    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
3107      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
3108    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
3109    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
3110      does not become too large (to avoid precision problems in implicit-diffusion
3111      solver); update ideal_2D_oce output.
3112    o pkg ggl90:
3113      - in ggl90_cal.F: compute only one set of visc/diff, used to
3114        step forward TKE/T/S/momentum
3115      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
3116        have Prandlt =1)
3117    o gmredi (fm07):
3118      - add lower limit on Transition layer thickness + lower limit on 1/lambda
3119      - allow to set few more params from data.gmredi
3120    o pkg ggl90:
3121          - add missing sqrt(2) factor in computation of mixing length
3122            scale in ggl90_calc.F
3123            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
3124    
3125    checkpoint61d (2008/09/25)
3126    o adjoint modifs
3127      - adapt to new field rhoInSitu
3128      - allow to revert from StoreDynVars2D, StoreDynVars3D
3129        to individual fields
3130        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
3131    o store 3-D (in-situ) density in commom block (DYNVARS.h)
3132     - save 1 rho computation.
3133     - no longer modify T & S inland when using down_slope pkg.
3134    o gad_som : allow to switch to SOM advection for T & S without corresponding
3135      pickup files (using new S/R: MDS_CHECK4FILE).
3136    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
3137      (for useSingleCpuIO to work in multi-threaded)
3138    o pkg/shelfice:
3139     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
3140       with SHELFICEtopoFile in data.shelfice
3141     - move code for reading ice shelf topography and modifying hFacC into separate
3142       subroutines of the shelfice package
3143     - separate initialisation of "fixed" and "variable" variables
3144     - kTopC is not (yet) replaced by kSurfC, although this is possible
3145    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
3146    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
3147      and rename:
3148      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
3149      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
3150    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
3151    
3152    checkpoint61c (2008/08/30)
3153    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
3154      to add mass source/sink of fluid in the interior (3-D generalisation
3155      of oceanic real-fresh water flux).
3156    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
3157    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
3158    o new pkg: down_slope
3159      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
3160      - presently, modify T & S inland (dwnslp_calc_rho.F).
3161        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
3162      - implementation for ocean in P-coords not tested.
3163      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
3164    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
3165      (to facilitate conversion of oceanic pkg to p-coordinate).
3166    o change FIND_RHO to FIND_RHO_2D :
3167      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
3168    o new pkg: cheapaml
3169    
3170    checkpoint61b (2008/08/05)
3171    o exch2:
3172      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
3173      - no longer depend on the order sequence (N,S,E,W).
3174      - 3rd exchange no longer needed (tested with 24 tiles).
3175      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
3176      - exch_UV_A-grid readily available (but not yet tested).
3177      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
3178      (both are no longer needed) in exch_uv: no effect in forward run; but
3179       get truncation error differences with adjoint exch.
3180    o exch2:
3181     - change index-bounds storage (moved from target to local tile,
3182       more intuitive this way) ; rename/remove some variables.
3183     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
3184    
3185    checkpoint61a (2008/07/29)
3186    o exch2/matlab-topology-generator:
3187      fix bug in index bounds for N-S internal exchange (hard to tell if this
3188      had any effect on the solution).
3189    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
3190      is exceeded
3191    o testreport: modify syntax of awk, so that it works also with
3192      awk, and not only with nawk and gawk
3193    
3194    checkpoint61 (2008/06/24)
3195    o autodiff
3196      Change default for TAF usage by removing argument '-nonew_arg'
3197      This changes TAF subroutine argument list (ordering of active var.)
3198      Omission of this flag leads to incompatibility w.r.t. TAMC
3199      To restore TAMC-compatibility, need following modifs:
3200      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
3201      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
3202      Tested TAF version is 1.9.22
3203      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
3204    
3205    checkpoint60 (2008/06/19)
3206    --->>> This is the last checkpoint for which generating the adjoint
3207    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
3208    --->>> by default.
3209    --->>> Future checkpoints will ommit this flag by default.
3210    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
3211    o pkg/grdchk: Add gradient check to etan0 perturbations.
3212    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
3213    o pkg/autodiff: more flexibility in zeroadj.
3214      model/src: modifying do_oceanic_phys.F accordingly.
3215    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
3216    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
3217      special setup of gmredi for which the adjoint is stable
3218      enough for parameter optimization.
3219    o bridging the gap between eddy stress and GM.
3220      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
3221          along with a change in CPP option (now ALLOW_EDDYPSI).
3222      -> when using GM w/ GM_AdvForm:
3223          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
3224          is applied either in the tracer Eq. or in momentum Eq.
3225          depending on data.gmredi (intro. GM_InMomAsStress).
3226      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
3227      The key modifications are in model/src/taueddy_external_forcing.F
3228      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
3229    
3230    checkpoint59r (2008/05/29)
3231    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
3232      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
3233      fix option to read coriolis(@ cell-corner) from files with CS-grid.
3234    o pkg/mnc: add some attributes to standard 1D-coordinate variables
3235    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
3236      mass points, when using mnc for output
3237      - add runtime parameter (missing_value, missing_value_int) to override
3238        default (which is the value of getcon('UNDEF'))
3239    o pkg/mnc: prepare mnc for the actual use of missing values with the
3240      diagnostics package: small fix in mnc_cw_readwrite.template and more
3241      initialisation of never used fields
3242      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
3243      versions
3244    o pkg/thsice/thsice_ini_vars.F added default initial values so that
3245      thermodynamics sea ice solver does not blow up when some initial fields
3246      are missing.
3247    o move from external_forcing_surf.F to ini_forcing.F
3248      the p-coord. hack consisting in using pLoad to set phi0surf ;
3249      update output of tutorial_global_oce_in_p (affected @ truncation level).
3250    o Freshen up a bit hs94.1x64x5, notably:
3251      remove rotationPeriod and tRef=5*0. (adjoint only), and add
3252      exactConserv=.TRUE.
3253    o pkg/generic_advdiff:
3254      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
3255      applies to files where Temperature & Salinity 2nd Order moments are used.
3256    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
3257      this uses a dynamically allocated internal state data structure
3258      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
3259      and requires a fortran 90 compiler
3260    
3261    checkpoint59q (2008/05/06)
3262    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
3263       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
3264    o Refresh tutorial_global_oce_biogeo, notably:
3265      - change bathymetry (put back seamounts in ACC, use hFacs)
3266      - change EOS (POLY3 --> JMD95Z)
3267      - use Bryan-Lewis vertical diffusivity
3268      - use multidimensional advection
3269      - remove old virtual virtual in dic pkg, now done through ptracer pkg
3270      - change a couple of parameters in dic pkg
3271    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
3272    o pkg/obcs: change default to OBCSfixTopo = .true.,
3273      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
3274      - replace "debugMode" with "debugLevel .GE. debLevB"
3275    o implementation of TAF directives for gchem,cfc,dic
3276    o remove "exp5" (replaced by tutorial_deep_convection).
3277    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
3278      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
3279      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
3280      --> changes results in exp4, seaice_obcs
3281    o tutorial_deep_convection :
3282      update the set-up and increase resolution and domain size ; start
3283      from pseudo initial conditions = output at t=120mn in order to see
3284      something happening when running testreport.
3285    o pkg/seaice: add os7mp as an advection scheme
3286                  add check for advection schemes
3287                  add a flag for restoring T and S underneath sea ice
3288    o pkg/my82: add netcdf-support and diagnostics
3289    o thsice pkg:
3290      - Now hsMax limits snow height by turning it into ice following
3291        flooding scheme (and now conserving energy)
3292      - Slight rewriting of the formula in thsice_calc_thick.F
3293      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
3294      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
3295    
3296    checkpoint59p (2008/04/10)
3297    o gchem / dic / cfc :
3298      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
3299      - add new parameter files: "data.dic" & "data.cfc" ;
3300      - various re-arrangement in initialisation & header file ;
3301      - fix tutorial_global_oce_biogeo for multi-threaded test.
3302    o pkg/dic: test for "pickup_dic" file when restarting ;
3303      if no pickup-file, can restart with a re-initialised pH (same as it did
3304      before) providing pickupStrictlyMatch is set to False.
3305    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
3306      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
3307    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
3308      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
3309    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
3310     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
3311       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
3312    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
3313       scheme to use for vorticty-term ;
3314     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
3315       (with default selectVortScheme, return to original discretisation)
3316     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
3317    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
3318    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
3319      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
3320      also fix diagnostics VISCAHW & VISCA4W.
3321    
3322    checkpoint59o (2008/03/07)
3323    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
3324    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
3325      move a few statemens out the main loop into separate loops
3326    o pkg/shelfice:
3327      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
3328        (kg/m^2/s), does not break tests, because in verification/isomip,
3329        rhoConstFresh=rhoConst (by accident)
3330      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
3331      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
3332        new file model/src/seawater.F, so that they are available for all pkgs.
3333      - convert potential temperature into in-situ temperature. This changes the
3334        isomip tests => update tests
3335    o add a flag writePickupAtEnd (default=true) to be able to suppress
3336      writing a pickup at the last timestep
3337    o tools/mpack-1.6 :
3338      - disable automake (not working) and autoconf (not needed).
3339      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
3340        also cleaner with much less compilation warnings.
3341    o pkg/profiles:
3342      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
3343      (for "less than 32 characters name" compiler requirement)
3344    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
3345      conditions that have a different sampling frequency than S/T/U/V obcs
3346    o pkg/diagnostics (stats-diags):
3347      - fix global Min/Max in case 1 processor get only empty tiles
3348    o genmake2: replace (4 times)
3349         make genmake_tc_1.o >> genmake_warnings 2>&1
3350      with
3351         COMM="$CC $CFLAGS -c genmake_tc_1.c"
3352         echo $COMM >> genmake_warnings
3353         $COMM >> genmake_warnings 2>&1
3354      to make genmake2 always see the value of CC as specified in the optfile.
3355    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
3356      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
3357      - modify verification advect_cs test to test SOM-advection on CS-grid.
3358    o pkg/ctrl:
3359      - Rewrite of ctrl_map_ini_ecco.F,
3360        introducing a generic routine (ctrl_map_ini_gen.F).
3361      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
3362    
3363    checkpoint59n (2008/02/09)
3364    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
3365      number in dedicate array "hdiag":
3366      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
3367        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
3368      - many small changes (integer format) for large number of diagnostics
3369      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
3370        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
3371    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
3372      usingSphericalGrid, this allows to define the rotated grid coordinates
3373      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
3374      geographical coordinates according to the inverse of the rotation defined
3375      by the Euler angles, so that Coriolis parameter and online-interpolation by
3376      exf works with the geographical coordinates on XC/YC/XG/YG.
3377      Naturally, this feature does not work with all packages, so some
3378      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
3379      profiles), because there the coordinates are assumed to be regular
3380      spherical grid coordinates.
3381    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
3382      - introduce isopycnal diffusion coefficient control.
3383    o tools/adjoint_options:
3384      - additional control vector components.
3385    o pkg/mnc: have mnc create marginally meaning full coordinate variables
3386      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
3387    o pkg/mypackage:
3388      - add example of read/write pickup for state-var ;
3389      - add entry points to the main code for state-vars diags & write-pickup.
3390    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
3391      transitions for useExfYearlyFields
3392      - add new subroutine that determines the file to read from for
3393        use*YearlyFields = .TRUE. and .FALSE.
3394      - add a verification experiment to global_with_exf that tests
3395        useExfYearlyFields with USE_EXF_INTERPOLATION defined
3396    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
3397      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
3398      subroutines (which could be generated from a template, because they are
3399      almost identical), for now they are included in obcs_prescribe_read.F for
3400      simplicity
3401    o pkg/exf:
3402      - add a little more diagnostic to exf_interp_read (in analogy to
3403        mds_read_field, can be turned off with debugLevel < debugLevA=1)
3404      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
3405        ugly but fast by unrolling short inner loops, inserting a unroll=8
3406        directive in routine lagran, and splitting a loop and making do while the
3407        outermost loop (the latter requires the intoduction of index arrays)
3408    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
3409    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
3410      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3411    o verification/seaice_obcs: updated for restart test and latest options
3412    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
3413      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
3414      for now this is only available for the C-grid code and also within
3415      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
3416    
3417    checkpoint59m (2008/01/14)
3418    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
3419      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
3420    o gad_som : fix flux output (& diagnostics) to have same units as other  
3421      advection scheme fluxes (was previously multiplied by deltaT).  
3422    o added verification/seaice_obcs both to test seaice open boundaries
3423      and to provide an example matlab scrpt for generating them
3424    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
3425    o pkg/salt_plume: clean up salt_plume_frac.F to
3426      remove redundancy in PlumeMethod 1 and 4
3427    o pkg/kpp: added saltplume diagnostics
3428    o pkg/obcs and pkg/seaice:
3429      - do not set uice and vice to zero when OB*icefile are unspecified
3430      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
3431      - moved seaice tracer obcs after call to seaice_growth
3432    o pkg/salt_plume: added various options for salt plume depth
3433      criterion and for vertical distribution of the salt
3434    
3435    checkpoint59l (2007/12/18)
3436    o pkg/ptracers: new version of ptracers pickup:
3437      read meta file and write only fields which are needed to restart.
3438      ( same logic as main pickup file ; also using pickupStrictlyMatch )
3439    o pkg/seaice:
3440      - add timescale for melting due to warm mixed layer as a means of
3441        setting SEAICE_availHeatFrac more conveniently
3442      - add a CPP-flag/runtime parameter check for flooding algorithm
3443      - reformulated availHeat in seaice_growth.F to be independent of AREA
3444    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
3445      unit changes
3446    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
3447    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
3448      SX vector computer.
3449    o pkg/seaice:
3450      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
3451        seaice forcing fields can now be read only through pkg/exf
3452      - removed some unused halos
3453    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
3454    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
3455      or U/VICE from U/VWIND before computing U/VSTRESS
3456    
3457    checkpoint59k (2007/11/30)
3458    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
3459      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
3460    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
3461      all experiments pass when compile with un-initialised var. checking option.
3462    o added pkg/salt_plume
3463    o script to test restart (for now, in MITgcm_contrib/jmc_script)
3464    o pkg/seaice: new read/write pickup version.
3465      read meta file and write only fields which are needed to restart.
3466      ( same logic as main pickup file ; also using pickupStrictlyMatch )
3467    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
3468    o lab_sea.hb87: modify the domain & update output.hb87.txt :
3469      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
3470      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
3471      process. Fixed here by closing the domain at the Northern boundary.
3472    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
3473    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
3474      a set of consecutive levels in/from a 3-D array.
3475    o pkg/ptracers:
3476      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
3477      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
3478    
3479    checkpoint59j (2007/11/09)
3480    o in pkgs: dic, obcs, offline, rbcs:
3481      standard way to compute coeff. for time interpolation between 2 time reccords
3482      which retains full precision (& make results less dependent on compiler).
3483      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
3484    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
3485      packages instead of reading ice cover and wind speed separately
3486    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
3487     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
3488      to allow to compile customized code before the update)
3489    o cleaning-up:
3490      - fix CPP instruction syntax in pkg/obcs
3491      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
3492        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
3493      - fix some threads issue in IO parts.
3494    o pkg/dic:
3495      - add tons of "_d 0" (--> much better testreports !)
3496       and then update outputs of tutorial_global_oce_biogeo
3497    o pkg/mom_fluxform:
3498      add a special version of momentum advection intended to conserve momentum
3499      next to a bathymetry step or a coastline edge. (default = off = #undef)
3500    o new read/write pickup version:
3501      - for now, only implemented for main (mdsio) pickup file.
3502      - write out only what is needed to restart; merge pickup_nh , pickup_ph
3503        and main pickup together.
3504      - read meta file; read only what is needed to restart; stop if a field
3505        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
3506        if it make sense (even if the restart is not perfect).
3507      - if no meta file, assume that pickup to read corresponds exactly to
3508        a pickup that would currently be written.
3509      - read pickup written in the old format (until checkpoint59i) if it
3510        recognizes an old meta file (no field-list).
