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revision 1.1469 by ifenty, Wed Jun 29 21:44:26 2011 UTC revision 1.1684 by jmc, Fri Jul 6 15:32:20 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63p (2012/07/06)
8    o pkg/autodiff:
9      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
10      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
11        which are now read from new parameter file "data.autodiff" (inAdExact
12        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
13      - add file "data.autodiff" in all verification/*/input_ad/ directories.
14      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
15        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
16    o verification/tutorial_tracer_adjsens/
17      - add extra sub-verification which uses "SOM" advection scheme
18        (2nd Order-Moment Advection Scheme, Prather Limiter) with
19          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
20        and in data:
21          multiDimAdvection=.TRUE.,
22          tempAdvScheme=81,
23          saltAdvScheme=81,
24    o model/src:
25      - introduce ALLOW_BALANCE_RELAX which allow the removal
26       of the global mean of relaxation terms by setting
27       balanceThetaClimRelax and balanceSaltClimRelax
28      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
29       This case is now treated appropriately in seaice_growth.F
30    o pkg/seaice:
31      - do balanceEmPmR and balanceQnet based on the net fluxes
32        (SItflux) that enter the ocean+ice system rather than QNET
33        and EMPMR. Works best in real fresh water.
34      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
35        out of the diagnotics bloc, and stored in global arrays.
36    
37    checkpoint63o (2012/06/29)
38    o vertical mixing schemes:
39      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
40      - replace computation of density (in Function STATE1, opps_calc.F) by a call
41        to S/R FIND_RHO_SCALAR
42      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
43        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
44        affects output (vermix.ggl90) at truncation level.
45    o testreport:
46      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
47        (nSx,nSy) for the number of threads (from eedata.mth)
48    o model/src:
49      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
50        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
51    o verification/tutorial_tracer_adjsens/
52      - compile with ALLOW_CG2D_NSA
53      - run with nonlinFreeSurf=3
54      - update reference output_adm.txt
55    o tools/genmake2:
56      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
57        refine usePROFILES switching off (only when NetCDF is not available).
58    o verification (atmospheric set-up):
59      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
60    o pkg/profiles : refine profiles and files handling.
61    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
62    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
63      - changes to use model/src/the_main_loop.F rather than the ecco version
64        in ecco type adjoint runs.
65    o model/src:
66      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
67      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
68      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
69    o model/src:
70      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
71        update output of test experiment bottom_ctrl_5x5.
72    o pkg/generic_advdiff:
73      - implement vertical bi-harmonic diffusion (for now, only for T & S and
74        only explicitly).
75    o verification/bottom_ctrl_5x5/
76      update reference output (results changed quite some time ago,
77      not sure when; but new reference results look ok in terms of grdchk)
78    o verification/1D_ocean_ice_column/
79      For verification purposes, the exact adjoint rather than an approx.
80      should be used (e.g., to comare against F.D. or TLM).
81      removed autodiff_inadmode*_ad.F routines in code_ad/
82      Update results/ accordingly.
83    o pkg/cal:
84      - change cal_getdate.F so that output date is function of input time only
85        (less ambiguous, not mixed up with input iteration number).
86      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
87    o pkg/diagnostics:
88      - implement calendarDumps also for stats-diags
89      - implement calendarDumps also for snap-shot output (negative freq)
90      - for now, ignores calendarDumps if non-zero phase-lag.
91    
92    checkpoint63n (2012/06/04)
93    o model/src:
94      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
95        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
96      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
97        similar to calc_r_star.F); update results of experiment internal_wave and
98        tutorial_global_oce_in_p (affected @ truncation level).
99    o pkg/shelfice:
100      - add parameterisation of advective-diffusive flux into the ice shelf
101        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
102      - simply eps3/3a computation
103    o eesupp:
104     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
105       between tiles, just fill-in edges assuming locally periodic subdomain) and
106       add corresponding exchange subroutines (EXCH0);
107     - new CG-solver version (_EX0) for disconnected-tiles special case.
