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revision 1.1484 by jmc, Mon Aug 1 20:47:39 2011 UTC revision 1.1686 by gforget, Tue Jul 10 15:47:30 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
8    o AD_CONFIG.h file:
9     - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
10     - remove #include "AD_CONFIG.h" from all included OPTIONS files and
11       add it explicitly in each fortran src file where it is needed.
12       motivation: header file AD_CONFIG.h is generated/modified after "make depend"
13       thus introducing potentially wrong dependency; therefore, better to include
14       it only where it's really needed, and after any other included OPTIONS file
15       (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
16       or ALLOW_TANGENTLINEAR_RUN).
17    
18    checkpoint63p (2012/07/06)
19    o pkg/autodiff:
20      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
21      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
22        which are now read from new parameter file "data.autodiff" (inAdExact
23        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
24      - add file "data.autodiff" in all verification/*/input_ad/ directories.
25      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
26        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
27    o verification/tutorial_tracer_adjsens/
28      - add extra sub-verification which uses "SOM" advection scheme
29        (2nd Order-Moment Advection Scheme, Prather Limiter) with
30          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
31        and in data:
32          multiDimAdvection=.TRUE.,
33          tempAdvScheme=81,
34          saltAdvScheme=81,
35    o model/src:
36      - introduce ALLOW_BALANCE_RELAX which allow the removal
37       of the global mean of relaxation terms by setting
38       balanceThetaClimRelax and balanceSaltClimRelax
39      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
40       This case is now treated appropriately in seaice_growth.F
41    o pkg/seaice:
42      - do balanceEmPmR and balanceQnet based on the net fluxes
43        (SItflux) that enter the ocean+ice system rather than QNET
44        and EMPMR. Works best in real fresh water.
45      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
46        out of the diagnotics bloc, and stored in global arrays.
47    
48    checkpoint63o (2012/06/29)
49    o vertical mixing schemes:
50      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
51      - replace computation of density (in Function STATE1, opps_calc.F) by a call
52        to S/R FIND_RHO_SCALAR
53      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
54        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
55        affects output (vermix.ggl90) at truncation level.
56    o testreport:
57      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
58        (nSx,nSy) for the number of threads (from eedata.mth)
59    o model/src:
60      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
61        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
62    o verification/tutorial_tracer_adjsens/
63      - compile with ALLOW_CG2D_NSA
64      - run with nonlinFreeSurf=3
65      - update reference output_adm.txt
66    o tools/genmake2:
67      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
68        refine usePROFILES switching off (only when NetCDF is not available).
69    o verification (atmospheric set-up):
70      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
71    o pkg/profiles : refine profiles and files handling.
72    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
73    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
74      - changes to use model/src/the_main_loop.F rather than the ecco version
75        in ecco type adjoint runs.
76    o model/src:
77      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
78      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
79      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
80    o model/src:
81      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
82        update output of test experiment bottom_ctrl_5x5.
83    o pkg/generic_advdiff:
84      - implement vertical bi-harmonic diffusion (for now, only for T & S and
85        only explicitly).
86    o verification/bottom_ctrl_5x5/
87      update reference output (results changed quite some time ago,
88      not sure when; but new reference results look ok in terms of grdchk)
89    o verification/1D_ocean_ice_column/
90      For verification purposes, the exact adjoint rather than an approx.
91      should be used (e.g., to comare against F.D. or TLM).
92      removed autodiff_inadmode*_ad.F routines in code_ad/
93      Update results/ accordingly.
94    o pkg/cal:
95      - change cal_getdate.F so that output date is function of input time only
96        (less ambiguous, not mixed up with input iteration number).
97      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
98    o pkg/diagnostics:
99      - implement calendarDumps also for stats-diags
100      - implement calendarDumps also for snap-shot output (negative freq)
101      - for now, ignores calendarDumps if non-zero phase-lag.
102    
103    checkpoint63n (2012/06/04)
104    o model/src:
105      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
106        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
107      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
108        similar to calc_r_star.F); update results of experiment internal_wave and
109        tutorial_global_oce_in_p (affected @ truncation level).
110    o pkg/shelfice:
111      - add parameterisation of advective-diffusive flux into the ice shelf
112        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
113      - simply eps3/3a computation
114    o eesupp:
115     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
116       between tiles, just fill-in edges assuming locally periodic subdomain) and
117       add corresponding exchange subroutines (EXCH0);
118     - new CG-solver version (_EX0) for disconnected-tiles special case.
119    o model/src (CG-solvers):
120     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
121       (similar final residual output and max-Iter number as with standard version);
122     - allows to store and use lowest-residual solution (standard & _SR versions);
123     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
124     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
125    o eesup/src:
126     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
127       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
128    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
129    
130    checkpoint63m (2012/04/27)
131    o pkg/shelfice:
132     - account for partical cells in surface level below ice-shelf for hydrostatic
133       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
134    o ad test experiments:
135     - update and rename to "ad_optfile.local" local AD-optfile specific to a
136       particular adjoint verification experiment (in verification/*/code_ad/)
137    o pkg/seaice & pkg/exf:
138     - Part two of ECCO-CLIVAR code merges.