3511      - add a meta file in exp. which starts from a pickup: 2 cases:
3512        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
3513         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
3514        b) a meta file describing the content of the associated pickup file
3515         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
3516    o pkg/mdsio & pkg/rw:
3517      - new routine to read a meta file ; new set of routine to read
3518        Multiple-fields file (with meta file).
3519    o added open boundary conditions capability for seaice
3520        HSNOW, HSALT, UICE, and VICE
3521    
3522    checkpoint59i (2007/10/21)
3523    o adjoint:
3524      * fix multiDimAdvection adjoint
3525        (partial recomputation problem by TAF for fVerT(:,:,kDown)
3526        and comlev1 size definition (maxpass vs. max. number of tracers)
3527      * verification/global_ocean.90x45x15 adjoint now tests
3528        NLFS and multiDimAdvection using DST3 (=30)
3529      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
3530    o pkg/kpp: add "_d 0" to real constant (if missing);
3531      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
3532      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
3533    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
3534      for internal parameters related to restart process (formerly from PARAMS.h)
3535      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
3536    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
3537      as argument. (only atm2d & obcs write_pickup have not yet been updated)
3538    o pkg/monitor:
3539      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
3540      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
3541      - account for deep Atmosphere factor and density factor (anelastic)
3542    o added open boundary conditions capability for seaice HEFF and AREA
3543    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
3544      thermodynamics
3545      - requires a little reorganization, which affects the testreport results
3546        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
3547        so that now the conservative form is tested
3548      - add a few comments
3549    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
3550    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
3551    o add new diagnostics to seaice: advective, diffusive fluxes (only for
3552      multidim-advection, for scheme 2 they are not filled) and transports,
3553      thermodynamic growth rates
3554    o change units of EmPmR (inside the code, + within coupling interface)
3555      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
3556      Affects results @ truncation level (cg2d match) and update output of
3557       experiments: lab_sea(6), global_ocean.90x40x15(10),
3558      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
3559      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
3560      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
3561      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
3562    
3563    checkpoint59h (2007/09/29)
3564    o pkg/exf:
3565      - improve vectorization by moving if-statement out of loops in
3566        exf_mapfields, exf_radiation
3567      - exf_bulkformulae.F: introduce 2D fields and vectorize code
3568    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
3569    o testreport:
3570      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
3571        monitor & update offline_exf_seaice exp. output.
3572      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
3573    o pkg/seaice:
3574      - bug fix in the evp solver: boundary conditions were affected be
3575        masking of zMax/zMin (changes results)
3576      - minor bug fix in boundary conditions in seaice_calc_strainrates
3577        (changes results for no_slip)
3578      - seaice_lsr.F: make interpolation of eta dependent on boundaries
3579      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
3580      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
3581        stress formulation and no-slip boundary conditions
3582    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
3583      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
3584    o pkg/seaice: a first HSALT time stepping equation has been checked in
3585    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
3586      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
3587      without requiring DO-IF statements
3588    o pkg/thsice:
3589      use continuous power-law function for partition of energy between lateral
3590      melting/freezing and thinning/thickening ; old code using step function
3591      still available with #undef THSICE_FRACEN_POWERLAW
3592      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
3593    o testreport: change AD testing : check against results/output_adm.txt
3594      using same scripts as for forward test.
3595    
3596    checkpoint59g (2007/09/17)
3597    o adjoint testing: in preparation for changing testreport:
3598      - output format: cost and grad written on separated lines
3599      - ad output results in directory "results" (instead of "results_ad")
3600    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
3601    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
3602    o pkg/ecco: allow user defined cost function contributions
3603    o testreport:
3604      Allow to choose (per experiment) the list of tested output variables
3605       and the main variable (used to issue a pass/FAIL ) ;
3606      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
3607      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
3608      Also modify printing of summary:
3609       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
3610       b) echo the list of tested variables in the individual summary.txt of
3611          each experiment.
3612    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
3613      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
3614      (but still depend on the tile decompostion of the domain).
3615    o pkg/seaice: change a discretization detail to make the B-grid code
3616      "more symmetric". This change is likely to remove all "ridges/leads" that
3617      where quasi-aligned with the grid in B-grid solutions. It may also be
3618      the solution to the stress coupling issues with the B-grid.
3619    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
3620      remove .cvsignore from input dir. (since testreport no longer run here).
3621    o pkg/thsice:
3622     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
3623     - fix reshaping of sea-ice just after advection:
3624       melt all the ice only if ice-volume is too small.
3625     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
3626       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
3627     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
3628    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
3629      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
3630    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
3631      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
3632      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
3633      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
3634      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
3635      -> update output.txt
3636    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
3637     this affects truncation error: -> update output.txt of exp:
3638      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
3639      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
3640    
3641    checkpoint59f (2007/08/21)
3642    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
3643    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
3644      a bounded range (in forward mode)
3645    o pkg/ecco, ctrl, autodiff and mom_common:
3646     internal parameter controls, completements of implementations
3647    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
3648    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
3649      (not seem any difference in testing results).
3650    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
3651       at face corners.
3652    o pkg/generic_advdiff:
3653     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
3654      loop range indices for computing vertical advection tendency
3655      and do the calculation in the interior only (no overlap) ;
3656      for now, only implemented for SOM advection (to save CPU time).
3657     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
3658    o exch2 adjoint
3659      First set of changes:
3660      - add exch2 hand-written adjoint templates
3661      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
3662        This will require cleanup in pkg/autodiff/*.F
3663        (changed routines currently kept separate in verif. code/)
3664      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
3665        that used to hide exch2 or cubed-sphere specific code
3666        (commented via 'cph-exch2')
3667    o pkg/seaice
3668      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
3669    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
3670       output of global_ocean.cs32x15.thsice .
3671    
3672    checkpoint59e (2007/07/26)
3673    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
3674      for B-grid vector (not yet tested) and C-grid vector (<- only used
3675      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
3676    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
3677      (#ifdef ALLOW_SALT_PLUME)
3678    o gather_2d/scatter_2d: removed halo regions
3679    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
3680      scheme and the corresponding test case (under front_relax dir). For now,
3681      only available with Skew-flux form and not yet tested in realistic set-up.
3682      adjoint: store directives updated, but gradient checks deteriorated,
3683      so maybe GM/Redi adjoint is now broken.
3684    o seaice adjoint
3685      * add AREA, HEFF, HSNOW as control variable
3686        (should not change lab_sea results)
3687      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
3688    o pkg/seaice:
3689      * added computation of saltFlux in seaice_growth;
3690        For time being, sea ice salinity is assumed constant
3691        contribution of snow flooding to freshening of sea ice is neglected.
3692        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
3693        defaults to 0.0 in order to maintain backward compatibility.
3694        Typical values for SEAICE_salinity are 4 to 10 g/kg.
3695      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
3696      * added SEAICE_availHeatFrac, which specifies fraction of surface level
3697        heat content used to melt or grow ice
3698      * commented out cap of HICE: it helps keep ice thinner
3699      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
3700      * applied OBCS T/S mask to HEFFM sea ice mask
3701    
3702    checkpoint59d (2007/06/21)
3703    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
3704     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
3705     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
3706    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
3707     and change default value of parameter "GM_Small_Number";
3708     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
3709       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
3710       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
3711    o pkg/ecco: cost function when applying pkg/smooth to controls
3712    o pkg/ctrl: add forcingPrecond run time parameter
3713    o pkg/seaice:
3714     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
3715     - fix bug in metric terms of u-equation in LSR solver (implicit part),
3716       changes verification/lab_sea
3717     - rearrange implicit part of u-equation in LSR solver to make it easier to
3718       read, understand, and debug. This causes changes at the truncation level.
3719     - fix (serious) bug in the boundary conditions (sign error in the implicit
3720       part) of the LSR solver. Changes all LSR results.
3721     - fixed problem with HSNOW initialization to avoid thick snow when AREA
3722       is initilized with small values - does not change lab_sea results.
3723     - added HsnowFile initialization capability
3724    o pkg/smooth: addition to model/src and pkg/ctrl so allow
3725     initialization of pkg/smooth and application to control vector
3726    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
3727    o dependencies: pkg/profiles requires pkg/cal
3728    o pkg/profiles:
3729     - added option ALLOW_PROFILES_GENERICGRID
3730         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
3731         that interpolation information (grid points and coefficients) is provided
3732         within the netcdf input files.
3733         -> sample matlab scripts can be found in MITgcm_contrib/gael
3734         that allow you to prepare netcdf input files.
3735     - also modified: cleaner include statements, cleaner error print statements,
3736       cleaner stops when error, and more tests of the netcdf input files consistency.
3737    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
3738    o pkg/seaice:
3739     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
3740       requires a new routine: seaice_diagnostics_fill.F
3741     - make sure that seaice does not move if not forced (pressure replacement
3742       method, Hibler and Ip, 1995), changes results
3743     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
3744     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
3745       It is turned off by default (=-1.), because it changes the results.
3746     - make it possible to read AREA from a file, too.
3747    
3748    checkpoint59c (2007/06/04)
3749    o add S/R and diagnostics for oceanic mixed-layer depth
3750    o move GMRedi call after all vertical mixing schemes (including KPP)
3751    o pkg/thsice:
3752     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
3753      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
3754    o pkg/obcs:
3755     - bug fix for balance code
3756    o pkg/seaice:
3757      - allow values of SEAICE_elasticParm > 1
3758      - add new parameter SEAICE_evpTauRelax as an alternative
3759        to SEAICE_elasticParm
3760      - make lsr boundary conditions free slip (by default), changes result
3761      - add code for no slip boundary conditions for lsr
3762      - set minimum of zeta to zero (and not 4e8) (changes results)
3763      - add a cap on AREA after advecting AREA if seaice_growth is not called
3764    o change calculation of Visbeck K:
3765      - no longer depend on tapering scheme; instead, compute slope (limited
3766        by GM_maxSlope). this is equivalent to what was comuted before with
3767        clipping or linear tappering.
3768      - fix vertical averaging (wrong by 1/2 level)
3769      - leave the old version (but will not be maintained) within
3770        #ifdef OLD_VISBECK_CALC / #endif
3771      - update output of exp. ideal_2D_oce
3772    o change error catch in calc_r_star to improve vectorization
3773    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
3774      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
3775    o adjoint:
3776      Re-organized adjoint checkpointing according to Matt Mazloff
3777      (but with modifs/completions/cleanups)
3778      Storing is now bundled into large arrays to optimized I/O
3779      (and second step in cleanup of the_main_loop)
3780    
3781    checkpoint59b (2007/05/16)
3782    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
3783      - export/import (between ocean & coupler) fields needed for ocean DIC.
3784    o pkg/seaice:
3785      - get rid of three more exchanges seaice_calc_viscosities (required
3786        different loop boundaries in seaice_lsr and seaice_ocean_stress)
3787      - bug fix in seaice_ocean_stress (update of lab_sea required)
3788      - reduce loop boundaries to necessary minimum also in seaice_evp
3789      - go back to the old way of computing deltaC/Z as the adjoint likes that
3790        better
3791    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
3792      passive tracer to an Age Tracer) + update output.txt
3793    o pkg/exf:
3794      - implement A-grid / C-grid selection for wind-stress input files.
3795      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
3796      for now, in exf_bulk_largeyeager04.F only :
3797      - change implementation for case where windspeed + 2. components wind-stress
3798        are read-in. AND use rhoConstFresh to convert evap.
3799    o pkg/seaice:
3800      - use correct EXCH_UV for wind-forcing (on A-grid).
3801      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
3802        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
3803    o pkg/exf:
3804      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
3805      EXF_INTERPOLATION:
3806      - merge global_with_exf/code version of exf_interp_read.F
3807        to the main code ;
3808      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
3809        reading the file ; Important: This options needs to be defined to recover
3810        previous code.
3811        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
3812      - no longer loose real*8 precision along the way when using exf_iprec=64.
3813    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
3814      - change discretisation of evp-solver in order to avoid another exchange
3815        (changes lab_sea) and clean up a little
3816      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
3817        help the adjoint (this also changes the results slightly)
3818      - add a few "_d 0" where they had been missing in seaice_evp.F
3819      - cleaning up: remove unused seaice_calc_rhs.F
3820    o pkg/exf: some cleaning-up:
3821      - change various "constants" into runtime parameters
3822      - cleaned-up Large&Yeager04 routine which should eventually
3823        replace exf_bulkformulae.F (changed names of S/R and CPP)
3824        and merged various ALLOW_ATM_WIND options
3825     only used with thsice pkg (in thsice_get_exf.F):
3826      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
3827        which are used when useStabilityFct_overIce=TRUE (= the default)
3828      - change default values of ice & snow emissivity and scale downward LW
3829        by ice & snow emissivity.
3830    o pkg/thsice:
3831     fix few little problems, in thsice_calc_thickn.F:
3832      - growth vertically (and not laterally) if iceFrac == iceMaskMax
3833      - melt only laterally if hIce < hThinIce (as the comments say)
3834      and in thsice_extend.F:
3835      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
3836      - start to form ice as soon as the minimum ice-volume is reachable.
3837     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
3838      and cpl_aim+ocn
3839    o pkg/kpp
3840     - move computation of surface related input fields to KPP into a new
3841       subroutine kpp_forcing_surf.F
3842     - remove wrong (within bi,bj loops) EXCH calls.
3843     - little cleaning (add argument myThid in last position, cvs header ...)
3844     - for now, fix conservation problem by exchanging KPPviscAz (may not
3845       be the best fix)
3846    o pkg/seaice
3847     - check for inconsistent evp parameter/cpp-flag combination
3848     - remove leftover errIO flat for obsolete name list error handling
3849    o OpenAD
3850     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
3851    
3852    checkpoint59a (2007/05/01)
3853    o pkg/seaice: some parameter clarifications and a little bit of clean up
3854    o pkg/thsice: rename run-time parameters:
3855       himin       -> hIceMin
3856       himin0      -> hThinIce
3857       hihig       -> hThickIce
3858       i0          -> i0swFrac
3859       transCoef   -> bMeltCoef
3860       frac_energy -> fracMelting
3861      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
3862       with default values (for now) that do not change the results.
3863      remove old version of thsice vars advection in pkg/seaice.
3864    o in FFIELDS.h:
3865      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
3866      - make pLoad & sIceLoad always available (but still only used if
3867         ATMOSPHERIC_LOADING is #define).
3868    o pkg/kpp: replaced _KPP_RL with _RL
3869    o bug fixes for vertical diffusivity computations when both KPP and
3870        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
3871        are no longer updating the vertical diffusivity array
3872        (passed as argument) but are (re-) setting those arrays.
3873    o pkg/seaice: fix bug in evp solver, while doing that
3874      - change (improve?) discretization of stress computations for both
3875        cgrid-lsr and evp solver
3876      - add a new routine to compute strain rates
3877      - the above changes lab_sea results
3878      - add no slip conditions for evp solver (off by default), lsr-version
3879        may follow
3880      - fix exchange for shear at Z-points (does not change lab_sea)
3881      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
3882        (to force the user to pick a time step since there is not "safe" way
3883        of choosing it)
3884      - add principal stress diagnostics
3885      - rearrange fields for evp a little to avoid having to call a: too many
3886        exchanges and b: exchanges for stress trensor components which we do
3887        not have.
3888      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
3889        of evp, complete rewrite for lsr case (latter is does not yet work
3890        in all cases)
3891    o pkg/kpp: add code to have mixing in shelf ice caverns
3892      - add myThid to all kpp routines (long overdue)
3893    
3894    checkpoint59 (2007/04/19)
3895    o pkg/exf:
3896      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
3897        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
3898      - move exf header files from lower_case.h to UPPER_CASE.h ;
3899        add missing cvs Header & Name
3900      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
3901      - add namelist param. selectStressGridPosition, exf_monFreq
3902      - retire many _CLIM routines, and remove data.exf_clim
3903        + params moved to data.exf
3904        + climsst, climsss now handled by exf_set_gen, i.e.
3905          climss?period=0 refers to constant field,
3906          climss?period=-12 to monthly forcing
3907      - split up namelists in data.exf
3908    o pkg/seaice:
3909      - remove seaice_exch and seaice_exch_uv
3910      - remove superfluous exchange of theta
3911      - add myThid to seaice_budget_ocean/ice
3912      - add new interface for atmospheric wind forcing (C-grid only)
3913        + new routine
3914        + two new field (taux, tauy for stress over ice)
3915        + removed one global field (DAIRN) for C-grid case only
3916    o pkg/thsise
3917      - 2nd set of modifs for thsice adjoint in conjunction with exf
3918    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
3919    
3920    checkpoint58y_post (2007/04/15)
3921    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
3922      vertical diffusivity, similar to that in MOM4; turned on using
3923      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
3924      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
3925    o Added capability for 3D specification of background vertical diffusion
3926      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
3927      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
3928      "data" file that contains the 3D vertical diffusivity coefficients.
3929    o ice dynamics (pkg/seaice) with thsice thermodynamics:
3930      - add code within pkg thsice to advect & diffuse sea-ice fields
3931      similar to (and will replace) what has been added in  seaice_advdiff.F,
3932      but: - conserving Mass, Heat & Salt.
3933           - better when using non-linear advection scheme (not yet fully tested)
3934           - can also be used in atmospheric set-up (for now, only the diffusion).
3935    
3936    checkpoint58x_post (2007/04/04)
3937    o IO option for global-file compact format:
3938      - add options when generating topology (utils/exch2/matlab-topology-generator)
3939      - add I/O capability (pkg/mdsio).