108    o model/src (CG-solvers):
109     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
110       (similar final residual output and max-Iter number as with standard version);
111     - allows to store and use lowest-residual solution (standard & _SR versions);
112     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
113     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
114    o eesup/src:
115     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
116       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
117    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
118    
119    checkpoint63m (2012/04/27)
120    o pkg/shelfice:
121     - account for partical cells in surface level below ice-shelf for hydrostatic
122       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
123    o ad test experiments:
124     - update and rename to "ad_optfile.local" local AD-optfile specific to a
125       particular adjoint verification experiment (in verification/*/code_ad/)
126    o pkg/seaice & pkg/exf:
127     - Part two of ECCO-CLIVAR code merges.
128       Completes merge of seaice area relax. code.
129       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
130       to be set in EXF_OPTIONS.h since this pkg controls its I/O
131       (and avoids second CPP option in SEAICE_OPTIONS.h)
132     - change default value of costIceStart & costIceEnd to a valid date.
133     - add snowPrecip to HSNOW in seaice_growth
134    o pkg/ptracers:
135     - move ptracers summary and setup check into separated S/R ; add a check for
136       valid PTRACERS_Iter0 value (error+stop or just warning).
137    o pkg/cal (+ pkg/ecco):
138     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
139       as input; and for AD, unless both are not differentiable (e.g., k index)).
140    o model/src:
141     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
142       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
143       temporary set to usingZCoords value (to be changed to F when using shelfice).
144     - hydrostatic pressure: implement partial cell near the surface also for
145       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
146       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
147    o pkg/ctrl/ctrl_init.F:
148     - add a formal parameter to s/r ctrl_init_rec to print
149       xx_$(ctrl_valiable)_file for easier debugging
150     - move call of cal_* routines into the if-block where they are really
151       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
152       to specify a startdate
153    o pkg/seaice:
154     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
155       global_ocean.cs32x15/code versions).
156     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
157       verification experiment global_ocean.cs32x15.seaice and update results.
158    o pkg/exf:
159     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
160       (according to useExfYearlyFields).
161    o pkg/cal:
162     - move calendar setting & summary (previously in cal_readparams.F) into new
163       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
164       length of the simulation is set (after SET_PARMS call); This is an attempt
165       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
166     - For safety: keep a record of pkg/cal parameter settings status
167               to allow to STOP if one pkg/cal S/R is called too early.
168     - add a stop in all basic pkg/cal subroutines if called before setting is done.
169     - modify cal_getdate.F: stop when nothing was returned;
170       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
171       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
172    
173    checkpoint63l (2012/04/04)
174    o pkg/bbl:
175      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
176        update global_with_exf output.yearly.txt file.
177    o pkg/cal:
178      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
179      - remove 2 unsused and very short (1 line only) functions ;
180      - remove unsused subroutines from AD-Diff list.
181    o model/src:
182      - start to implement clean wait to stop in initialization S/R (config_check.F,
183         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
184    o folowing PRINT_MESSAGE changes:
185      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
186    o pkg/bbl:
187      - modification so it can work with z*
188      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
189      - global_with_exf/input.yearly verification; changes output.yearly.txt
190    o eesupp/src:
191      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
192        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
193      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
194        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
195      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
196      - when using MPI, always set usingMPI=T ; set default accordingly and stop
197        if not consistent.
198      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
199        argument is zero (in case called within single-thread section).
200    o pkg/fizhi:
201        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
202        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
203    o pkg/exch2:
204      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
205        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
206      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
207        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
208        with bad ones coming from a not-yet-updated halo.
209        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
210    o pkg/frazil:
211        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
212        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
213    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
214    o verification/lab_sea
215      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
216      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
217      * nTimeSteps 3 -> 4
218      * changed reference output accordingly
219    o pkg/ctrl:
220      * fix ctrl_get_gen for xx_sst, xx_sss
221    o pkg/fizhi:
222      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
223        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
224      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
225        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
226        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
227    o pkg/gmredi:
228      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
229    o pkg/fizhi:
230      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
231        (old)aces open64 tuv test.
232    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
233    o pkg/mom_vecinv:
234      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
235        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
236        with non-lin free-surf).