139       Completes merge of seaice area relax. code.
140       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
141       to be set in EXF_OPTIONS.h since this pkg controls its I/O
142       (and avoids second CPP option in SEAICE_OPTIONS.h)
143     - change default value of costIceStart & costIceEnd to a valid date.
144     - add snowPrecip to HSNOW in seaice_growth
145    o pkg/ptracers:
146     - move ptracers summary and setup check into separated S/R ; add a check for
147       valid PTRACERS_Iter0 value (error+stop or just warning).
148    o pkg/cal (+ pkg/ecco):
149     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
150       as input; and for AD, unless both are not differentiable (e.g., k index)).
151    o model/src:
152     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
153       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
154       temporary set to usingZCoords value (to be changed to F when using shelfice).
155     - hydrostatic pressure: implement partial cell near the surface also for
156       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
157       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
158    o pkg/ctrl/ctrl_init.F:
159     - add a formal parameter to s/r ctrl_init_rec to print
160       xx_$(ctrl_valiable)_file for easier debugging
161     - move call of cal_* routines into the if-block where they are really
162       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
163       to specify a startdate
164    o pkg/seaice:
165     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
166       global_ocean.cs32x15/code versions).
167     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
168       verification experiment global_ocean.cs32x15.seaice and update results.
169    o pkg/exf:
170     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
171       (according to useExfYearlyFields).
172    o pkg/cal:
173     - move calendar setting & summary (previously in cal_readparams.F) into new
174       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
175       length of the simulation is set (after SET_PARMS call); This is an attempt
176       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
177     - For safety: keep a record of pkg/cal parameter settings status
178               to allow to STOP if one pkg/cal S/R is called too early.
179     - add a stop in all basic pkg/cal subroutines if called before setting is done.
180     - modify cal_getdate.F: stop when nothing was returned;
181       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
182       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
183    
184    checkpoint63l (2012/04/04)
185    o pkg/bbl:
186      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
187        update global_with_exf output.yearly.txt file.
188    o pkg/cal:
189      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
190      - remove 2 unsused and very short (1 line only) functions ;
191      - remove unsused subroutines from AD-Diff list.
192    o model/src:
193      - start to implement clean wait to stop in initialization S/R (config_check.F,
194         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
195    o folowing PRINT_MESSAGE changes:
196      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
197    o pkg/bbl:
198      - modification so it can work with z*
199      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
200      - global_with_exf/input.yearly verification; changes output.yearly.txt
201    o eesupp/src:
202      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
203        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
204      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
205        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
206      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
207      - when using MPI, always set usingMPI=T ; set default accordingly and stop
208        if not consistent.
209      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
210        argument is zero (in case called within single-thread section).
211    o pkg/fizhi:
212        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
213        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
214    o pkg/exch2:
215      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
216        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
217      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
218        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
219        with bad ones coming from a not-yet-updated halo.
220        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
221    o pkg/frazil:
222        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
223        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
224    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
225    o verification/lab_sea
226      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
227      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
228      * nTimeSteps 3 -> 4
229      * changed reference output accordingly
230    o pkg/ctrl:
231      * fix ctrl_get_gen for xx_sst, xx_sss
232    o pkg/fizhi:
233      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
234        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
235      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
236        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
237        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
238    o pkg/gmredi:
239      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
240    o pkg/fizhi:
241      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
242        (old)aces open64 tuv test.
243    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
244    o pkg/mom_vecinv:
245      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
246        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
247        with non-lin free-surf).
248    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
249      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
250      some compilers (gfortran 4.6.0 on MacOS)
251    o momentum:
252      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
253        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
254        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
255    
256    checkpoint63k (2012/03/17)
257    o model/src:
258       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
259         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
260       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
261         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
262    o model/src: solve_*diagonal.F
263       - replace division with multiplication by inverse (similar to original version)
264         update output of AD exp. global_ocean.90x40x15.
265       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
266         to enable the use of the vectorized & differentiable solve_tridiagonal.F
267       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
268         vertical advection (to get solve_tridiagonal tested in AD mode).