3940      - adapt utils/matlab/rdmds.m to read this format.
3941      for now long-line format not yet supported by pkg/mdsio (& exch2).
3942    o shelfice: add a few diagnostics
3943    
3944    checkpoint58w_post (2007/03/13)
3945    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
3946      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
3947      (and replace horiVertRatio in NH code).
3948      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
3949                         and tutorial_plume_on_slope (sensitive to truncation)
3950    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
3951      directly to drive seaice model (C-grid only)
3952    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
3953     - reintroduce computation of wind from stress,
3954     - compute tau (in exf_bulkformulae.F) from windstress averaged to
3955       mass points to avoid tau = 0
3956     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
3957    o rdmnc.m: make it work with "global" files created with gluemnc
3958    o rdmnc.m : some improvements in dealing with singleton dimension
3959      (tested on all testreport mnc output files).
3960    o genmake2: disable pkg/profiles if netcdf test fails.
3961    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
3962    o move call to cal_readparms up to make calendar parameters/variable available
3963      to all packages
3964    
3965    checkpoint58v_post (2007/02/08)
3966    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
3967      useDynP_inEos_Zc tested.
3968    o pkg/exf: changes to properly interpolate/mask/scale initial fields
3969    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
3970      and portions thereof.  See read_cs.txt for description and examples.
3971    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
3972      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
3973      following the great-circle arc between those 2 points.
3974    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
3975      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
3976    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
3977     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
3978     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
3979     - still needs work (not working with some options ; efficiency to improve)
3980       and serious testing.
3981     - use this scheme for temperature & salinity in 2 advection test exp.:
3982       advect_xy & advect_xz, respectively.
3983    
3984    checkpoint58u_post (2007/01/12)
3985    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
3986    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
3987    o testreport: add option "-skipdir" to skip some test.
3988    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
3989      momentum calculation.
3990    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
3991    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
3992      remove checkpoint.F and the_correction_step.F (no longer used);
3993      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
3994    o add option (linFSConserveTr) to correct for tracer source/sink due to
3995      Linear Free surface
3996    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
3997    o pkg/thsice: fix reading mnc-pickups
3998    
3999    checkpoint58t_post (2006/12/30)
4000    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
4001    o pkg/mdsio:
4002     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
4003       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
4004       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
4005     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
4006     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
4007       either MDS_READ_FIELD or MDS_WRITE_FIELD )
4008     - new S/R (to replace MDSWRITEMETA), which allows to write more
4009       informations (variable names, time ...) to meta files.
4010     - modify rdmds.m to give back the meta file content.
4011    o pkg/diagnostics: change vertical interpolation to be safer, and more
4012       flexible (define p-levels to interpolate to in data.diagnostics);
4013      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
4014       diagnostic pointer.
4015    o pkg/seaice: more cleaning up of seaice_growth, added many comments
4016    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
4017    o fix multi-category seaice:
4018     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
4019       SEAICE_MULTICATEGORY
4020     - fix short wave heat flux
4021    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
4022       and allow to use EVP solver. Change forward lab_sea: test both EVP
4023       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
4024    o Initial check-in of lab_sea adjoint
4025      (very similar to natl_box_adjoint/code_seaice)
4026      * used C-grid and EVP solver
4027      * used KPP, GM/Redi
4028      * uses inAdExact=.TRUE.
4029      * gradient checks fail for both ADM and TLM
4030        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
4031        f.d. gradients actually seem more problematic than ADM, TLM gradients;
4032        issue is related to forward mismatch between g77 an ifort
4033    o pkg/seaice: overhaul of thermodynamics
4034     - growth.F and groatb.F are replaced by new routine seaice_growth.F
4035     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
4036     - move a few global fields out of SEAICE.h into seaice_growth.F and
4037       make them 2D (FICE/QNETO/ ...)
4038     - remove FO (it is the same as QNETO)
4039     - introduce a few local fields to avoid modifying external fields such
4040       as atemp, etc.
4041    
4042    checkpoint58s_post (2006/12/11)
4043    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
4044      changed exf_set_gen.F so that
4045        genperiod=0 means input file is one time-constant field and
4046        genperiod=-12 means input file contains 12 monthly means
4047    o CG2D: use pre-computed solver main-diagonal (stored in common block);
4048      this affects truncation error ; generate new output file for exp. which
4049      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
4050        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
4051        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
4052        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
4053        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
4054        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
4055    o start implementation of deep-atmosphere and anelastic formulation
4056    o verification: remove 2nd copy of input files and use script "prepare_run"
4057      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
4058    o mom_common/vecinv/fluxform: fix a few initialisation isssues
4059    o profiles: fix for multithreaded case
4060    
4061    o diagnostics: rename few diags:
4062      s/'PRESSURE'/'RCENTER '/g
4063      s/'TICE    '/'oceFreez'/g
4064      s/'TAUX    '/'oceTAUX '/g
4065      s/'TAUY    '/'oceTAUY '/g
4066      s/'SWFLUX  '/'oceQsw  '/g
4067      s/DIFx/DFxE/g
4068      s/DIFy/DFyE/g
4069      and add few ocean-forcing diagnostics:
4070      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
4071    o modifications to pkg/seaice/growth.F and budget.F, which change results of
4072      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
4073      as actual snow thickness.  It now refers everywhere to effective snow
4074      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
4075    
4076    checkpoint58r_post (2006/11/17)
4077    o modifications to pkg/seaice/growth.F, which change results of
4078      lab_sea experiment: fixes pertain to melting snow over open water, to
4079      masking EVAP under sea ice, and to using the correct AREA variable for
4080      computations of EVAP, PRECIP, HSNOW, and GHEFF
4081    o add ability to read bathy, salt, and theta using MNC (off by def)
4082    o add flooding algorithm and advection of HSNOW for pkg/seaice;
4083      both are turned off by default and do no change any results
4084    o seaice advection with pkg/thsice: a step toward the use of non-linear
4085      advection scheme, but #ifdef or commented out for now (requires more EXCH).
4086    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
4087      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
4088      in natl_box (affects results @ truncation level: update output.txt)
4089    o multi-threading and IO:
4090      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
4091      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
4092        (needed to work with SingleCpuIO): tested in all verif. exp.
4093    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
4094      affects the results (but none of the verification test uses this scheme).
4095    o Adding some pkg/diagnostics capability to pkg/seaice
4096      (will certainly be subject to changes)
4097    o ctrl: adding new control variables:
4098      lwflux, lwdown, evap, snowprecip, apressure, runoff
4099    
4100    checkpoint58q_post (2006/10/20)
4101    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
4102      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
4103      high_res_cube configuration by 4% on Columbia.
4104    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
4105      add (in global_with_exf/code) a version of EXF_INTERP_READ without
4106      dynamical allocation (seems to work in multi-threaded).
4107    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
4108      single CPU io) so that TAF does not have to see EESUPPORT.h
4109    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
4110    
4111    checkpoint58p_post (2006/09/08)
4112    o obcs: stop if obcs is used with useCDscheme = .true.
4113    o shelfice:
4114     - fix a sign error so that no slip at shelfice interface works
4115     - remove stop for combination non-hydrostatic code and shelfice. That does
4116       not mean, that the results are correct, but at least they are numerically
4117       stable
4118    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
4119    o added adjoint exch routined for all exch*3d* routines
4120      and updated flow directives
4121    
4122    checkpoint58o_post (2006/08/28)
4123    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
4124      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
4125    o change controling S/R for writing pickup file (new S/R do_write_pickup)
4126      and clean-up reading/writing of pickup files.
4127    o fix local version of read/write pickup (NH part) in rotating_tank/code
4128    o simplify EXCH interface:
4129     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
4130     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
4131    o added the regrid package
4132    o shelfice:
4133     - add a simple boundary layer scheme to reduce noise
4134     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
4135    
4136    checkpoint58n_post (2006/08/14)
4137    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
4138       local variable (not in common block).
4139    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
4140      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
4141      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
4142        to work with SingleCpuIO.
4143    o add "_d 0" to real constant of pkg/cfc subroutines ;
4144       update exp. cfc_exemple & tutorial_cfc_offline output files.
4145    o multi-threading and IO:
4146      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
4147        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
4148      - barrier before and after reading.
4149      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
4150      - avoid using MDS_WRITELOCAL for LAND pkg output.
4151      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
4152        common-block variables ; Allows multi-threading with master-thread IO.
4153    o change default MAX_NO_THREADS from 32 to 4 ;
4154      and stop cleanly when MAX_NO_THREADS is too small.
4155    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
4156    
4157    checkpoint58m_post (2006/07/17)
4158    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
4159       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
4160    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
4161       keep global_ocean.90x40x15 (for AD testing) with former secondary test
4162       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
4163    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
4164        add MITgcm_tutorials (= code + all the tutorials)
4165    o ecco, option to compute cost for total ssh (mean+anom)
4166    o consistent with addition of ptracer and ssh in pkg/profiles
4167    o profiles: adding ptracer and ssh
4168    o testreport: change multi-test output-file name
4169      (from output.txt.{name} to output.{name}.txt)
4170    o profiles: now ok for mutli-tiles case
4171    o seaice: add 4 parameters for different advection schemes for area,
4172      (effective) seaice thickness, enthalphy, and snow height. Their default
4173      is the standard parameter SEAICEadvScheme
4174    o calc_gw:
4175     - add cosFacU in zonal viscous flux (harmonic.visc.).
4176     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
4177       of tutorial_plume_on_slope.
4178    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
4179    o calc_gw: true flux-form, account for horizontal grid spacing.
4180      update rotating_tank results, but not plume_on_slope (affected at
4181      truncation level, 11 digits).
4182    
4183    checkpoint58l_post (2006/07/12)
4184    o calc_gw:
4185     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
4186     - remove side-drag for now (need to fix it); update plume_on_slope results.
4187     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
4188    o commit code to make SST/SSS weights spatially variable
4189      (based on either variable in-situ or variable initial T/S weights)
4190    o pkg/ecco:
4191      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
4192        now based on horizontally varying weights wthetaLev, wsaltLev
4193      * cost_averagesflags now returns year indices in addition to day, month
4194      * sflux balance is performed on annual basis
4195        (sflxumm, sfluxmm2, bal_sfluxmm)
4196      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
4197        including separate counting and multipliers
4198    o pkg/rbcs
4199      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
4200    
4201    checkpoint58k_post (2006/07/06)
4202    o testreport:
4203     - always build in dir. "build" (if not there, mkdir build instead of building
4204       & running in input)
4205     - run in dir run (if it exists), in build otherwise.
4206     - call prepare_run (if input/prepare_run exists)
4207     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
4208    o pkg/exf modifications to interpolation and rotation routines for more
4209       reasonable treatment of North Pole singularity: for tracers North Pole
4210       value is set to northernmost zonal-mean value, for zonal velocity it is
4211       set to zero, and for meridional velocity it is set to northernmost value.
4212    o pkg/exf/exf_check_range.F
4213     - add tile index to diagnostics and move stop statement to the very
4214       end of the routine.
4215    o pkg/diagnostics: (diagnostics_main_init.F)
4216      define title of isomorphic variables according to the current config.
4217    o pkg/thsice with pkg/seaice dynamics:
4218    - fix domain of computation (interior only, required for exf) and do exchanges
4219    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
4220    o towards a standard way of dealing with multi-threading in MONITOR
4221      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
4222    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
4223       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
4224    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
4225    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
4226    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
4227       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
4228    o tracer advection:
4229     - clean-up and simplify calc_common_factors.F
4230     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
4231       advection subroutine (but still not used within DST advection S/R)
4232    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
4233    
4234    checkpoint58j_post (2006/06/15)
4235    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
4236      from file (collects calls previously in FORWARD_STEP)
4237    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
4238    o adjoint store dir. adjusted accordingly
4239    o genmake2
4240      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
4241    
4242    checkpoint58i_post (2006/06/14)
4243    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
4244      on wind stress (SEAICEstressFactor defaults to 1.)
4245    o Total number of Timers is finite (<=40): comment out 2 non-essential one
4246      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
4247    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
4248      on CS-grid: no longer loosing mass.
4249    o exf & curvilinear-grid: no longer modify longitude xC & xG.
4250    o pkg/ggl90: fix sloppy output and fix a bug
4251    o pkg/seaice: added SEAICEuseEVPpickup parameter
4252      - Set to false in order to start EVP solver with
4253        non-EVP pickup files when using SEAICEuseEVP
4254      - fix sign error in diffusion in seaice_calc_rhs
4255    
4256    checkpoint58h_post (2006/06/07)
4257    * Modifications for bottom topography control
4258      o replace hFacC by _hFacC at various places
4259      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
4260      o add non-self-adjoint cg2d_nsa
4261      o update autodiff support routines
4262      o re-initialise hfac after ctrl_depth_ini
4263      o works for 5x5 box, doesnt work for global_ocean.90x40x15
4264    * Adding verification for 5x5 box (4-layer) bottom topography control
4265    
4266    checkpoint58g_post (2006/06/07)
4267    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
4268       used for mean seasonal cycle, mean diurnal cycle); add an example
4269       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
4270    o pkg/ggl90:
4271      - add parameter (minimum surface kinetic energy)
4272      - fix bug (avoiding division by zero)
4273    o couple pkg/thsice to pkg/seaice:
4274      - modify advection in seaice to accomodate new scalar fields to be advected
4275      - only muliDimAdection scheme work with seaice/thsice
4276      - mapping of thsice-variables to seaice-variables, back and forth
4277      - does not break the verification experiments, but does not give the
4278        desired results either
4279    o pkg/seaice
4280      - make (default) second order advection a bit less confusing?
4281    
4282    checkpoint58f_post (2006/06/05)
4283    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
4284      to pkg/seaice):
4285      - new routines thsice_map_exf and thsice_get_exf provide the interface
4286      - add an additional formal parameter to thsice_solve4temp
4287    o pkg/exf:
4288      - add new fields wspeed, snowprecip (to be able to couple to thsice)
4289      - correct Stefan-Boltzmann constant
4290      - new parameter for longwave surface emittance
4291      - separate some stuff from exf_bulkformulae into new routines  
4292        exf_radiation, exf_wind
4293      - add new parameters and constants: longwave emissivity for ocean, ice
4294        and snow, evaporation parameters over ice
4295      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
4296        either wind from stress or stress from wind
4297    o pkg/thSIce:
4298    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
4299    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
4300       and THSICE_CALC_THICKN
4301    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
4302    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
4303      to make debugging easier.
4304    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
4305    o pkg/bulk_force:
4306      - clean-up comments and parameters ;
4307      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
4308    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
4309      generate new output for test-experiment: aim.5l_cs.thSI
4310    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
4311      testreport accordingly
4312    
4313    checkpoint58e_post (2006/05/17)
4314    o SEAICE_CGRID adjoint done
4315    o R_STAR adjoint implemented.
4316      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
4317      * need to sort out init. of h0facc, etc.
4318    o Make pkg/profile fully independent of ecco,cost, etc. stuff
4319      to be able to use it in pure forward.
4320    
4321    checkpoint58d_post (2006/04/21)
4322    o upgrade simple test-experiment to tutorial example:
4323     step.1: duplicate the experiment and (step.2) will remove the old copy.
4324      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
4325      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
4326      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
4327      tutorial_global_oce_biogeo    <- copy of dic_example
4328      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
4329      tutorial_plume_on_slope       <- copy of plume_on_slope
4330      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
4331      tutorial_global_oce_optim     <- empty for now (David ?)
4332      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
4333     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
4334    o correct a sign problem in cost_scat.F
4335    o obcs and ptracers: fix boundary conditions for advections schemes
4336      with larger stencil
4337    o thsice adjoint: start
4338    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
4339      completeness
4340    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
4341      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
4342    o ptracers adjoint:
4343      * avoid extensive recomputatations
4344      * fix missing re-init. of gptr (missed by TAF)
4345    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
4346      me to turn off the excessive output to STDOUT that this package produces
4347    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
4348      and add those terms in Vector-Invariant formulation.
4349    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
4350      if the control period (xx_hfluxperiod etc) is 0
4351    o in profiles pkg, clean routines and fix details
4352    o in ecco pkg, reading ssh data:
4353      fix problem in case the model does not start at iter0=0
4354    o fix mnc-pickup/restart for ptracers
4355    o new package prifiles:
4356      code to compute profile-based cost by Gael Forget
4357      (modifs in ecco, ctrl, autodiff)
4358    o Benign bug fix in initialization (spotted by M. Mazloff) of
4359      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
4360    
4361    checkpoint58c_post (2006/03/23)
4362    o adjoint: finish NLFS adjoint and provide reference output in
4363      verification/global_ocean.90x40x15/results_ad_nlfs
4364    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
4365      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
4366      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
4367      with SEAICE_CGRID defined.