269    o pkg/seaice: ECCO-CLIVAR merge:
270      1. seaice AREA relaxation
271         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
272         * runtime flag: SEAICE_tauAreaObsRelax
273      2. modified global mean cost imbalance code: CPP option
274          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
275    o another iteration on solve_*diagonal.F
276       Make choices independent of AUTODIFF
277       Default will be the adjoinable vectorized version.
278       Alternative choices are:
279       * non-adjoinable original version with low memory footprint:
280         #define SOLVE_DIAGONAL_LOWMEMORY
281       * still adjoinable but does not vectorize (k as inner-most loop):
282         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
283    o testreport
284     - add option to use a home made wrapper around "make"
285     - remove MITGCM_IEEE env. variable (no longer active)
286    o pkg/shelfice
287     - improve computation of friction velocity for velocity dependent
288       exchange coefficients: include velocities into SHELFICEBoundaryLayer
289       block to average velocities vertically
290     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
291    o Modify diagonal solvers, now three versions (upon request):
292      #ifndef SOLVE_DIAGONAL_AUTODIFF
293        1. default version (dating back a while ago)
294      #else /* def SOLVE_DIAGONAL_AUTODIFF */
295      # ifdef SOLVE_DIAGONAL_KINNER
296        2. adjoinable version with k-innermost loop (G. Forget)
297      # else
298        3. adjoinable vectorized version of 2.
299      # endif
300      #endif /* SOLVE_DIAGONAL_AUTODIFF */
301      All flags are currently set within routines, but could/should be moved to CPP-options.
302      Array bounds for 1. are as before, for 2.,3. cover the entire domain
303      (could be changed for 1. too).
304    o verification/lab_sea (fwd):
305      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
306        use 7 categories (except hb87), new solve4temp params (except salt_plume),
307        constant salinity (=4) or variable salinity (salt_plume) done through
308        SItracer.
309    o pkg/seaice:
310      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
311      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
312         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
313        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
314        SEAICE_freeze got retired) but already better than previously with
315        SEAICE_freeze=123456.7 deg.C;
316      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
317        (safer multi-threaded setting); always set SEAICEuseEVP;
318      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
319        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
320        stop if multiple specifications for the same coeff; make sure default
321        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
322    o pkg/obcs:
323      - allow to switch to upwind 1rst order advection scheme for the advective
324        flux computation at the open-boundary; disabled for adjoint built.
325    o pkg/ptracers:
326      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
327      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
328      - add parameter to decide when to start a tracer; use internal flag to
329        know which tracer to step-forward; switch this internal flag at the top
330        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
331        for adjoint built.
332    o pkg/seaice:
333      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
334      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
335      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
336    o pkg/ecco:
337      - fix writing of output file DiagnosCost_ClimSalt/Theta
338        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
339    o pkg/seaice:
340      - add missing initialisation of COR_ICE array in dynsolver.F
341      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
342        compiled either way, and is tested in all exps (multidim was only tested
343        in lab_sea ad before).
344      - cosmetic change to prepare for future addition of ITD. no change to results.
345        no defaults change.
346      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
347      - by lack of adequate verification experiments, I further used custom versions
348        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
349        should be correct.
350      - avoid recomputations in ad.
351    o array initialisation in adjoint mode:
352      1) pkg/mom_common/mom_calc_ke.F:
353        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
354        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
355        part this initialisation is gone, resulting in Floating Point Exception
356        (caught by open64 compiler with debug option).
357      2) model/src/convective_weights.F
358        set output convectCount over the full array range (instead of doing
359        an update): this fix a similar issue when called within recomputation (adjoint)
360        which could by-pass the initialisation (normally done in the caller S/R).
361    o pkg/seaice:
362      - final version of turbulent flux params, as agreed at MIT ice meet:
363           SEAICE_mcPheePiston (default is ~ 0.000875)
364           SEAICE_mcPheeTaper (default is 0.)
365           SEAICE_frazilFrac (defualt is 1.)
366           SEAICE_mcPheeStepFunc (default is false)
367      - changes results at trunction error level
368      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
369    o added pkg/frazil:
370      - see frazil_description.tex for details
371      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
372    o pkg/shelfice/shelfice_thermodynamics.F
373      - fix exponents for velocity dependent exchange coefficients: change
374        from 2/3(=0) to 0.66666666666666667
375      - move computation of velocity dependent exchange coefficients into
376        separate loop, so that it applies to both thermodynamics
377      - move some divisions by constants out of loops
378    
379    checkpoint63j (2012/02/16)
380    o pkg/seaice:
381      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
382      - SItracer:  added run time params, and allow coupling to ocn salinity.
383    o pkg/seaice: remove (almost) all divisions by constants within loops
384      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
385      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
386      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
387      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
388    o pkg/seaice :
389      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
390        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
391      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
392      - add permanent SItflux diag that corresponds to TFLUX but includes
393        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
394      - allow activation/testing of a fix for suspected missing term in
395        ocn-ice heat budget (to be confirmed). To test this, you want to
396        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
397        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
398      - no change in results, fwd or ad.
399    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
400      - switch to variable freezing point.
401           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
402      - bug fix : the sublimation term that was missing is now activated.
403           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
404      - bug fix : flooding sign term for SIsal0.NE.0.