4368    o move calendarDumps from "data" to "data.cal" and clean-up the code
4369      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
4370    o add useEXF & useCAL flags (for now, set in hard-coded way)
4371    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
4372      (were missing in NH mode, and wrong in quasihydrostatic mode).
4373      waiting for Chris updated version of calc_gw to add those CALLs.
4374    o fix bug in quasihydrostatic S/R ;
4375      add a test for this option: global_ocean.90x40x15.qshyd
4376    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
4377      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
4378    o add on/off flag useOffLine for package OFFLINE
4379    o seaice:
4380      - modify advection so that it works also on the C-grid
4381      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
4382        problem in multi-tile runs with C-grid
4383      - add flags for clipping ice velocities and/or masking solver forcing
4384      - fix drag (ocean on ice) formulation and a bug that caused noise in the
4385        C-grid solver
4386      - added a few comments to seaice_diffusion.F
4387      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
4388        are now exclusive)
4389      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
4390        required re-ordering the code a little:
4391       + make DAIRN global variable (defined in SEAICE)
4392       + move computation of the viscosities eta and zeta into a new separate
4393         routine (because I need to recompute them in seaice_ocean_stress.F)
4394    
4395    checkpoint58b_post (2006/03/13)
4396    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
4397      update output.txt of exp. aim.5l_cs.thSI
4398    o various mnc cleanups and improvements:
4399      + shrink lookup tables by factor of ~4
4400      + better error reporting when running out of lookup space
4401      + able to handle longer path/file names (up to 500 chars)
4402    o adjoint:
4403      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
4404      - TBD: "hidden" mom_vecinv recomp. in dynamics
4405    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
4406     (allow to differentiate between forcing components using new integer flags:
4407      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
4408     and add new flag to put Dissipation tendency out of Adams-Bashforth.
4409    o ecco
4410      - enable trend removal from SSH anomaly obs.
4411    o adjoint
4412      - a fix for PmEpR when #undef EXACT_CONSERV
4413      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
4414      - try to fix "hidden" recomp. in forward_step for NLFS
4415        (NLFS seems broken sometimes after I checked it in)
4416    o seaice:
4417     - add c-grid version of the dynamic solver:
4418       + three new routines that are the c-grid substitute lsr, dynsolver
4419         and ostres
4420       + put a few fields that were local to dynsolver into global common
4421         blocks, so that I can move the computation of stresses etc into
4422         seaice_lsr (saves coding but may break the adjoint).
4423     - replace more hardwired parameters by runtime parameters
4424     - add ice masks that mask the rhs of the implicit solvers where there
4425       is no ice (commented out in seaice_dynsolver, because i am not sure
4426       if this works properly), eventually this should replace the clipping
4427       of ice velocities in seaice_dynsolver to +/-40cm/s.
4428    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
4429      include it only where its needed
4430    o move balancing of fluxes before the call of external_forcing_surf
4431    o seaice:
4432      - correct units of turning angles (now they are really in degrees)
4433      - move computation of GWATX/Y out of main routine into dynsolver
4434      - initialize GWATX/Y in seaice_init
4435    o Apply mask on Fresh-Water flux (needed for SSH forcing).
4436      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
4437    o seaice: add runtime flags for turning angles (default to zero)
4438    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4439      and trend from exf forcing and ctrl control adjustments
4440    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
4441      (since checkpoint57x_post)
4442    o change the default rotation period to 86164.s = the Earth rotation
4443    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
4444      and based on a reference stratification. Tested within hs94.cs-32x32x5.
4445    o seaice advection: add code for choosing between the default (2nd order
4446      central differences) and multiDim advection schemes provided by
4447      pkg/generic_advdiff
4448    o seaice:
4449      - removed all references to SEAICE_GRID.h fields from
4450        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
4451        (cubed-sphere configuration will change a little)
4452      - grid computations in seaice_init are obsolete now.
4453      - cleaned up code a little so that is easier to read (hopefully).
4454      - added new (better?) discretizations of default advection and diffusion
4455        (turn on with SEAICEuseFluxForm)
4456      - replace 1 in 3d global fields by kSurface in growth.F
4457      
4458    checkpoint58a_post (2006/02/13)
4459    o seaice:
4460      - bug fix in advect.F
4461    o shelfice:
4462      - separate shelfice load anomaly from pload (breaks with time
4463        dependent forcing), => introduce constant field shelficeLoadAnomaly.
4464        Its default is 0., but it may be computed more cleverly from (unknown)
4465        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
4466        done offline. A good approximation of the pressure load anomaly is
4467        necessary to avoid large initial adjustment processes underneath
4468        deep-reaching shelfice.
4469      - small fix in ISOMIP shelfice_thermodynamics
4470      - add more sophisticated thermodynamics of Hellmer (1989), this is
4471        now the default
4472      - give a few constants more intuitive names
4473    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
4474      if bulk formulae are used in long integration (especially EmPmR). Turn
4475      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
4476      if balancePrintMean, the imbalance that is substracted is printed to
4477      STDOUT.
4478    o fix bug (typo) in obcs_apply_eta.F
4479    o add a new package shelfice which enables us to model the circulation
4480      underneath shelf-ice with draughts of hundreds of meters.
4481     - works
4482     - to do: + include improved thermodynamics
4483              + check whether kSurfC (from model/inc/SURFACE.h) can be used
4484                instead of new field kTopC
4485              + can we use topoFile, Ro_surf and existing code in ini_depth.F
4486                instead of new field R_shelfIce and new code in ini_depth.F
4487                and ini_mask_etc.F?
4488              + adjust vertical mixing schemes?
4489    o seaice pkg:
4490     - add a cpp-flag to include a simple formula for a salinity dependent
4491       freezing point of sea water at the surface
4492     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
4493       meridional stresses are now different (and hopefully correct)
4494    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
4495       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
4496       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
4497    o pkg/diagnostics: add options and parameters for regional-statistics
4498       diagnostics ; define regions by reading a region-mask from a file
4499       (might add other options later)
4500    o pkg/bulk_force:
4501     - add option and parameters to use AIM surface-flux formulae.
4502     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
4503       others forcing fields (defined in PARM05, parameter file "data") are loaded
4504       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
4505     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
4506     - use the right EXCH call for uwind,vwind (to work on CS-grid).
4507     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
4508       and parameters (note: calcWindStress replaces .NOT.readwindstress).
4509     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
4510    
4511    checkpoint58 (2006/01/12)
4512    o add "--embed-source" option to genmake2 which, when the supporting
4513      tools can be compiled (as determined by genmake2) will turn on the
4514      embed_files package which then embeds the entire MITgcm source code
4515      (*.[fFhc] + Makefile) used for the build within the executable
4516      - requested by CNH but off by default
4517      - adds a paltry <9MB to the mitgcmuv executable in most cases
4518      - only writes the output when useEMBEDSRC in eedata is true
4519    o clean up 3-dim. relaxation codes:
4520      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
4521      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
4522      * Thanks to Tom Haine for testing!
4523    
4524    checkpoint57z_post (2005/12/31)
4525    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
4526      affects output (@ truncation level) of exp. plume_on_slope ; updated.
4527    o fix the pickup behavior for obcs in combination with ptracers
4528    o fix a bug in ptracers_external_fields_load
4529    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
4530      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
4531    o transfered surface NH pressure to eta field (if exactConserv).
4532    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
4533         and update lab_sea output.txt file.
4534    o completing 3-dim. relaxation code: additional term
4535         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
4536      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
4537      * At compile time, in "EXF_OPTIONS.h" set
4538          #define  ALLOW_CLIMTEMP_RELAXATION
4539          #define  ALLOW_CLIMSALT_RELAXATION
4540      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
4541          tauThetaClimRelax3Dim = 15552000.0,
4542          tauSaltClimRelax3Dim  = 15552000.0,
4543      * 3 cases:
4544          1) Use a constant-in-time 3-dim. field
4545          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
4546          3) Real-time relax. to time-evolving prescribed field
4547    o Adding Laplacian-type smoothness constraint on
4548      initial and boundary (forcing) controls (ic, bc)
4549      * enable at compile-time via
4550        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
4551      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
4552      * Absolute scale somewhat unclear so far
4553      * no area weighting was included since no other cost term does so far
4554    
4555    checkpoint57y_post (2005/12/08)
4556    First step for a NLFS adjoint
4557    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
4558    o new init. routines for calc_r_star, calc_surf_dr
4559    o still need to deal with ini_masks_etc
4560    o testreport seemed happy
4561    checkpoint57y_pre (2005/12/08)
4562    
4563    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
4564    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
4565    o add new offset feature to offline pkg (plus minor cleanup)
4566    o cfc fixes for final year of integration
4567    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
4568      be in GCHEM_OPTIONS).
4569    
4570    checkpoint57x_post (2005/12/04)
4571    o fix testreport Pb in multiple test experiment.
4572    o cleanup our namelist syntax in verification:
4573      - make it more F95 standards compliant (some work still needed)
4574      - allows the vast majority of our tests to work with gfortran
4575    o Non-Hydrostatic:
4576     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
4577     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
4578    o Allow to apply AB on T,S rather than on AB(gT,gS):
4579     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
4580     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
4581       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
4582     - need a "clever" read_pickup to restart from the other AB formulation
4583    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
4584    o remove some unused variables (reduces number of compiler warnings)
4585    o adjoint
4586      * Disable useVariableViscosity for adjoint for time being
4587        (there are a number of extensive recomputations)
4588      * Initialize certain variables needed for adjoint
4589    
4590    checkpoint57w_post (2005/11/03)
4591    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
4592                 fix the singleCpuIO RS version of MDSWRITEFIELD
4593       and add a WARNING if using globalFiles=T with multi-processors.
4594    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
4595      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
4596    o tracer advection scheme:
4597      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
4598       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
4599       was not very convenient).
4600      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
4601       (further tests needed for the implicit DST & Flux-Limiter schemes).
4602    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
4603      and sRef for convenience, handy, when you want to initialize
4604      ptracers in a large domain with a constant non-zero value. Also,
4605      untangle ptracers_init.F a little.
4606    
4607    checkpoint57v_post (2005/10/13)
4608    o change dome exp. to use variable viscosity in side-drag terms.
4609    o remove all the files from the cfc_offline test since they are now
4610      incorporated into tutorial_cfc_offline which has been producing
4611      identical results for a few days of testing
4612    o add new parameter: sideDragFactor to enable half-slip-side BC
4613      and change side-drag S/R to use viscosity from mom_calc_visc
4614      (can switch back by setting sideDragFactor=0.); affects results at
4615      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
4616       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
4617    o vorticity & strain are now computed without masking, to account for
4618      no-slip-side BC in variable viscosity calculation ; mask is applied
4619      anyway later on, before computing advection/coriolis terms.
4620    o modify exp4 to test new obcs support for reading from external files
4621      and for passive tracers
4622    o fix behavior of ptracers_monitor when monitor output is written to a
4623      netcdf-file; still not independent of monitor.F (writes in the same
4624      file).
4625    o change default value of tRef (put a uniform, meaningful value for ocean
4626      & atmos) and initialize sRef (was missing, as Martin mentioned).
4627    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
4628      to be proportional to enstrophy dissipation length.  Thus,
4629       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
4630      This is now consistent with Smagorinsky and with the manual.
4631    
4632    checkpoint57u_post
4633    o OBCS and PTRACERS: add open boundary support for passive tracers
4634      - either use homogenous (pseudo) v.Neumann conditions or prescribe
4635        OB-values from file; this is not different from the way theta and salinity
4636        are treated
4637      - however, Orlanski-radiation conditions are not supported, and the model
4638        will stop if you use pTracers and Orlanski at the same time.
4639      - beefed up the rountine obcs_external_fields_load: now only those open
4640        boundary values are overwritten with values from files for which there
4641        are really files, otherwise the OB-fields remain untouched. This makes
4642        it possible to use different OBs at different ends of the domain (as
4643        with EXF)
4644    o reduce number of exch calls in shap_filt (s2).
4645    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
4646      truncation level) 4/5 MLAdjust test results (11&12 digits match).
4647    
4648    checkpoint57t_post (2005/10/03)
4649    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
4650    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
4651      same truncation, independent of the face number: affects affects several
4652      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
4653    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
4654      note that biharmonic viscosity + no-slip was not tested in any experiment.
4655    o fix bug in non-linear free-surf side-drag ; generate new output for
4656      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
4657    o make mnc honor the writeBinaryPrec flag for most kinds of output
4658    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
4659    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
4660      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
4661    o add brackets in multi-terms sum to get same truncation, independent of
4662      the face number (manage to get exactly same value of gU,gV at the cs-edge)
4663      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
4664    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
4665      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
4666      a maximum grid-scale Reynolds number.  Also, changes all length calculations
4667      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
4668      Suggested values of viscosity parameters found in mom_calc_visc.
4669      Many new viscosity diagnostics available.
4670    
4671    checkpoint57s_post (2005/09/20)
4672    o Add clearing-house for viscosity calculations, mom_calc_visc and
4673      correct numerous bugs in LeithD and Smagorinsky discretizations.  
4674      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
4675      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
4676      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
4677      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
4678      The Strain-Tension form is now called with useStrainTensonVisc=.true.
4679      ViscAhStrain and viscAhTension are now retired.
4680    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
4681    o In response to JMC's bug report, genmake2 now ignores any soft-links
4682      that it finds in the *current* directory when searching for files.
4683      Soft-links found in any other source directories will still work as
4684      they did before.
4685    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
4686      a C routine to unlimit the stack size
4687    o mnc-ify pkg/aim snapshot vars
4688    o mnc-ify pkg/land as requested by Daniel
4689    o various changes to mnc including:
4690      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
4691      - output can now be grouped so that all files within a group
4692          change the ITER portion of their names in lock-step together
4693      - can now read ("global") PER-FACE (in addition to PER-TILE) files
4694          and works with both EXCH1 and EXCH2 (but needs more testing)
4695      - writing works for all verification test cases w/ g77 on Linux
4696    
4697    checkpoint57r_post (2005/09/07)
4698    o make MNC variable initialization happen earlier
4699    o add diagnostics for (almost) each term of the momentum Eq.
4700    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
4701    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
4702    o remove MINIMAL_TAVE_OUTPUT option ;
4703      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
4704    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
4705      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
4706    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
4707    o add time-dependent SST, SSS control
4708    o cost terms in ecco/ modularized (new cost_generic.F)
4709    o cost_averages routines are modularized (new cost_averagesgeneric.F)
4710    o new infrastructure for seaice model vs. obs misfits in seaice/
4711      * driver from the_main_loop.F is seaice_cost_driver.F
4712      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
4713      * gradient check in Exp. 6a of natl_box_adjoint/
4714    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
4715      (see README file)
4716    
4717    checkpoint57q_post (2005/08/19)
4718    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
4719    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
4720      - bug was reported by Jean-Michel and Ian Fenty
4721    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
4722      update exp. cpl_aim+ocn output.
4723    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
4724      Needed for high-res. runs with large global files
4725      to be able to limit tapelev size
4726    o Changed some tests for adjoint:
4727      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
4728      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
4729      * global_ocean.90x40x15/ back to default 3-level checkpointing
4730    o Modifications to enable scripted COMMON to MODULE conversion
4731      * verification/OpenAD/code/ has necessary scripts and description;
4732      * converts, compiles and runs successfully;
4733    
4734    checkpoint57p_post (2005/08/01)
4735    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
4736    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
4737      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
4738    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
4739    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
4740      (was already the case for dissipation with mom_vecinv,
4741       and also the case for grad.PhiHyd when staggered-timeStep)
4742      This will allow to put dissipation out-off the AB time-stepping.
4743     Unfortunately, affects truncation error. Update output of exp. that "fails"
4744      (cg2d matching number) and leave the others for later: front_relax(10),
4745      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
4746      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
4747    
4748    checkpoint57o_post (2005/07/30)
4749    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
4750      (2) its ready to be documented during the 20050801 DocFest
4751    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
4752      for ideal_2D_oce and lab_sea on linux_ia32_g77
4753    o set to #undef CTRL_SET_OLD_MAXCVARS_30
4754      in global1x1_tot/code_seaice_adj to access indices 32, 33
4755      (worth another tag)
4756    
4757    checkpoint57n_post (2005/07/29)
4758    o adding precip control xx_precip 32
4759    o adding swflux control xx_swflux 33
4760    o Replacing 10 forcing penalty cost routines by 1 generic.
4761    o Implementing partitioning in time-mean and variable adjustment
4762      for atmos. state.
4763    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
4764    o in natl_box_adjoint:
4765      * updated exp 1 to 10
4766        (but does not have time-mean vs. variable split results yet)
4767    o updated global1x1/*_seaice_adj/
4768      to incorporate latest changes
4769    o enable useSingleCpuIO for mdsio vector routines
4770      (applies in particular to tapelev I/O)
4771    o removed inefficient K-loop in all active_file*control*.F
4772    
4773    checkpoint57m_post (2005/07/28)
4774    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
4775      and advect_cs (use EXCH-2 and standard cs-32 grid files).
4776    o pkg/exch2: filling of face-corner halo regions is optional
4777      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
4778    
4779    checkpoint57l_post (2005/07/14)
4780     tag before updating tutorials (pre-release-2)
4781    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
4782       for output and interpolation of input fields onto model grid)
4783    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
4784       Affects results of exp. rotating_tank ; update output.txt.
4785    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
4786          and taking the square quantity and/or using a fraction-weight field.
4787    o fix aim_diagnostics_init.F mate numbers.
4788    o add mnc output capability to diagnostics/diagstat and update
4789      our cvsignore files for the ACSII output generated
4790    
4791    checkpoint57k_post (2005/07/02)
4792    o lab_sea now uses diagnostics package and provides a suite of
4793      new EXF diagnostics output.
4794    
4795    checkpoint57j_post (2005/06/30)
4796    o exf
4797      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
4798        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
4799        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
4800      * extended diagnostics output
4801        - now includes all EXF variables
4802        - hs, hl moved to common block
4803        - separate S/R for diagnostics, called after ctrl vector is added
4804        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
4805        - EXFqnet contains true Qnet (i.e. includes qsw)
4806      * updated verif. lab_sea, global_with_exf
4807      * Rearranging hflux (exf_mapfields -> exf_getforcing)
4808        to ensure that diagnostics sees a true EXFqnet
4809    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
4810    o diagnostics pkg: change pointers so that 1 diagnostic can be used
4811      several times with different frequencies.
4812    o mnc-ify the thsice package as requested by Daniel Enderton
4813      - the monitor--MNC output needs work
4814      - many attributes need to be added (most are currently blank)
4815    o mnc-ify theaim_v23 package as requested by Daniel Enderton
4816      - many attributes need to be added (most are currently blank)
4817    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
4818    o add Sadourny like discretization to the 4th.O vorticity advection scheme
4819    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
4820      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
4821         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
4822    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
4823     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
4824    
4825    checkpoint57i_post (2005/06/19)
4826    o Diagnostics package was changed: diagnostic allocation is now deactivated
4827      by setting an empty file name in the namelist (used to be by setting 0 frequency)
4828    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
4829      add 1rst Order upwind vertical Shear.
4830    o add a quick fix for A/B checkpointing in OFFLINE mode
4831    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
4832      end-run around the C/Fortran linking horror in eesup/src/timers.F
4833    o added pkg/runclock: allows user to terminate run based on wall clock
4834    o added non-hydrostatic scaling parameter: nh_am2
4835    o pkg/my82: futile attempt to make results compiler-independent by adding
4836      some "_d 0", etc. no effect.
4837    o for mnc output, fill the 'T' coordinate var with myTime and create a
4838      separate 'iter' variable for iteration count
4839    o pkg/diagnostics:
4840      add new capability: output of Global/Regional & per-level statistics ;
4841      tested against monitor output (including land & thSIce) on various exp.
4842    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
4843    
4844    checkpoint57h_done (2005/05/19)
4845      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
4846      data.diagnostics, data.gchem, data.ptracers) is done.
4847    
4848    o pkg/diagnostics: prepare for Global/Regional statistics.
4849      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
4850    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
4851      and rename it: DIFFERENT_MULTIPLE
4852    
4853    checkpoint57h_post (2005/05/14)
4854    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
4855    o pkg/diagnostics: change output frequency, now in seconds (instead
4856      of Nb of iterations). This requires to change data.diagnostics.
4857    checkpoint57h_pre (2005/05/12)
4858    
4859    o in mnc, let the user create the output dir if both mnc_outdir_date
4860      and mnc_outdir_num are false
4861    o add fflags() to pkg/diagnostics which allows one to specify, on a
4862      per-file basis, the file precision [default behavior is unchanged]
4863    o added diagnostics to pkg/kpp, including computation of mixed layer
4864      depth based on a temperature/density criterion
4865    o updated verification/natl_box to test the new pkg/kpp diagnostics
4866    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
4867    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
4868    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
4869      not mnc -- this mistake was found by JMC and is now corrected
4870    
4871    checkpoint57g_post (2005/04/15)
4872    o add Adams-Bashforth 3rd Order time stepping:
4873      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
4874      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
4875    checkpoint57g_pre (2005/04/15)
4876    
4877    o make lambda[Theta,Salt]ClimRelax spatially varying
4878      (default remains spatially uniform constant based on tau)
4879    o added new control variables
4880      * init. uVel, vVel, etanN
4881      * lambda[Theta,Salt]ClimRelax
4882    o separate masks used for ctrl_pack/unpack 'from write_grid' output
4883      (suggested by G. Forget)
4884    
4885    checkpoint57f_post (2005/04/06)
4886    o add parameter "baseTime" = model base time = time at iteration zero
4887      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
4888      account for baseTime shift
4889    o move Coriolis arrays from PARAMS.h to GRID.h
4890    checkpoint57f_pre (2005/04/06)
4891    
4892    o mnc-ifying the seaice package
4893    o introduced an alternative length scale calculation for use in the limiting
4894      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
4895    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
4896    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
4897      as well as grad(vort3).  Made it compatible with both approximate form
4898      for the cubed sphere and full form of these gradients.  Added flag
4899      useFullLeith to select between approximate and full form.  
4900    o add "d0" in getcon.F to reduce differences between compilers/platforms
4901      update output.txt of exp. fizhi-gridalt-hs
4902    o change port_rand funtion to allow to set the seed.
4903    o fix obscure MNC bug involving conversion between reals and integers
4904      - it caused no problems with certain (eg. gcc, ifc) compilers but the
4905        new version is now more standards-compliant
4906    o adjoint-related modifications
4907      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
4908      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
4909      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
4910    
4911    checkpoint57e_post (2005/02/28)
4912    o Adding eddy stress controls a la Ferreira et al.
4913    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
4914    
4915    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
4916      update output.txt of exp. fizhi-gridalt-hs
4917    o add more "Z" dimensions and associated coordinate vars to MNC
4918    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
4919    o parameter calendarDumps: when set, approximate months (30-31 days) and years
4920      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
4921      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
4922      months and years.  Requires pkg/cal.
4923    o diagnostics: add pickup functionality
4924      - off by default for backwards compatibility
4925      - current version only uses MDSIO -- MNC will be added
4926    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
4927    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
4928    
4929    checkpoint57d_post (2005/02/11)
4930    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
4931    o modify verification/ideal_2D_oce so that it tests the creation of mnc
4932      output from the diagnostics package
4933    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
4934    o make genmake2 more portable by using ".$FS" instead of ".f" for more
4935      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
4936    o add coordinate variables to the MNC output from the diagnostics package
4937    o change MNC-flags default value: true when useMNC=TRUE
4938    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
4939      the ability (off by default) to read the grid information using MNC
4940    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
4941    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
4942    o do snap-shot diagnostics at the middle of the time-interval (instead of
4943      at the end).
4944    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
4945      new test for AIM with thSIce + slab-ocean
4946    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
4947    o move state variable diagnostics to the beginning of the time step ;
4948      (note: still needs some work specially for snap-shot diagnostics)
4949      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
4950    
4951    checkpoint57c_post (2005/01/27)
4952    o Change testing option (-ieee) to get closer agreement between g77 & ifort
4953    o generate new output.txt files on faulks with g77 & the new -ieee option
4954    checkpoint57c_pre (2005/01/27)
4955    
4956    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
4957      update output.txt of exp. global_ocean.90x40x15
4958    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
4959      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
4960    o add saltFlux(+File) forcing capability with periodicExternalForcing
4961    o allow to use pkg diagnostics for GM-Redi & ThSIce output
4962    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
4963    o improvements for the MNC output from DIAGNOSTICS:
4964      - correct handling of the unlimitied dimension
4965      - all dims now have associated coordinate variables
4966      - variables located at U, V, and Corner ("Z") points are now written
4967        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
4968        *all* data points are output
4969    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
4970    o added pkg/seaice/seaice_monitor.F
4971    o mdsio_readfield.F can now read files visible only to master MPI process.
4972    o pkg/seaice: some test code for ice-modified ocean stress
4973    o exf_getffields interpolation defaults to bilinear for all scalar forcing
4974      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
4975      spurious negative numbers for precipitation and humidity.  Will cause
4976      some small numerical differences for integrations using pkg/exf/exf_interp.F.
4977    o pkg/ctrl/
4978      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
4979        May be enabled via doPackDiag
4980      *  introduce z-scaling of
4981         + gradient (doZscalePack) and
4982         + control (doZscaleUnpack)
4983    o pkg/mdsio/
4984      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
4985      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4986    
4987    checkpoint57b_post (2004/12/20)
4988    o simplify options in diagnostics_fill arguments (remove weird combinations)
4989    o fix MNC coordinate variables so that they now contain per-face index
4990      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
4991      general, EXCH2 grids are only aligned to a "local" coordinate system
4992    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
4993    o Implement instantaneous output within pkg diagnostics:
4994      setting a negative frequency in data.diagnostics produces
4995     "snap-shot" output (as opposed to time-average if freq > 0)
4996    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
4997      NOTE: change ptracer diagnostics name: use 2 characters to work with
4998            more than 9 tracers. Add also diagnostics of advect & diffus flux.
4999    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
5000      becomes the coordinate variable for the 'T' dimension
5001    o add CF-style coordinate variables to MNC
5002      - just a first cut:  numbers are meaningless on the cubesphere and
5003        missing along the T axis but otherwise it works!
5004    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
5005    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
5006    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
5007      this is based directly on what the model compute, so that the content of
5008      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
5009    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
5010    o clean up build options files for SunOS, in particular
5011      - remove -traditional from xmakedepend
5012      - change -xarch=v9 to -xarch=native for f77
5013      - restore use of make (not gmake)
5014      - add CC=gcc if using g77
5015    o changes per discussion of AM, JMC, & EH3 today:
5016      - move redundant "grid" variables out of "state" -- in preparation of
5017        creating proper CF-style coordinate variables and in recognition
5018        that any/all grid variables can be easily copied (eg. w/NCO) from
5019        the grid files into any of the other NetCDF files
5020      - *always* output grid variables with MDSIO (this will eventually be
5021        changed)
5022      - output MNC grid file if useMNC is true
5023    o every instance of _END_MASTER() has been found and replaced with
5024      _END_MASTER( myThid ) in order to satisfy certain picky Sun
5025      preprocessors
5026    o re-arrange diagnostics pkg initialisation:
5027     - allow each package to extend the available diagnostics list
5028     - add some checking and fix small problems (multi-threaded, ...)
5029     - new S/R diagnostics_fill (replace fill_diagnostics):
5030       look through the short list of active diag. (instead of the long list)
5031       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
5032    
5033    checkpoint57a_post (2004/12/10)
5034    o this set of changes restores TAMC compatibility
5035      tested for global_ocean.90x40x15 adjoint on trough
5036      (what a pain)
5037    
5038    checkpoint57a_pre (2004/12/10)
5039    o some modifs in tools/build_options for sunos
5040    o call ctrl_pack for ctrl at end for optimcycle=0
5041    
5042    checkpoint57 (2004/12/09)
5043    o add horizontal bi-harmonic viscosity for vertical velocity
5044      - new parameter viscA4W (defaults to viscA4)
5045      - affects only non-hydrostatic code
5046      - to be done: no-slip lateral boundary conditions
5047    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
5048    o implement Implicit Vertical advection for pTracers
5049  o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)  o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
5050    (implemented also for implicit vertical diffusion & advection)    (implemented also for implicit vertical diffusion & advection)
5051  o OBCS: extend application of tracer open boundary conditions  o OBCS: extend application of tracer open boundary conditions
# Line 11  o add call monitor to TAF set of require Line 5054  o add call monitor to TAF set of require
5054    and include in natl_box_adjoint    and include in natl_box_adjoint
5055  o untangle a few ifdefs related to cost, ctrl, autodiff  o untangle a few ifdefs related to cost, ctrl, autodiff
5056    untangel a few ALLOW_ECCO_OPTIMIZATION    untangel a few ALLOW_ECCO_OPTIMIZATION
5057    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
5058      (theta2, salt2 in ecco_cost_weights)
5059    
5060  checkpoint56c_post  checkpoint56c_post (2004/12/03)
5061  o OBCS as control variables  o OBCS as control variables
5062    - update ctrl_ad_diff.list, obcs_ad_diff.list    - update ctrl_ad_diff.list, obcs_ad_diff.list
5063    - remove balance of obcs controls from default    - remove balance of obcs controls from default
# Line 30  o exf: Line 5075  o exf:
5075  o mdsio:  o mdsio:
5076    - i/o-vector change debugLevel from debLevA to debLevB    - i/o-vector change debugLevel from debLevA to debLevB
5077    
5078  checkpoint56b_post  checkpoint56b_post (2004/12/01)
5079  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that  o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
5080    is called from DO_THE_MODEL_IO    is called from DO_THE_MODEL_IO
5081    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE    - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
# Line 45  o testreport previously did a lousy job Line 5090  o testreport previously did a lousy job
5090    testreport.    testreport.
5091  o ptracers_monitor: bug fix for MPI  o ptracers_monitor: bug fix for MPI
5092    
5093  checkpoint56a_post  checkpoint56a_post (2004/11/28)
5094  o GCHEM: finish reorganizating the package  o GCHEM: finish reorganizating the package
5095    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency    - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
5096      (introduces another 3D-array for each passive tracer, but only if      (introduces another 3D-array for each passive tracer, but only if
# Line 90  o GCHEM: Line 5135  o GCHEM:
5135    - cleaning up    - cleaning up
5136  o small cleaning of exch2: remove files that are also in eesupp/src  o small cleaning of exch2: remove files that are also in eesupp/src
5137    
5138  checkpoint56  checkpoint56 (2004/11/17)
5139  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0  o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
5140  o mnc: cleanup "full" files--fixes out-of-memory problem  o mnc: cleanup "full" files--fixes out-of-memory problem
5141  o ECCO-GODAE  o ECCO-GODAE
# Line 120  o mdsio: filename info to both stderr, s Line 5165  o mdsio: filename info to both stderr, s
5165  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]  o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
5166    from sign change    from sign change
5167    
5168  checkpoint55j_post  checkpoint55j_post (2004/11/10)
5169  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.  o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
5170    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5171  o add consistent build directories and .cvsignore files to verification  o add consistent build directories and .cvsignore files to verification
# Line 131  o make all subroutines 30 or less charac Line 5176  o make all subroutines 30 or less charac
5176  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;  o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
5177    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)    affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5178    
5179  checkpoint55i_post  checkpoint55i_post (2004/10/28)
5180  o change arrays for total vertical diffusivity (2.D if explicit,  o change arrays for total vertical diffusivity (2.D if explicit,
5181    3.D if implicit) ; each ptracer uses its own background value.    3.D if implicit) ; each ptracer uses its own background value.
5182  o added mnc/NetCDF output capability to ocn_compon_interf  o added mnc/NetCDF output capability to ocn_compon_interf
# Line 146  o give MNC the ability to create additio Line 5191  o give MNC the ability to create additio
5191  o Compute the non-local term using either KPP vertical diffusivity (=default)  o Compute the non-local term using either KPP vertical diffusivity (=default)
5192     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
5193    
5194  checkpoint55h_post  checkpoint55h_post (2004/10/20)
5195  o add verification test "vermix"  o add verification test "vermix"
5196  o remove all the *_ioinc flags and replace with the single global  o remove all the *_ioinc flags and replace with the single global
5197    outputTypesInclusive flag    outputTypesInclusive flag
# Line 154  o allow to set a vertical profile of ver Line 5199  o allow to set a vertical profile of ver
5199  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS  o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
5200  o useMNC moved from data.mnc to data.pkg  o useMNC moved from data.mnc to data.pkg
5201    
5202  checkpoint55g_post  checkpoint55g_post (2004/10/14)
5203  o Renaming carbon AD experiments to comply with testreport conventions  o Renaming carbon AD experiments to comply with testreport conventions
5204  o Updating adjoint of Held-Suarez hs94.1x64x5  o Updating adjoint of Held-Suarez hs94.1x64x5
5205  o Fixing directives for non-ECCO forward_step, after ECCO directives  o Fixing directives for non-ECCO forward_step, after ECCO directives
# Line 164  o Fixing directives for non-ECCO forward Line 5209  o Fixing directives for non-ECCO forward
5209  o Updating adjoint output for natl_box_adjoint after  o Updating adjoint output for natl_box_adjoint after
5210    pkg/ecco has been modified (see taga c55d_post)    pkg/ecco has been modified (see taga c55d_post)
5211    
5212  checkpoint55f_post  checkpoint55f_post (2004/10/13)
5213  o rename to timeave_init_fixed  o rename to timeave_init_fixed
5214    
5215  checkpoint55e_post  checkpoint55e_post (2004/10/13)
5216  o some delicate re-shuffle of store directives to avoid one  o some delicate re-shuffle of store directives to avoid one
5217    extra call of do_oceanic_physics    extra call of do_oceanic_physics
5218    affects ecco_the_main_loop.F, do_oceanic_physics.F    affects ecco_the_main_loop.F, do_oceanic_physics.F
# Line 175  o some delicate re-shuffle of store dire Line 5220  o some delicate re-shuffle of store dire
5220  o NB: this may break global_ocean adjoint temporarily,  o NB: this may break global_ocean adjoint temporarily,
5221    but it is clear how to fix it. Will do later, need this now.    but it is clear how to fix it. Will do later, need this now.