405           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
406    o pkg/seaice:
407      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
408        is now the default, and the old default constant freezing point is recovered
409        with SEAICE_tempFrz0    = -1.96,
410             SEAICE_dTempFrz_dS = 0.,
411      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
412      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
413      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
414        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
415      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
416        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
417      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
418        seaice_growth r149 for legacy branch (no results change).
419      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
420        from I. Fenty).
421      - results did not change except for global_ocean.cs32x15, mostly due to the
422        switch to variable freezing point (see above item for detail).
423    o pkg/thsice:
424      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
425        seawater freezing in thsice_calc_thickn (not used).
426    o pkg/seaice: turbulent flux term specification via run time params.
427      - replace CPP switches with run time switches to facilitate testing
428      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
429                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
430      - added runtime parameter : SEAICEturbFluxFormula
431      - move Mcphee constants to SEAICE_PARAMS.h
432      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
433                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
434                 remove seaice_summary call (moved to seaice_init_fixed)
435      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
436        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
437      - seaice_summary.F : add missing report of read turbulent flux term set up
438                           and SITRACER.
439      - seaice_check.F : check range; inform and stop if retired CPPs are used
440                         (incl. SEAICE_AGE).
441      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
442             CPP switch, same computation as before for the different options.
443      - change results at the truncation level.
444    o pkg/seaice:
445      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
446        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
447        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
448      - update verification/*/input*/data.seaice:
449        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
450        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
451        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
452        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
453    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
454      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
455        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
456        difference in results only due to machine truncation.
457      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
458        MaykutPolySatVap; keep MIN_LWDOWN.
459      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
460      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
461        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
462    o pkg/salt_plume:
463      - isolate saltPlumeFlux array exch into a specific S/R called from
464        do_oceanic_phys.F
465      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
466    o verification:
467      - move untested set-up to MITgcm_contrib/verification_other.
468    o pkg/seaice:
469      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
470    o pkg/seaice:
471      - seaice_solve4temp.F (keeping results unchanged):
472        * add 2 future run-time params to select which saturation vapor pressure
473          formula is used and how post-iteration fluxes are set.
474          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
475        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
476          the linearized expression to stay consistent with tsurf finding.
477      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
478        can be < 0.
479    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
480      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
481        conductive heat flux F_c , and add it explicitly when updating tsurf as
482        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
483        so that now F_ia has a consistent meaning through the entire routine.
484        This causes differences at truncation level: update output of fwd exp.
485        global_ocean.cs32x15.seaice.
486    o pkg/seaice:
487      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
488        of arrays, sign/direction of fluxes; no effect on results.
489      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
490        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
491        note: this should have been done before changing celsius2K default.
492      - to keep results unchanged, add back old value of celsius2K in verification
493        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
494      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
495        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
496        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
497        freezing temp is consistent with value in seaice_growth.F ; this causes
498        differences at machine truncation level: update lab_sea AD output (3/4).
499    o pkg/seaice:
500      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
501        and climsst/sss even when using seaice (to prevent calculation that might
502        use SST on land); does not affect any verification exp.
503      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
504        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
505    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
506      over land (non-legacy code)
507    o vectorize salt_plume package:
508      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
509      - this code computes plumebk everywhere (also over land), thus requires
510        code to avoid divisions by zero and catch the case of kLev=Nr.
511      - efficiency of salt_plume_frac is still sub-optimal
512    o tools (genmake2):
513      - fix makefile NAME specification (option: -makefile NAME) by adding
514        "-f $MAKEFILE" in few places where it was missing including makedepend
515        command (contribution from Paul).
516    
517    checkpoint63i (2012/01/24)
518    o model/src:
519      - add factorized versions of some EOS code to find_rho.F,
520        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
521    o model/src:
522      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
523      - change default celsius2K from 273.16 to 273.15
524      - to keep results unchanged, add back old value of celsius2K in verification
525        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
526         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
527    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
528      to make TAF generate vectorizable code
529    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
530       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
531       have flags that do this more efficiently.
532    o pkg/diagnostics/diagstats_calc.F
533      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
534    o pkg/obcs (with exch2):
535      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
536        and remove code (in obcs_readparms.F) which was based on EXCH of indices
537        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
538    o pkg/exf and seaice exp:
539      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
540        so that switching off area & heff advection flags does not affect results.
541      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
542      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
543        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
544        results of verification experiments: 1D_ocean_ice_column(fwd),
545        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
546        and offline_exf_seaice (all 4).
547    o pkg/seaice:
548      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
549        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
550      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
551        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
552        not multi-dim advection;
553      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
554        SHORTWAVE_HEATING #undef.
555    o optim: make Makefile more robust (?)