5222    
5223  checkpoint55d_post  checkpoint55d_post (2004/10/11)
5224  o ECCO specific cost function terms (up-to-date with 1x1 runs)  o ECCO specific cost function terms (up-to-date with 1x1 runs)
5225  o ecco_cost_weights is modified to 1x1 runs  o ecco_cost_weights is modified to 1x1 runs
5226  o modifs to allow observations to be read in as  o modifs to allow observations to be read in as
5227    single file or yearly files    single file or yearly files
5228  o enable to read exf forcing fields as either  o enable to read exf forcing fields as either
5229    single file or yearly files (flag useExfYearlyFields)    single file or yearly files (flag useExfYearlyFields)
5230  checkpoint55d_pre  checkpoint55d_pre (2004/10/08)
5231    
5232  o switch between 2-level and 3-level checkpointing  o switch between 2-level and 3-level checkpointing
5233  o add ability of MNC to write local and "partial" (eg. 2D slices where  o add ability of MNC to write local and "partial" (eg. 2D slices where
# Line 230  o more obcs stuff Line 5275  o more obcs stuff
5275    - changed argument list of OBCS_CALC to myTime+deltaTclock    - changed argument list of OBCS_CALC to myTime+deltaTclock
5276    - fixed about 35 bugs in obcs_external_fields_load    - fixed about 35 bugs in obcs_external_fields_load
5277    
5278  checkpoint55c_post  checkpoint55c_post (2004/09/23)
5279  o obcs stuff  o obcs stuff
5280    - new runtime flags useOBCSprescribe, useOBCSbalance    - new runtime flags useOBCSprescribe, useOBCSbalance
5281    - re-arranged obcs_calc    - re-arranged obcs_calc
# Line 244  o obcs stuff Line 5289  o obcs stuff
5289  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments  o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
5290    which simplifies the calls and passes the ifc check-bounds test    which simplifies the calls and passes the ifc check-bounds test
5291    
5292  checkpoint55b_post  checkpoint55b_post (2004/09/22)
5293  o add a 2D scalar, Z location, exchange_2 routine.  o add a 2D scalar, Z location, exchange_2 routine.
5294  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows  o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
5295    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]    to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
# Line 255  o use a more standard discretization for Line 5300  o use a more standard discretization for
5300  o fix gad_advection.F (CubedSphere part), back to version 1.23  o fix gad_advection.F (CubedSphere part), back to version 1.23
5301  o fix bug in mom_vi_del2uv.F (CubedSphere part).  o fix bug in mom_vi_del2uv.F (CubedSphere part).
5302    
5303  checkpoint55a_post  checkpoint55a_post (2004/09/20)
5304  o merged code to  o merged code to
5305    * prescribe/read time-dependent open boundaries    * prescribe/read time-dependent open boundaries
5306      (works in conjunction with exf, cal)      (works in conjunction with exf, cal)
# Line 263  o merged code to Line 5308  o merged code to
5308    * each boundary N/S/E/W now has its own CPP option    * each boundary N/S/E/W now has its own CPP option
5309      (healthy for the adjoint)      (healthy for the adjoint)
5310    
5311  checkpoint55  checkpoint55 (2004/09/17)
5312  o up-to-date adjoint of previous breaks  o up-to-date adjoint of previous breaks
5313    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix    - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
5314    - global_ocean_ebm: adjoint still needs fix (TLM ok)    - global_ocean_ebm: adjoint still needs fix (TLM ok)
# Line 273  o up-to-date adjoint of previous breaks Line 5318  o up-to-date adjoint of previous breaks
5318  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)  o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
5319    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)    (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
5320    
5321  checkpoint54f_post  checkpoint54f_post (2004/09/16)
5322  o in verification/carbin/ remove experiment related to  o in verification/carbin/ remove experiment related to
5323    ALLOW_PASSIVE_TRACER (array tr1 etc)    ALLOW_PASSIVE_TRACER (array tr1 etc)
5324    code_ad/ input_ad/ results_ad    code_ad/ input_ad/ results_ad
# Line 299  o overhaul of IO so that we now have fla Line 5344  o overhaul of IO so that we now have fla
5344    - numerous small formatting cleanups for ProTeX    - numerous small formatting cleanups for ProTeX
5345  o add version info (via BUILD_INFO.h) to MNC and stdout  o add version info (via BUILD_INFO.h) to MNC and stdout
5346    
5347  checkpoint54e_post  checkpoint54e_post (2004/09/02)
5348  o add two new packages  o add two new packages
5349    - pp81 (Packanowski and Philander, 1981), Richardson number and    - pp81 (Packanowski and Philander, 1981), Richardson number and
5350      stratification dependent mixing      stratification dependent mixing
5351    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
5352    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
5353      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
5354      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
5355  o add offline package  o add offline package
5356  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
5357    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
5358  o genmake2: add ability to search for C compilers and cleanup test output  o genmake2: add ability to search for C compilers and cleanup test output
5359    - fixes recent SX-6 problems and should help with others (eg. HP-UX)    - fixes recent SX-6 problems and should help with others (eg. HP-UX)
5360    
5361  checkpoint54d_post  checkpoint54d_post (2004/07/27)
5362  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed  o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
5363  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,  o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
5364    leading to additional shift by 5 days each year of integration    leading to additional shift by 5 days each year of integration
# Line 329  o fix a bug in Flux deriv. vs Ts (pkg/ai Line 5374  o fix a bug in Flux deriv. vs Ts (pkg/ai
5374  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")  o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
5375  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)  o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
5376    
5377  checkpoint54c_post  checkpoint54c_post (2004/07/18)
5378  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr  o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
5379    this affects (truncation error) output.txt of test-exp:    this affects (truncation error) output.txt of test-exp:
5380     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
# Line 340  o define the max number of passive trace Line 5385  o define the max number of passive trace
5385  o start to test mnc routinely in exp0  o start to test mnc routinely in exp0
5386  o add sea-ice loading (sIceLoad) as a new forcing field.  o add sea-ice loading (sIceLoad) as a new forcing field.
5387    
5388  checkpoint54b_post  checkpoint54b_post (2004/07/08)
5389  o add testreport "-j JOBS" option for parallel builds (tested and pretty  o add testreport "-j JOBS" option for parallel builds (tested and pretty
5390     impressive on Altix and Opteron systems)     impressive on Altix and Opteron systems)
5391  o diagnostics can now write NetCDF files through the mnc package  o diagnostics can now write NetCDF files through the mnc package
# Line 350  o staggerTimeStep & NLFS: rescale T & S Line 5395  o staggerTimeStep & NLFS: rescale T & S
5395    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
5396  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
5397    
5398  checkpoint54a_post  checkpoint54a_post (2004/07/06)
5399  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).  o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
5400  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)  o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
5401  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)  o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
5402  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)  o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
5403    + internal_wave (shift in writing cg2d_ini_res)    + internal_wave (shift in writing cg2d_ini_res)
5404  checkpoint54a_pre  checkpoint54a_pre (2004/07/05)
5405    
5406  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice  o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
5407    - modified verification/lab_sea and natl_box_adjoint accordingly    - modified verification/lab_sea and natl_box_adjoint accordingly
5408    
5409  checkpoint54  checkpoint54 (2004/07/02)
5410  checkpoint53g_post  checkpoint53g_post (2004/07/02)
5411  o prepare splitting of thermodynamics: store convect.counter in common block  o prepare splitting of thermodynamics: store convect.counter in common block
5412  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)  o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
5413    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave    output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
# Line 371  o new parameter "nShapS": allow to treat Line 5416  o new parameter "nShapS": allow to treat
5416  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)  o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
5417  o restore adjointability  o restore adjointability
5418    
5419  checkpoint53f_post  checkpoint53f_post (2004/06/25)
5420  o modifications that affect AIM experiment results (update output.txt):  o modifications that affect AIM experiment results (update output.txt):
5421    - no advection of S at top interface Nr (pkg/generic_advdiff)    - no advection of S at top interface Nr (pkg/generic_advdiff)
5422    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)    - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
# Line 384  o merged cylindrical coord configuration Line 5429  o merged cylindrical coord configuration
5429  o added rotating_tank experiment  o added rotating_tank experiment
5430  checkpoint53e_pre  checkpoint53e_pre
5431    
5432  checkpoint53d_post  checkpoint53d_post (2004/06/14)
5433  o faulks upgraded: re-generate output.txt that have changed:  o faulks upgraded: re-generate output.txt that have changed:
5434     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
5435  o Added Bryan and Lewis, 1979, vertical diffusivity profile  o Added Bryan and Lewis, 1979, vertical diffusivity profile
# Line 403  o regenerated output for global_ocean_eb Line 5448  o regenerated output for global_ocean_eb
5448  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation  o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
5449    of mom_common/    of mom_common/
5450    - simple re-arrangement of instructions within computing loop    - simple re-arrangement of instructions within computing loop
5451  checkpoint53d_pre  checkpoint53d_pre (2004/05/21)
5452    
5453  checkpoint53c_post  checkpoint53c_post (2004/05/21)
5454  o new version of coupler for AIM+thSIce and Ocean models  o new version of coupler for AIM+thSIce and Ocean models
5455   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler   - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
5456   - land: change Evaporation of snow   - land: change Evaporation of snow
# Line 422  o Adjoint of EBM package + verification Line 5467  o Adjoint of EBM package + verification
5467    * TLM OK    * TLM OK
5468    * ADM not sufficient accuracy yet (needs further testing)    * ADM not sufficient accuracy yet (needs further testing)
5469    
5470  checkpoint53b_post  checkpoint53b_post (2004/05/14)
5471  o Commiting new energy balance model to repository  o Commiting new energy balance model to repository
5472    * package is pkg/ebm    * package is pkg/ebm
5473    * verif. is verification/global_ocean_ebm    * verif. is verification/global_ocean_ebm
# Line 440  C        Destabilization of the thermoha Line 5485  C        Destabilization of the thermoha
5485  C        by atmospheric eddy transports.  C        by atmospheric eddy transports.
5486  C        J. Climate 7(12), 1870-1882  C        J. Climate 7(12), 1870-1882
5487  o Will need long integration testing.  o Will need long integration testing.
5488  checkpoint53b_pre  checkpoint53b_pre (2004/05/14)
5489    
5490  o created pkg/mom_common in preparation for variable viscosity code  o created pkg/mom_common in preparation for variable viscosity code
5491  o renamed and split ini_mnc_io  o renamed and split ini_mnc_io
# Line 448  o pkg/land: only liquid water can diffus Line 5493  o pkg/land: only liquid water can diffus
5493  o AIM using land: soil wetness availability account for snow  o AIM using land: soil wetness availability account for snow
5494  o added printMapIncludesZeros to EEPARMS namelist  o added printMapIncludesZeros to EEPARMS namelist
5495    
5496  checkpoint53a_post  checkpoint53a_post (2004/05/11)
5497  o restore TAMC compatiility for exf_constants.h  o restore TAMC compatiility for exf_constants.h
5498    (no usage of _d in .h)    (no usage of _d in .h)
5499  o Additional storing in KPP in an attempt to fix  o Additional storing in KPP in an attempt to fix
# Line 461  o Fixed verification/natl_box_adjoint ex Line 5506  o Fixed verification/natl_box_adjoint ex
5506    and hence gives results closer to that of Experiment 2.    and hence gives results closer to that of Experiment 2.
5507    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.    Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
5508    
5509  checkpoint53  checkpoint53 (2004/05/06)
5510  o stable checkpoint with up to date adjoint  o stable checkpoint with up to date adjoint
5511    TLM tests only run for 1st grdchk at the moment. Its unclear if    TLM tests only run for 1st grdchk at the moment. Its unclear if
5512    this is a code problem or a problem with resetting code for g_    this is a code problem or a problem with resetting code for g_
# Line 471  o stable checkpoint with up to date adjo Line 5516  o stable checkpoint with up to date adjo
5516     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
5517       are both still in chaos following their security messes.       are both still in chaos following their security messes.
5518    
5519  checkpoint52n_post  checkpoint52n_post (2004/05/06)
5520  o various build (mostly genmake2) changes including:  o various build (mostly genmake2) changes including:
5521    - ability to build/run more easily within Cygwin and MacOS X    - ability to build/run more easily within Cygwin and MacOS X
5522    - more complicated Makefiles with a stronger dependence on Gnu Make    - more complicated Makefiles with a stronger dependence on Gnu Make
# Line 502  o fix in pkg/thsice: Line 5547  o fix in pkg/thsice:
5547    - maintain snow precipitation unchanged (even if Tsf >=0).    - maintain snow precipitation unchanged (even if Tsf >=0).
5548   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice   both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
5549    
5550  checkpoint52m_post  checkpoint52m_post (2004/04/18)
5551  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;  o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
5552    this does not change any of the results, because myIter=0 in swfrac always    this does not change any of the results, because myIter=0 in swfrac always
5553    lead to jwtype=2 (the default anyway), but the call makes little sense    lead to jwtype=2 (the default anyway), but the call makes little sense
# Line 534  o test exp. advect_cs: use the standard Line 5579  o test exp. advect_cs: use the standard
5579  o Added functionality to grdchk:  o Added functionality to grdchk:
5580    pick global i,j,k position (or nearest wet) where to perform check.    pick global i,j,k position (or nearest wet) where to perform check.
5581    
5582  checkpoint52l_post  checkpoint52l_post (2004/03/11)
5583  o new land formulation:  o new land formulation:
5584    a) use ground enthalpy as prognostic variable to ensure exact    a) use ground enthalpy as prognostic variable to ensure exact
5585       energy conservation.       energy conservation.
# Line 545  o aim_v23 modification for new land mode Line 5590  o aim_v23 modification for new land mode
5590    a) Treat separately land / ocean / sea-ice surface fluxes    a) Treat separately land / ocean / sea-ice surface fluxes
5591       to allow implicit computation of land & sea-ice surface temp.       to allow implicit computation of land & sea-ice surface temp.
5592    b) add snow precipitation.    b) add snow precipitation.
5593  checkpoint52l_pre  checkpoint52l_pre (2004/03/11)
5594    
5595  o fix problem (when 1 tile is empty) in min/max monitor.  o fix problem (when 1 tile is empty) in min/max monitor.
5596  o fix bug in timeAve (u,vZetatave in common block)  o fix bug in timeAve (u,vZetatave in common block)
# Line 558  o fix ini_curvilinear_grid ; test CS exp Line 5603  o fix ini_curvilinear_grid ; test CS exp
5603  o aim.5l_cs: modify sea-ice fraction input file ; update output  o aim.5l_cs: modify sea-ice fraction input file ; update output
5604  o exf: Adding simple range check routine for exf fields after read  o exf: Adding simple range check routine for exf fields after read
5605    
5606  checkpoint52k_post  checkpoint52k_post (2004/02/23)
5607  o removed top-level directory "diags"  o removed top-level directory "diags"
5608    - we migrated these functions to pkg/timeave a long time ago    - we migrated these functions to pkg/timeave a long time ago
5609  o fixed bug introduced in pkg/monitor  o fixed bug introduced in pkg/monitor
# Line 571  o set all ...Freq to zero after cost_fin Line 5616  o set all ...Freq to zero after cost_fin
5616    taveFreq, dumpFreq, pChkptFreq    taveFreq, dumpFreq, pChkptFreq
5617  o MAIN and ECCO differentiability restored  o MAIN and ECCO differentiability restored
5618    
5619  checkpoint52j_post  checkpoint52j_post (2004/02/18)
5620  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
5621  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
5622  o Really weird thing!  o Really weird thing!