556    o pkg/obcs:
557      * fix treatment of obcs_read_pickup for TAF
558    o pkg/shelfice:
559      * add missing initialisation of num_shifwflx
560      * new adjoint verification exp. for isomip
561      * change Prandtl and Schmidt numbers from generic formulations
562        (in terms of model diffus. and visc.) to separate runtime
563        parameters, with Holland and Jenkins (1999) default values.
564    o pkg/exf (interpolation):
565      - extended input field (2 rows) near the N & S poles:
566        * fill in with the symetric value (when even Nb of data in longitude)
567        * add average value at the poles only for scalar quantities ; for vector
568          component interpolation, skip the averaging and keep duplicated values,
569          unless the 2 components have same location (uvInterp=T) in which case
570          interpolate the 2 components together using S/R EXF_INTERP_UV.
571      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
572        together: this allows to account properly for local orientation when
573        averaging at N & S pole.
574      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
575        exf-interpolation near N & S poles. Undef by default.
576      - add debug check/print on 1rst iter if debugLevel >=2.
577    o pkg/exf:
578      - change masking flags definition (no longer "parameter"), put them in
579        common block and set them in S/R EXF_INIT_FIXED.
580      - change recognized masking flag from s,u,v to c,w,s since the mask
581        to use (maskC,W,S) depends on position on model grid and has little to
582        do with scalar/vector difference; fix masking if using P-coordinates.
583      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
584        and update results of exp. global_with_exf (x2).
585      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
586    o pkg/obcs
587      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
588    o pkg/exf (interpolation):
589      - assume periodicity in X only if input field cover full longitude range.
590      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
591        and should vectorise).
592      - fix input lat of the 2 added row (in case we provide N.pole data).
593    
594    checkpoint63h (2011/12/30)
595    o pkg/seaice:
596      - change declaration of UVM from _RL to _RS in order to get B-grid
597        uIce,vIce monitor when _RS = real*4
598    o pkg/offline:
599      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
600      - compute vertical velocity if not read from file (switch on exactConserv
601        & staggerTimeStep);
602      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
603    o verification:
604      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
605        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
606        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
607      - update output of exp. global_ocean.cs32x15.viscA4 after changing
608        grid-file angles (used here for coriolis-3d);
609      - remove (or gzip) few files not needed to run fizhi-cs experiments.
610    o pkg/exf (vector interpolation):
611      - rotate vector component toward local grid-axis orientation using grid-angles
612        (stored in GRID.h) instead of locally computed rotation angle; keep old code
613        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
614    o pkg/seaice:
615      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
616        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
617    o pkg/PKG_OPTIONS.h files:
618      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
619        outside of the #ifdef ALLOW_THISPKG / #endif block.
620      - update verification/*/code/PKG_OPTIONS.h files.
621    o add a verification experiment (offline_exf_seaice/input.seaice) that test
622      the B-grid LSOR solver
623    o pkg/seaice: sort out emissivity and long wave radiation step 2:
624      - add emissivity for snow and ice as new run-time parameters
625        (unfortunately) that default to the corresponding exf values; this
626        changes results in most verification experiments so that for backward
627        compatibility these parameter have to be set explicitly to inconsistent
628        values (ugly);
629      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
630        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
631        until we agree how to handle this bug properly
632    o pkg/exf (interpolation):
633      - add a set of run-time param ({inputfield}_interpMethod), one for
634        each interpolated input field, to select the interpolation method
635        with a value of zero switching off the interpolation;
636      - print interpolation parameters to standard output;
637      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
638        (to use instead runoff_interpMethod=0 in data.exf).
639      - simplify default setting of interpolation parameters (for all fields,
640        set position to match model grid cell-center position, leading to trivial
641        interpolation in case of regular Lat-Lon grid) and fix for the case of
642        non-uniform delY.
643    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
644       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
645       this factor is absolutely required, because the lw exitance (= out-going
646       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
647       where the reflectivity rho = 1-emissivity for conservation reasons. Once
648       this is established, we can remove the CPP-Flag (if we want to).
649    o pkg/seaice:
650      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
651        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
652      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
653        what the name implies (and not emissivity*BoltzmannConstant), this means
654        the old default value of 5.5e-8 now means
655        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
656        S/R exf_readparms
657      - FV-discretization of the B-grid LSOR solver, turn on with
658        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
659        of the calling routine dynsolver, so that B and C-grid code look a
660        little more alike.
661      - fix index bugs in ostres.F (B-grid code)
662    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
663    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
664      default for SEAICE_emissivity, if useEXF; requires setting a wrong
665      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
666      backward compatiblity
667    o model/src: use sigmaR in calc_ivdc
668    
669    checkpoint63g (2011/12/16)
670    o pkg/seaice/seaice_growth.F:
671      fix heat conservation of the coupled ocean-seaice system.
672      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
673      solid vs liquid water treatment is resolved via QNET.
674    o pkg/seaice/seaice_growth.F:
675      add missing term for sublimation in saltFlux, which was breaking conservation.