# Line 579  o Really weird thing! Line 5624  o Really weird thing!
5624    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
5625    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
5626    after cost_final call which should not be there!    after cost_final call which should not be there!
5627  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
5628    
5629  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
5630    error messages    error messages
# Line 596  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 5641  o merged mom_vi_calc_relvort3.F, mom_vi_
5641    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
5642  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
5643    
5644  checkpoint52i_post  checkpoint52i_post (2004/01/21)
5645  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
5646  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
5647  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
5648    
5649  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
5650    the old pkg/aim).    the old pkg/aim).
5651    
5652  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
5653  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
5654  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
5655  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 615  o added temporary hack for sea-ice dynam Line 5660  o added temporary hack for sea-ice dynam
5660    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
5661    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
5662    
5663  checkpoint52f_post  checkpoint52f_post (2004/01/09)
5664  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
5665  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
5666  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
5667  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
5668    
5669  checkpoint52e_post  checkpoint52e_post (2004/01/07)
5670  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
5671    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
5672  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 629  o step.1 : rewrite (as in MultiDimAdvec) Line 5674  o step.1 : rewrite (as in MultiDimAdvec)
5674  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
5675  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
5676   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
5677  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
5678    
5679  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
5680  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 640  o added exf_offset_atemp for Celsius to Line 5685  o added exf_offset_atemp for Celsius to
5685  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
5686  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
5687    
5688  checkpoint52d_post  checkpoint52d_post (2003/12/16)
5689  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
5690    - updated output accordingly    - updated output accordingly
5691    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 669  o check-in the first version of the coup Line 5714  o check-in the first version of the coup
5714  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
5715     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
5716    
5717  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
5718  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
5719  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
5720    
5721  checkpoint52c_post  checkpoint52c_post (2003/11/25)
5722  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
5723    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
5724    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 687  o Removed all CPP options for cal packag Line 5732  o Removed all CPP options for cal packag
5732  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
5733  o corrected key comp. for passkey  o corrected key comp. for passkey
5734    
5735  checkpoint52b_post  checkpoint52b_post (2003/11/23)
5736  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
5737   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
5738   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 695  o new version: "thsice" of thermodynamic Line 5740  o new version: "thsice" of thermodynamic
5740   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
5741     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
5742  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
5743  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
5744    
5745  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
5746  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 705  o missing PTRACERS headers in some routi Line 5750  o missing PTRACERS headers in some routi
5750  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
5751    to ensure proper customization    to ensure proper customization
5752    
5753  checkpoint52a_post  checkpoint52a_post (2003/11/17)
5754  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
5755    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
5756    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 720  o fix problem with ECCO-related divided Line 5765  o fix problem with ECCO-related divided
5765    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
5766    but no warning issued by TAF    but no warning issued by TAF
5767    
5768  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
5769  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
5770    
5771  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
5772  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
5773    
5774  checkpoint51u_post  checkpoint51u_post (2003/11/06)
5775  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
5776    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
5777  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 741  o top level routines the_main_loop, forw Line 5786  o top level routines the_main_loop, forw
5786    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
5787  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
5788    
5789  checkpoint51t_post  checkpoint51t_post (2003/11/04)
5790  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
5791    
5792  checkpoint51s_post  checkpoint51s_post (2003/11/04)
5793  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
5794  o pkg/grdchk  o pkg/grdchk
5795    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 753  o pkg/grdchk Line 5798  o pkg/grdchk
5798    - additional high-precision output for testreport    - additional high-precision output for testreport
5799      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
5800    
5801  checkpoint51r_post  checkpoint51r_post (2003/11/03)
5802  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
5803  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
5804    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
5805    
5806  checkpoint51q_post  checkpoint51q_post (2003/10/30)
5807  o cd_code:  o cd_code:
5808    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
5809    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 774  o ctrl package totally restructured Line 5819  o ctrl package totally restructured
5819    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
5820  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
5821    
5822  checkpoint51p_post  checkpoint51p_post (2003/10/30)
5823  o create initial cd_code package  o create initial cd_code package
5824    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
5825      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 789  o create initial cd_code package Line 5834  o create initial cd_code package
5834  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
5835  o cleanup testreport  o cleanup testreport
5836    
5837  checkpoint51o_post  checkpoint51o_post (2003/10/27)
5838  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
5839    - carbon/    - carbon/
5840    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 810  o Correcting initialisations for fVerU, Line 5855  o Correcting initialisations for fVerU,
5855  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
5856    fVerU, fVerV    fVerU, fVerV
5857  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
5858  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
5859    
5860  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
5861  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 818  o added the [#include "AD_CONFIG.h"] sta Line 5863  o added the [#include "AD_CONFIG.h"] sta
5863   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
5864   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
5865    
5866  checkpoint51n_post  checkpoint51n_post (2003/10/23)
5867  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
5868    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
5869    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 827  o modifications to make FREEZE flux visi Line 5872  o modifications to make FREEZE flux visi
5872       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
5873  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
5874    
5875  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
5876  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
5877  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
5878    defines:    defines:
# Line 835  o added [#include "AD_CONFIG.h"] to all Line 5880  o added [#include "AD_CONFIG.h"] to all
5880    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
5881    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
5882    
5883  checkpoint51m_post  checkpoint51m_post (2003/10/21)
5884  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
5885    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
5886    - various cleanups related to package handling    - various cleanups related to package handling
5887    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
5888    
5889  checkpoint51l_post  checkpoint51l_post (2003/10/20)
5890  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
5891   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
5892   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
5893   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
5894     model integration time     model integration time
5895    
5896  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
5897  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
5898  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
5899  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
5900     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
5901    
5902  checkpoint51k_post  checkpoint51k_post (2003/10/16)
5903  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
5904   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
5905     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 868  o added an include barrier to the defaul Line 5913  o added an include barrier to the defaul
5913    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
5914  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
5915    
5916  checkpoint51j_post  checkpoint51j_post (2003/10/10)
5917  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
5918  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
5919  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 882  o Moving pkg-specific flow directives to Line 5927  o Moving pkg-specific flow directives to
5927         - pkg_ad_diff.list         - pkg_ad_diff.list
5928         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
5929    
5930  checkpoint51i_post  checkpoint51i_post (2003/10/09)
5931  o merge of the branch-genmake2  o merge of the branch-genmake2
5932    - knowingly breaks the older genmake    - knowingly breaks the older genmake
5933    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
5934    - new testreport supersedes older testscript    - new testreport supersedes older testscript
5935  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
5936  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
5937    
5938  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
5939  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 900  o modify gchem pkg to be more versatile Line 5945  o modify gchem pkg to be more versatile
5945  o modifications to clean up dic pkg  o modifications to clean up dic pkg
5946  o add pkg/cfc  o add pkg/cfc
5947    
5948  checkpoint51g_post  checkpoint51g_post (2003/10/02)
5949  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
5950  o start removing verification/vero/  o start removing verification/vero/
5951  o update AD-related stuff  o update AD-related stuff
# Line 908  o update AD-related stuff Line 5953  o update AD-related stuff
5953  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
5954    vector invariant setup    vector invariant setup
5955    
5956  checkpoint51f_post  checkpoint51f_post (2003/10/02)
5957  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
5958  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
5959    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
5960    
5961  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
5962  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
5963      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
5964    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 925  o Bug fix to pkg/ptracers, pkg/generic_a Line 5970  o Bug fix to pkg/ptracers, pkg/generic_a
5970      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
5971      non-local transport term.      non-local transport term.
5972    
5973  checkpoint51e_post  checkpoint51e_post (2003/08/03)
5974  o pkg/mom_vecinv:  o pkg/mom_vecinv:
5975    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
5976    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 935  o atmospheric geopotential: - include wa Line 5980  o atmospheric geopotential: - include wa
5980  o land pkg: read initial state from files.  o land pkg: read initial state from files.
5981  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
5982    
5983  checkpoint51d_post  checkpoint51d_post (2003/07/18)
5984  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
5985    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
5986  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 948  o Use cluster local disks for purely loc Line 5993  o Use cluster local disks for purely loc
5993    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
5994    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
5995    
5996  checkpoint51c_post  checkpoint51c_post (2003/07/08)
5997  o introducing integer flag debugLevel  o introducing integer flag debugLevel
5998    - debLevZero: suppress all output    - debLevZero: suppress all output
5999    - debLevA: standard    - debLevA: standard
# Line 971  o added verification for adjoint with pt Line 6016  o added verification for adjoint with pt
6016    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
6017  <<<checkpoint51b_pre  <<<checkpoint51b_pre
6018    
6019  checkpoint51a_post  checkpoint51a_post (2003/06/25)
6020  o added code for biogeochemistry package  o added code for biogeochemistry package
6021    - new pkgs: dic, gchem    - new pkgs: dic, gchem
6022    - new subroutine in ptracers    - new subroutine in ptracers
6023  o modify code for biogeo packages  o modify code for biogeo packages
6024    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
6025    
6026  checkpoint51  checkpoint51 (2003/06/24)
6027  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
6028    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
6029    kept separate packages    kept separate packages
# Line 986  o merged improved packages from ecco-bra Line 6031  o merged improved packages from ecco-bra
6031  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
6032    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
6033    
6034  checkpoint50i_post  checkpoint50i_post (2003/06/23)
6035  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
6036    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
6037    - 1st step: this one is differentiable    - 1st step: this one is differentiable
6038    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
6039                from ecco-branch)                from ecco-branch)
6040    
6041  checkpoint50h_post  checkpoint50h_post (2003/06/20)
6042  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
6043  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
6044  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 1002  o New variable in PARM03 for more flexib Line 6047  o New variable in PARM03 for more flexib
6047  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
6048    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
6049    
6050  checkpoint50g_post  checkpoint50g_post (2003/05/23)
6051  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
6052    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
6053    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
6054      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
6055    
6056  checkpoint50f_post  checkpoint50f_post (2003/05/23)
6057  o exf totally restructured  o exf totally restructured
6058    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
6059      and made sure it's still differentiable      and made sure it's still differentiable
# Line 1016  o exf totally restructured Line 6061  o exf totally restructured
6061    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
6062    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
6063    
6064  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
6065   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
6066        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
6067   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 1026  checkpoint50f_pre Line 6071  checkpoint50f_pre
6071   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
6072   o removed lots of single quotes from comments   o removed lots of single quotes from comments
6073    
6074  checkpoint50e_post  checkpoint50e_post (2003/05/14)
6075  o make KPP work with PTRACERS  o make KPP work with PTRACERS
6076   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
6077     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
6078   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
6079     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
6080  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
6081  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
6082    
6083  checkpoint50d_post  checkpoint50d_post (2003/05/13)
6084  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
6085    files analogous to write_state.F    files analogous to write_state.F
6086  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
6087    analogous to the cg2d-related output.    analogous to the cg2d-related output.
6088  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
6089    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
6090  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
6091    
6092  checkpoint50c_post  checkpoint50c_post (2003/05/12)
6093  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
6094  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
6095  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
6096  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
6097  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
6098    
6099  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
6100  Merging from release1_p13:  Merging from release1_p13:
6101  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
6102  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
6103    
6104  checkpoint50b_post  checkpoint50b_post (2003/04/17)
6105  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
6106  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
6107    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 1065  o new flag "useCDscheme" (default=F); re Line 6110  o new flag "useCDscheme" (default=F); re
6110  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
6111     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
6112    
6113  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
6114  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
6115  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
6116    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
6117    
6118  checkpoint50a_post  checkpoint50a_post (2003/03/21)
6119  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
6120    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
6121    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
6122    in contradiction with new key itdkey.    in contradiction with new key itdkey.
6123    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
6124    
6125  checkpoint50  checkpoint50 (2003/03/08)
6126  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
6127    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
6128  - bug fix in find_alpha  - bug fix in find_alpha
# Line 1085  checkpoint50 Line 6130  checkpoint50
6130  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
6131  - merged some sliced AD support routines  - merged some sliced AD support routines
6132    
6133  checkpoint49  checkpoint49 (2003/03/06)
6134  merged from ecco-branch:  merged from ecco-branch:
6135  o exf:  o exf:
6136    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 1123  o DIVA: Line 6168  o DIVA:
6168    (see MITgcm manual).    (see MITgcm manual).
6169  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
6170    
6171  checkpoint48i_post  checkpoint48i_post (2003/03/05)
6172  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
6173    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
6174    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 1141  o Modif. for DIVA: Line 6186  o Modif. for DIVA:
6186    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
6187    only relevant for ecco-branch)    only relevant for ecco-branch)
6188    
6189  checkpoint48h_post  checkpoint48h_post (2003/02/28)
6190  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
6191  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
6192  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
6193  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
6194    
6195  checkpoint48g_post  checkpoint48g_post (2003/02/18)
6196  --- EOS:  --- EOS:
6197  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
6198    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 1161  o accurate phiHyd when using interface-W Line 6206  o accurate phiHyd when using interface-W
6206   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
6207  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
6208    
6209  checkpoint48f_post  checkpoint48f_post (2003/02/18)
6210  Merging from release1_p12:  Merging from release1_p12:
6211  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
6212    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 1189  o pkg/seaice: Line 6234  o pkg/seaice:
6234    - adjoint-friendly modifications    - adjoint-friendly modifications
6235    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
6236    
6237  checkpoint48e_post  checkpoint48e_post (2003/02/12)
6238  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
6239  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
6240    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 1200  o following exp works with Olx=Oly=2 (an Line 6245  o following exp works with Olx=Oly=2 (an
6245      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
6246    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
6247    
6248  checkpoint48d_post  checkpoint48d_post (2003/02/09)
6249  o in preparation for r*:  o in preparation for r*:
6250   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
6251      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 1208  o in preparation for r*: Line 6253  o in preparation for r*:
6253      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
6254    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
6255    
6256  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
6257  o in preparation for r*:  o in preparation for r*:
6258    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
6259    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
6260    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
6261  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
6262    
6263  checkpoint48c_post  checkpoint48c_post (2003/02/06)
6264  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
6265  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
6266    
6267  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
6268  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
6269  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
6270    
6271  checkpoint48b_post  checkpoint48b_post (2003/01/27)
6272  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
6273   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
6274  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
6275    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
6276    
6277  checkpoint48a_post  checkpoint48a_post (2003/01/24)
6278  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
6279     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
6280    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
6281                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
6282    
6283  checkpoint48  checkpoint48 (2003/01/23)
6284  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
6285    
6286  checkpoint47j_post  checkpoint47j_post (2003/01/21)
6287  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
6288  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
6289  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 1257  o Yet more changes in gmredi: Line 6302  o Yet more changes in gmredi:
6302      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
6303  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
6304    
6305  checkpoint47i_post  checkpoint47i_post (2003/01/13)
6306  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
6307  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
6308    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 1273  o case GM_BOLUS_ADVEC should be cleaned Line 6318  o case GM_BOLUS_ADVEC should be cleaned
6318    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
6319  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
6320    
6321  checkpoint47g_post  checkpoint47g_post (2003/01/10)
6322  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
6323    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
6324  o After TAF bug fix:  o After TAF bug fix:
# Line 1299  Gradient checks OK for Line 6344  Gradient checks OK for
6344  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
6345  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
6346    
6347  checkpoint47f_post  checkpoint47f_post (2002/12/28)
6348  Merging from release1_p10:  Merging from release1_p10:
6349  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
6350    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 1311  o modifications for using pkg/exf with p Line 6356  o modifications for using pkg/exf with p
6356    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
6357      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
6358    
6359  checkpoint47e_post  checkpoint47e_post (2002/12/27)
6360  o created a tag prior to creating a branch  o created a tag prior to creating a branch
6361    
6362  checkpoint47d_post  checkpoint47d_post (2002/12/16)
6363  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
6364    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
6365  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
6366    oceanic pressure coordinates code    oceanic pressure coordinates code
6367  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
6368    also described in the tutorial section of the manual    also described in the tutorial section of the manual
6369  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
6370    
6371  checkpoint47c_post  checkpoint47c_post (2002/12/16)
6372  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
6373    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
6374    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 1335  o OCEANICP & realFreshWater: include P-E Line 6380  o OCEANICP & realFreshWater: include P-E
6380    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
6381  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
6382    
6383  checkpoint47b_post  checkpoint47b_post (2002/12/05)
6384  Merging from release1_p9:  Merging from release1_p9:
6385  o pkg/seaice  o pkg/seaice
6386    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 1352  o verification/lab_sea Line 6397  o verification/lab_sea
6397    - added missing matlab routines    - added missing matlab routines
6398    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
6399    
6400  checkpoint47a_post  checkpoint47a_post (2002/11/23)
6401  o new pkg: aim_v23  o new pkg: aim_v23
6402   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
6403     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 1369  o bulk_force and therm_seaice Line 6414  o bulk_force and therm_seaice
6414  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
6415     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
6416    
6417  checkpoint47  checkpoint47 (2002/11/15)
6418  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
6419  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
6420  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 1398  o Updated verification/carbon/ Line 6443  o Updated verification/carbon/
6443    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
6444    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
6445    
6446  checkpoint46n_post  checkpoint46n_post (2002/11/12)
6447  Merging from release1_p8:  Merging from release1_p8:
6448  o verification/natl_box:  o verification/natl_box:
6449    updating new external_fields_load routine    updating new external_fields_load routine
# Line 1452  o Adding new verification experiment glo Line 6497  o Adding new verification experiment glo
6497    the exf (and cal) package instead of the    the exf (and cal) package instead of the
6498    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
6499    
6500  checkpoint46m_post  checkpoint46m_post (2002/11/07)
6501  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
6502  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
6503    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 1465  o introduced flag for controllin non-hyd Line 6510  o introduced flag for controllin non-hyd
6510  o removed gravitySign from PARM04  o removed gravitySign from PARM04
6511  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
6512    
6513  checkpoint46l_post  checkpoint46l_post (2002/11/01)
6514  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
6515   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
6516     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 1478  o made convective adjustment work with p Line 6523  o made convective adjustment work with p
6523     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
6524     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
6525     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
6526  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
6527    
6528  checkpoint46k_post  checkpoint46k_post (2002/10/23)
6529  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
6530   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
6531   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 1494  o S/R aim_initialise.F replace S/R aim_i Line 6539  o S/R aim_initialise.F replace S/R aim_i
6539   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
6540   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
6541    
6542  checkpoint46j_post  checkpoint46j_post (2002/10/07)
6543  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
6544  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
6545  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
6546  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
6547  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
6548    
6549  checkpoint46i_post  checkpoint46i_post (2002/09/25)
6550  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
6551    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
6552    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
6553    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
6554    
6555  checkpoint46h_post  checkpoint46h_post (2002/09/25)
6556  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
6557    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
6558      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 1517  o introduced new parameter rhoConstFresh Line 6562  o introduced new parameter rhoConstFresh
6562    value is 999.8 kg/m^3    value is 999.8 kg/m^3
6563  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
6564    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
6565  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
6566    
6567   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
6568   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
6569   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
6570    
6571  checkpoint46g_post  checkpoint46g_post (2002/09/18)
6572  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
6573    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
6574    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 1541  o cleaned up find_rho Line 6586  o cleaned up find_rho
6586    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
6587  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
6588    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
6589  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
6590    
6591  checkpoint46f_post  checkpoint46f_post (2002/09/16)
6592  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
6593    - extended active file handling to g_... files    - extended active file handling to g_... files
6594    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 1551  o Enable tangent linear (forward mode) g Line 6596  o Enable tangent linear (forward mode) g
6596  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
6597  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
6598    
6599  checkpoint46e_post  checkpoint46e_post (2002/09/05)
6600  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
6601    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
6602    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 1560  o Added new equation of state -> MDJWF Line 6605  o Added new equation of state -> MDJWF
6605    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
6606      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
6607      expect perfect matches for those      expect perfect matches for those
6608  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
6609    
6610  checkpoint46d_post  checkpoint46d_post (2002/08/19)
6611  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
6612    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
6613    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
6614    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
6615  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
6616    in find_alpha/beta.    in find_alpha/beta.