676    o pkg/seaice/seaice_model.F:
677      Remove this patholigical case treatment in evolution branch,
678      where it is un-necessary and breaks conservation.
679      Update global_ocean.cs32x15/results accordingly for
680      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
681    o model/src:
682      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
683      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
684    o pkg/obcs:
685      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
686      tendency for temperature and salinity that is then applied to update
687      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
688      horizontal advection and diffusion contributions on the boundary (in
689      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
690      removing the mask in S/R timestep_tracer. The advantage of this approach is
691      that the updated tracer values include contributions from the surface
692      forcing and vertical diffusion.
693      This modification changes exp4.stevens because of vertical diffusion.
694    o model/src:
695      change non-curvilinear grid setting to also work with exch2 + blank tiles:
696      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
697        face dimensions.
698      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
699        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
700        and INI_SPHERICAL_POLAR_GRID.
701      change test-experiment global_ocean.90x40x15:
702      - split the domain in many more tiles (9x4 tiles of 10x10 each);
703      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
704      - update results of both test (std & dwnslp).
705    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
706       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
707    o model/src:
708      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
709        and fix initialisation when using sigma-coords.
710    o model/src:
711     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
712       to their current value at the beginning of forward_step.F": add a new run-time
713       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
714     - set doResetHFactors=T in the following test exp:
715        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
716        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
717        and tutorial_global_oce_in_p (nonLinFS in p)
718    o pkg/ecco
719      - added IES cost term
720    o verification/advect_xz
721      - scale down the depth by 1/100 (from 200 km to just 2.km)
722      - add secondary test using divergent flow, r-star and implicit vertical advection.
723      - add note (check_conserve_TS.txt) and matlab script to check global
724        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
725    o pkg/rbcs:
726      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
727    o pkg/obcs (Stevens BCs):
728      - fix various problems in the phase speed computations of the Stevens
729        boundary conditions:
730        - sign error for western and southern boundaries,
731        - time tendencies were underestimated by factor of dTracerLev and some just
732          zero (for multidim advection schemes) -> now estimate time tendencies
733          from difference between previous (n) time level and the one before (n-1);
734          this requires storing a field per tracer per boundary, also in the pickup
735          files.
736        - replace deltaTmom in cflMer/Zon computation with dTracerLev
737        - set default phase velocity to cflMer/Zon
738      - update verification experiment exp4.stevens
739    o pkg/generic_advdiff (implicit_r):
740      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
741        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
742      - fix implicit vertical diffusion or advection with NonLin FreeSurf
743        (was using current recip_hFacC instead of future recip_hFacC): set future
744        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
745        solver S/R ;
746      - fill diagnostics of vertical advective fluxes (computed from tendency)
747        when using implicit vert. advection;
748      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
749         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
750         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
751         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
752    o pkg/diagnostics:
753      - add diags for T & S tendency which goes through Adams-Bashforth.
754    
755    checkpoint63f (2011/11/30)
756    o pkg/obcs/obcs_calc_stevens.F:
757      - join some loops to reduce number of if-statements
758      - fix a bug in code for northern and southern boundaries.
759    o pkg/seaice/seaice_init_varia.F
760      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
761        caused zero ice-velocities for the B-grid code
762    o pkg/seaice/seaice_init_fixed.F
763      - fix a bug in the initialisation of the second metric terms
764        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
765      - this affects all seaice configurations with useCurviLinearGrid = .true.
766        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
767        = .true. (default)
768      - the only verification experiment affected is global_ocean.cs32x15:
769        icedyn, seaice, and seaice_dynmix (AD)
770    o pkg/thsice/thsice_diagnostics_state.F
771      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
772        not contain garbage that can lead to surprises in diagstats_calc.F
773    o model/src:
774      - move bi,bj loops inside INTEGR_CONTINUITY ;
775      - call INTEGR_CONTINUITY directly from forward_step.F
776        (previously called from momentum_correction_step.F)
777      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
778        forward_step.F and pkg/ecco/the_main_loop.F
779    o model/src/do_oceanic_phys.F:
780      - reset addMass to zero only if useICEFRONT ;
781      - separated k-loop for rhoInSitu calculation ;
782      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
783        and at constant T,S (= WdRHOdP);
784      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
785        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
786        transport of locally-referenced potential density);
787        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
788    o gluemnc:
789      - replace ncrcat with ncks when adding variables to *.glob.nc
790      - change the way variables without record dimensions are handled so that
791        files that have variables with and without record variables can be glued:
792        add a record dimension with a new unique name to be able to differentiate
793        between variable with and without a-prior record dimensions. Remove
794        this record dimension before adding the variable to the *.glob.nc file.
795        This procedure automatically works also for grid.*.nc files that do not
796        have any record dimension.
797    o verification/cpl_aim+ocn:
798      - generate new reference output on baudelaire (gfortran, mpich2) (previously
799        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
800    o pkg/obcs/obcs_calc_stevens.F:
801      - add code for northern and southern boundaries.
802      - reorder some loops to save some operations and so that drFBar can be scalar
803    o model/src:
804      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
805        truncation) and add diagnostics for Adams-Bashforth tendency increment.
806      - update test-exp. AD output:
807        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
808      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
809        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
810        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
811        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
812        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
813        tutorial_plume_on_slope.
814    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
815      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
816      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
817      does not even come with an F77 compiler anymore, this should not be
818      a limitation
819    
820    checkpoint63e (2011/11/06)
821    o pkg/seaice adjoint of LSR:
822      - substantially rework STORE dirs.
823      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
824        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
825        and only perform SOLV_MAX_FIXED adjoint iters.
826        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
827        always goes to same record, meaning that the last forward field will be
828        the one used in the adjoint - an approximation.
829      - now produces non-zero LSR-related gradients, and acceptable gradients for
830        An's zonal (x-z) test case (to be checked in)
831      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
832        (but these are screwed up by the thermodynamics in the first place);
833        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
834        output_adm.txt also reflects changes to seaice_lsr
835      - global_ocean.cs32x15:
836        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
837          (output_adm.seaice.txt was updated)
838        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
839          (output_adm.seaice_dynmix.txt)
840    o test-exp. exp4+stevens:
841      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
842    o pkg/seaice (lsr solver):
843      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
844        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
845      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
846      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
847        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
848      - compute (with new S/R) and print initial (+ free-driff sol. if available)
849        and final residual of linearised system.
850    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
851      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
852    o pkg/obcs: Stevens BCs (still only for east and west)
853      - fix Stevens BCs by using intermediate velocities of previous
854        time step as "baroclinic" contribution rather velocity of one grid cell
855        inside the boundaries; more consistent but makes the entire treatment
856        more complicated, requires new pickup files and two new S/Rs:
857        obcs_copy_uv_n and obcs_save_uv_n
858        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
859        (undefined by default)
860      - silently move computation of some grid factors into separate loops to
861        save some recomputations
862      - add a hack for non-linear free surface
863      - add a verification experiment to exp4 that tests this code
864    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
865    
866    checkpoint63d (2011/10/25)
867    o pkg/obcs + seaice-dynamics:
868      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
869        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
870        values (consistent with an implicit method).
871      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
872        return to older implementation (same results as before); note that none of
873        the "experimental" OBCS_SEAICE options are implemented in the new version.
874      - switch test exp. seaice_obcs to use new version (update output).
875    o pkg/seaice:
876      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
877      - add parenthesis in Water-Ice drag calculations (evp & lsr);
878      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
879        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
880      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
881        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
882    o pkg/layers:
883      - Include potential density as new coordinate (Thanks to David Munday)
884    o pkg/dic:
885      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
886        carbonate computation/output to CALC_PCO2_APPROX
887    o pkg/generic_advdiff
888      - make TAF generate code that vectorizes:
889        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
890    o model/src:
891      - improve vectorization also for adjoint code of
892        solve_tridiagonal and solve_pentadiagonal. As this requires up to
893        5 new 3D-fields, this code is only turned on for the combination of
894        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
895        for singular matrix check (only for TARGET_NEC_SX).
896      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
897        ALLOW_AUTODIFF. This flag now needs to be set outside of
898        solve_tri/pentadiagonal.F
899    o pkg/exf:
900      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
901        optional namelist EXF_NML_OBCS).
902      - add many debug-print (to trace down where pkg/cal error msg comes from)
903    o pkg/mom_vecinv/mom_vi_hdissip.F
904      - rearrange loops so that vectorization is improved and in particular
905        the adjoint routine vectorizes. The code is a little longer now, but I
906        think easier to read.
907        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
908    o pkg/seaice:
909      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
910    o pkg/exch2:
911      - alternative code (without tile x tile matrix) for cumulated (global) sum;
912        used as default; keep using matrix version in adjustment.cs-32x32x1.
913    o tools/build_options:
914      - after merging some MPI and/or multi-threads specific optfiles so that
915        the modified default optfile support both built (using genmake2 -mpi
916        for the MPI built, using genmake2 -omp for OpenMP built),
917        move now obsolete optfiles to tools/build_options/unsupported/
918       (add copy of email sent to support list in doc/optfiles_changes.txt)
919    
920    checkpoint63c (2011/09/28)
921    o pkg/ebm:
922      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
923        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
924    o pkg/seaice (SItracer pickup)
925    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
926      To be done:
927      - thorough testing of missing fields in S/R seaice_read_pickup
928      - thorough matching between generic tracers and specific fields used
929        (e.g. volume-weighted age, area-weighted age, salinity, ...)