6617  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
6618    
6619  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
6620    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
6621    
6622  checkpoint46c_post  checkpoint46c_post (2002/08/15)
6623  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
6624   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
6625   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
6626      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
6627   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
6628   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
6629  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
6630    
6631  checkpoint46b_post  checkpoint46b_post (2002/08/07)
6632  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
6633    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
6634    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1592  o Added UNESCO EOS, but not recommended Line 6637  o Added UNESCO EOS, but not recommended
6637    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
6638  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
6639    unesco.f to be used with POLY3    unesco.f to be used with POLY3
6640  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
6641    
6642  checkpoint46a_post  checkpoint46a_post (2002/07/31)
6643  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
6644    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
6645    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
6646  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
6647  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
6648  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
6649    
6650  checkpoint46  checkpoint46 (2002/07/13)
6651  further merges from release1_p5  further merges from release1_p5
6652  o new ctrl package  o new ctrl package
6653    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1629  o added hooks for Eliassen Palm fluxes ( Line 6674  o added hooks for Eliassen Palm fluxes (
6674  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
6675  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
6676    
6677  checkpoint45d_post  checkpoint45d_post (2002/07/12)
6678  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
6679  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
6680    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1643  o add new flags: Line 6688  o add new flags:
6688   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
6689  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
6690    
6691  checkpoint45c_post  checkpoint45c_post (2002/05/30)
6692  o Removed f90 comments ("!")  o Removed f90 comments ("!")
6693  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
6694    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1651  o modifications to gradient check packag Line 6696  o modifications to gradient check packag
6696    - enable centered differences    - enable centered differences
6697    - modified format of standard output    - modified format of standard output
6698    
6699  checkpoint45b_post  checkpoint45b_post (2002/05/30)
6700  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
6701  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
6702  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1663  o in initialise_varia, moved call packag Line 6708  o in initialise_varia, moved call packag
6708    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
6709  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
6710    
6711  checkpoint45a_post  checkpoint45a_post (2002/05/01)
6712  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
6713  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
6714  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 1683  o errorMessageUnit set non-equal zero in Line 6728  o errorMessageUnit set non-equal zero in
6728    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
6729  o modified carbon verif.  o modified carbon verif.
6730    
6731  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
6732  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
6733    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
6734  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
6735    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
6736    
6737  checkpoint44g_post  checkpoint44g_post (2002/03/05)
6738  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
6739    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
6740    
# Line 1754  o merge of relevant stuff from the ecco- Line 6799  o merge of relevant stuff from the ecco-
6799  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
6800  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
6801    
6802  checkpoint44  checkpoint44 (2002/01/18)
6803  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
6804  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
6805  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 1762  o update AIM experiments (NCEP input fil Line 6807  o update AIM experiments (NCEP input fil
6807  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
6808  o added some stuff for AD  o added some stuff for AD
6809    
6810  checkpoint43  checkpoint43 (2001/09/28)
6811  o added two new advection tests  o added two new advection tests
6812  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
6813  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
6814  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
6815    
6816  checkpoint42  checkpoint42 (2001/09/27)
6817    Fixed AD-related problems:    Fixed AD-related problems:
6818  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
6819    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1780  o Modified store directives for split of Line 6825  o Modified store directives for split of
6825    for the case ALLOW_KPP    for the case ALLOW_KPP
6826  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
6827    
6828  checkpoint41  checkpoint41 (2001/09/27)
6829  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
6830    to work with protex    to work with protex
6831    
6832  checkpoint40  checkpoint40 (2001/09/27)
6833  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
6834  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
6835  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1793  o more mods for non-linear free-surface Line 6838  o more mods for non-linear free-surface
6838  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
6839  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
6840    
6841  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
6842  o added DST advection schemes  o added DST advection schemes
6843  o fix MPI bug on SGI's  o fix MPI bug on SGI's
6844  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1803  o changes to commenting of arguments for Line 6848  o changes to commenting of arguments for
6848  o added/updated many matlab scripts  o added/updated many matlab scripts
6849  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
6850        
6851  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
6852  o new package rw/  o new package rw/
6853    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
6854    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1822  o TAMC-related update to cope with mom_f Line 6867  o TAMC-related update to cope with mom_f
6867    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
6868    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
6869    
6870  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
6871  o bug fix in dynamics.F  o bug fix in dynamics.F
6872    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
6873  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
6874  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
6875    related to TAF    related to TAF
6876    
6877  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
6878  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
6879  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
6880    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1837  o corresponding split of calc_diffusivit Line 6882  o corresponding split of calc_diffusivit
6882  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
6883  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
6884    
6885  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
6886  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
6887    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
6888  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 1851  o added new expt "solid-body.cs-32x32x1" Line 6896  o added new expt "solid-body.cs-32x32x1"
6896    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
6897      is not necessarily any better than the current one...      is not necessarily any better than the current one...
6898    
6899  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
6900  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
6901    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
6902  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1859  o extended iMin,jMin range for calc_comm Line 6904  o extended iMin,jMin range for calc_comm
6904  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
6905  o a few minor updates and fixes  o a few minor updates and fixes
6906    
6907  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
6908  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
6909  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
6910  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
6911    
6912  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
6913  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
6914  o Added gradient check package  o Added gradient check package
6915  o Added routines for passive tracer handling  o Added routines for passive tracer handling
6916  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
6917    
6918  checkpoint39  checkpoint39 (2001/05/14)
6919   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
6920     (mainly missing or wrong directives)     (mainly missing or wrong directives)
6921   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 1884  checkpoint39 Line 6929  checkpoint39
6929           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
6930   o disabled some packages by default in genmake   o disabled some packages by default in genmake
6931    
6932  checkpoint38  checkpoint38 (2001/04/10)
6933   o see notes_c37_adj.txt   o see notes_c37_adj.txt
6934   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
6935   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1892  checkpoint38 Line 6937  checkpoint38
6937     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
6938   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
6939    
6940  checkpoint37  checkpoint37 (2001/03/13)
6941   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
6942     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
6943      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1909  checkpoint37 Line 6954  checkpoint37
6954   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
6955   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
6956    
6957  checkpoint36  checkpoint36 (2001/02/20)
6958   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
6959   o recover Time-Average diagnostics   o recover Time-Average diagnostics
6960   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
6961   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
6962    
6963  checkpoint35  checkpoint35 (2001/02/08)
6964   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
6965   o allows staggered time-stepping   o allows staggered time-stepping
6966   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
6967   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
6968    
6969  checkpoint34  checkpoint34 (2001/01/30)
6970   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
6971   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
6972     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1932  checkpoint34 Line 6977  checkpoint34
6977   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
6978   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
6979    
6980  checkpoint33  checkpoint33 (2000/11/30)
6981   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
6982   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
6983     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1950  checkpoint33 Line 6995  checkpoint33
6995       possibly use them.       possibly use them.
6996   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
6997    
6998  checkpoint32  checkpoint32 (2000/11/13)
6999   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
7000     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
7001   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1961  checkpoint32 Line 7006  checkpoint32
7006   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
7007   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
7008    
7009  checkpoint31  checkpoint31 (2000/09/11)
7010   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
7011     -> new routines packages_...F     -> new routines packages_...F
7012     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1978  checkpoint31 Line 7023  checkpoint31
7023     - not yet tested for GMRedi.     - not yet tested for GMRedi.
7024     - not yet tested for KPP.     - not yet tested for KPP.
7025    
7026  checkpoint30  checkpoint30 (2000/07/13)
7027   o Updates for OBCs   o Updates for OBCs
7028   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
7029   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1987  checkpoint30 Line 7032  checkpoint30
7032   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
7033     and entry for T90 in genmake     and entry for T90 in genmake
7034    
7035  checkpoint29  checkpoint29 (2000/06/21)
7036   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
7037    
7038  checkpoint28  checkpoint28 (2000/06/09)
7039   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
7040   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
7041   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 2003  checkpoint28 Line 7048  checkpoint28
7048     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
7049   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
7050    
7051  checkpoint27  checkpoint27 (2000/04/10)
7052   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
7053     formulation works properly with variable resolution.     formulation works properly with variable resolution.
7054   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 2011  checkpoint27 Line 7056  checkpoint27
7056   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
7057     in new routine ini_psurf()     in new routine ini_psurf()
7058    
7059  checkpoint26  checkpoint26 (2000/04/05)
7060   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
7061     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
7062   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 2021  checkpoint26 Line 7066  checkpoint26
7066     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
7067   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
7068    
7069  checkpoint25  checkpoint25 (2000/03/15)
7070   o updates for OBCs and NH   o updates for OBCs and NH
7071   o dramatically reduced memory usage   o dramatically reduced memory usage
7072   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 2032  checkpoint25 Line 7077  checkpoint25
7077      an explicit free-surface option)      an explicit free-surface option)
7078   o initial state input files for U and V   o initial state input files for U and V
7079    
7080  checkpoint24  checkpoint24 (1999/08/02)
7081   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
7082   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
7083   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
7084    
7085  checkpoint23  checkpoint23 (1999/05/26)
7086   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
7087   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
7088    
7089  checkpoint22  checkpoint22 (1999/05/18)
7090   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
7091   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
7092    
7093  checkpoint21  checkpoint21 (1999/05/18)
7094   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
7095   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
7096   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
7097   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
7098    
7099  checkpoint20  checkpoint20 (1999/03/22)
7100   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
7101   o Added non-hydrostatic code   o Added non-hydrostatic code
7102   o Fixed some input data   o Fixed some input data
7103   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
7104    
7105  checkpoint19  checkpoint19 (1998/12/15)
7106   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
7107   o Added new code for open boundaries.   o Added new code for open boundaries.
7108   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 2065  checkpoint19 Line 7110  checkpoint19
7110   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
7111   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
7112    
7113  checkpoint18  checkpoint18 (1998/11/30)
7114   o Further changes for optional code generation with   o Further changes for optional code generation with
7115     CPP - ugh!     CPP - ugh!
7116    
7117  checkpoint17  checkpoint17 (1998/11/03)
7118   o Beginning to incorporating modularity   o Beginning to incorporating modularity
7119     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
7120   o Small changes for TAMC complinace   o Small changes for TAMC complinace
7121   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
7122     configuration "exp0".     configuration "exp0".
7123    
7124  checkpoint16  checkpoint16 (1998/10/28)
7125   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
7126     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
7127     assignment is an addition.     assignment is an addition.
# Line 2084  checkpoint16 Line 7129  checkpoint16
7129     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
7130     limit ).     limit ).
7131    
7132  checkpoint15  checkpoint15 (1998/09/29)
7133   Rewrote exchange routines to allow   Rewrote exchange routines to allow
7134   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
7135   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 2093  checkpoint15 Line 7138  checkpoint15
7138     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
7139     communication method.     communication method.
7140    
7141  checkpoint14  checkpoint14 (1998/09/09)
7142   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
7143   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
7144    
7145  checkpoint13  checkpoint13 (1998/07/17)
7146   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
7147   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
7148   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 2112  branch-point-rdot Line 7157  branch-point-rdot
7157   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
7158   we've actually tested it...   we've actually tested it...
7159    
7160  checkpoint12  checkpoint12 (1998/07/08)
7161   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
7162   configure script).   configure script).
7163   Released to testers.   Released to testers.
7164    
7165  checkpoint11  checkpoint11 (1998/07/02)
7166   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
7167   and ini_masks_etc().   and ini_masks_etc().
7168    
7169  checkpoint10  checkpoint10 (1998/07/01)
7170   Introduced the configure script.   Introduced the configure script.
7171   Separated out the diags package.   Separated out the diags package.
7172   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
7173   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
7174    
7175  checkpoint9  checkpoint9 (1998/06/22)
7176   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
7177   General tidy-up.   General tidy-up.
7178   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
7179    
7180  checkpoint8  checkpoint8 (1998/06/22)
7181   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
7182   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
7183    
# Line 2142  checkpoint7-4degree-ref Line 7187  checkpoint7-4degree-ref
7187   model etc..   model etc..
7188   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
7189    
7190  checkpoint7  checkpoint7 (1998/06/15)
7191   Created by cnh   Created by cnh
7192   Simple 4 degree global simulation   Simple 4 degree global simulation
7193   configuration.   configuration.
# Line 2150  checkpoint7 Line 7195  checkpoint7
7195   hydrography, bathymetry etc   hydrography, bathymetry etc
7196   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
7197    
7198  checkpoint6  checkpoint6 (1998/06/08)
7199   Created by cnh   Created by cnh
7200   merged checkpoint5 with CD and   merged checkpoint5 with CD and
7201   spherical polar code.   spherical polar code.
7202   Still some problems with GM Redi   Still some problems with GM Redi
7203   abd full topography.   abd full topography.
7204    
7205  checkpoint5  checkpoint5 (1998/06/08)
7206   Created by AJA   Created by AJA
7207   contains updates to GM Redi   contains updates to GM Redi
7208   and reordered timestepping loop   and reordered timestepping loop
7209   for Implicit Diffusion.   for Implicit Diffusion.
7210    
7211  checkpoint4  checkpoint4 (1998/05/30)
7212   Created by cnh   Created by cnh
7213   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
7214   grid variations are limited.   grid variations are limited.
7215   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
7216   for generation.   for generation.
7217    
7218  checkpoint3  checkpoint3 (1998/05/26)
7219   Created by cnh   Created by cnh
7220   Added extra flags for runtime options   Added extra flags for runtime options
7221   Added this file   Added this file

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