930    o pkg/grdchk:
931      - all procs calculate and print finite-difference gradient (for testreport)
932      - change description output used by testreport;
933      - AD testing: also compare and report Finite-difference gradient;
934        => update all output_adm*.txt
935    o test exp. global_ocean_ebm:
936      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
937        and turn on exactConserve; update (fwd) output.
938    o pkg/seaice (LSR):
939      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
940      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
941        * identical results with non-CS topology (but save up to half of EXCH calls)
942        * no much changes in cs-32 verification tests since no ice at face edges
943         (differences due to convergence criteria, since nb of iterations changed)
944        * expect some differences on lat-lon-cap grid.
945        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
946    o pkg/exch2:
947      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
948        many tiles); until alternative coding is added, just add a stop.
949    o pkg/kpp:
950      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
951        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
952    o optfiles:
953      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
954        into corresponding standard one, which now support different build:
955        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
956      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
957    o pkg/obcs (seaice):
958      - add missing EXCH for uIce,vIce after applying OBCS;
959      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
960        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
961        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
962      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
963      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
964        and eedata.mth for MPI and mutlti-threaded testing.
965    o pkg/flt:
966      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
967      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
968      - fix pickup and trajectories + profiles output with multi-threads;
969      - add parameter to select group of fields to write along trajectory and
970        profile (default unchanged);
971      - only call PORT_RAND* function when flt_noise <> 0;
972      - add multi-threaded test for verification exp. flt_example.
973    o eesupp/src:
974      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
975      - USE_OMP_THREADING: check that number of threads (from eedata) matches
976        actual number (from env.var. setting).
977    o pkg/ebm:
978      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
979      - add multi-threaded test for verification exp. global_ocean_ebm
980    
981    checkpoint63b (2011/08/29)
982    o pkg/ebm:
983      - fix sign of runoff;
984      - update directly forcing fields (Qnet,EmPmR) to use standard
985        external_forcing_surf.F (remove ebm_forcing_surf.F);
986      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
987      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
988        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
989      - update global_ocean_ebm parameters file data and update output (fwd+ad).
990    o verification/matrix_example:
991      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
992        MPI and mutlti-threaded testing.
993    o pkg/matrix:
994      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
995      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
996      - fix for multi-threaded (remove DATA statement);
997      - use standard DIFFERENT_MULTIPLE function;
998      - add MATRIX_OPTIONS.h
999    o verification/matrix_example:
1000       To allow to split the domain in several tiles, change the domain size
1001        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1002        Western side) of land points.
1003    o (*_)write_pickup:
1004      - fix few bugs in mypackage_read/write_pickup.F
1005      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1006        array of length 1 (was caught by compiler syntax-check).
1007    o pkg/diagnostics (velocity potential solver):
1008      - fix initialisation of main diagonal matrix (for overlap values)
1009    o tools/build_options:
1010      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1011        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1012      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1013        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1014        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1015        and use "-devel" testreport option for standard testing on baudelaire.
1016    o pkg/grdchk:
1017      - Assume that all gradient-check position are within the same tile
1018        corresponding to global indices (iGloTile,jGloTile) and that
1019        positions (i,j indices or nbeg) are local to this tile;
1020      - set tile local-indices and proc. number according to tile global-indices;
1021      - remove grdchkwhichproc from namelist (retired param);
1022      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1023      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1024    o adding package bbl (Bottom Boundary Layer)
1025      description in MITgcm/pkg/bbl/bbl_description.tex
1026      example/test experiment in MITgcm_contrib/bbl
1027    o adjoint verifications
1028      - changed 5 experiments to multi-tiles
1029        * global_ocean.90x40x15
1030        * obcs_ctrl
1031        * offline_exf_seaice
1032        * tutorial_dic_adjoffline
1033        * tutorial_tracer_adjsens
1034        changed reference output for those that crossed tile boundaries
1035        (changed choices of gradient check positions)
1036      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1037      - temporary bug fix in grdchk_loc.F for obcs
1038    o genmake2 & testreport
1039      - add target "obj" (just for OBJFILES files) to Makefile;
1040      - add option to specify FEXTRAFLAGS on command line.
1041    o pkg/mypackage:
1042      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1043    
1044    checkpoint63a (2011/08/02)
1045  o pkg/diagnostics (velocity potential):  o pkg/diagnostics (velocity potential):
1046    - fix velocity-potential calculation when using OBCS: balance net inflow    - fix velocity-potential calculation when using OBCS: balance net inflow
1047      at each level (new S/R OBCS_DIAG_BALANCE).      at each level (new S/R OBCS_DIAG_BALANCE).
# Line 54  o pkg/gmredi: Line 1092  o pkg/gmredi:
1092     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1093     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1094    
1095  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
1096  o pkg/exch2:  o pkg/exch2:
1097   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1098   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
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