237    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
238      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
239      some compilers (gfortran 4.6.0 on MacOS)
240    o momentum:
241      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
242        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
243        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
244    
245    checkpoint63k (2012/03/17)
246    o model/src:
247       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
248         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
249       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
250         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
251    o model/src: solve_*diagonal.F
252       - replace division with multiplication by inverse (similar to original version)
253         update output of AD exp. global_ocean.90x40x15.
254       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
255         to enable the use of the vectorized & differentiable solve_tridiagonal.F
256       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
257         vertical advection (to get solve_tridiagonal tested in AD mode).
258    o pkg/seaice: ECCO-CLIVAR merge:
259      1. seaice AREA relaxation
260         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
261         * runtime flag: SEAICE_tauAreaObsRelax
262      2. modified global mean cost imbalance code: CPP option
263          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
264    o another iteration on solve_*diagonal.F
265       Make choices independent of AUTODIFF
266       Default will be the adjoinable vectorized version.
267       Alternative choices are:
268       * non-adjoinable original version with low memory footprint:
269         #define SOLVE_DIAGONAL_LOWMEMORY
270       * still adjoinable but does not vectorize (k as inner-most loop):
271         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
272    o testreport
273     - add option to use a home made wrapper around "make"
274     - remove MITGCM_IEEE env. variable (no longer active)
275    o pkg/shelfice
276     - improve computation of friction velocity for velocity dependent
277       exchange coefficients: include velocities into SHELFICEBoundaryLayer
278       block to average velocities vertically
279     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
280    o Modify diagonal solvers, now three versions (upon request):
281      #ifndef SOLVE_DIAGONAL_AUTODIFF
282        1. default version (dating back a while ago)
283      #else /* def SOLVE_DIAGONAL_AUTODIFF */
284      # ifdef SOLVE_DIAGONAL_KINNER
285        2. adjoinable version with k-innermost loop (G. Forget)
286      # else
287        3. adjoinable vectorized version of 2.
288      # endif
289      #endif /* SOLVE_DIAGONAL_AUTODIFF */
290      All flags are currently set within routines, but could/should be moved to CPP-options.
291      Array bounds for 1. are as before, for 2.,3. cover the entire domain
292      (could be changed for 1. too).
293    o verification/lab_sea (fwd):
294      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
295        use 7 categories (except hb87), new solve4temp params (except salt_plume),
296        constant salinity (=4) or variable salinity (salt_plume) done through
297        SItracer.
298    o pkg/seaice:
299      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
300      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
301         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
302        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
303        SEAICE_freeze got retired) but already better than previously with
304        SEAICE_freeze=123456.7 deg.C;
305      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
306        (safer multi-threaded setting); always set SEAICEuseEVP;
307      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
308        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
309        stop if multiple specifications for the same coeff; make sure default
310        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
311    o pkg/obcs:
312      - allow to switch to upwind 1rst order advection scheme for the advective
313        flux computation at the open-boundary; disabled for adjoint built.
314    o pkg/ptracers:
315      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
316      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
317      - add parameter to decide when to start a tracer; use internal flag to
318        know which tracer to step-forward; switch this internal flag at the top
319        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
320        for adjoint built.
321    o pkg/seaice:
322      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
323      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
324      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
325    o pkg/ecco:
326      - fix writing of output file DiagnosCost_ClimSalt/Theta
327        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
328    o pkg/seaice:
329      - add missing initialisation of COR_ICE array in dynsolver.F
330      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
331        compiled either way, and is tested in all exps (multidim was only tested
332        in lab_sea ad before).
333      - cosmetic change to prepare for future addition of ITD. no change to results.
334        no defaults change.
335      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
336      - by lack of adequate verification experiments, I further used custom versions
337        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
338        should be correct.
339      - avoid recomputations in ad.
340    o array initialisation in adjoint mode:
341      1) pkg/mom_common/mom_calc_ke.F:
342        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
343        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
344        part this initialisation is gone, resulting in Floating Point Exception
345        (caught by open64 compiler with debug option).
346      2) model/src/convective_weights.F
347        set output convectCount over the full array range (instead of doing
348        an update): this fix a similar issue when called within recomputation (adjoint)
349        which could by-pass the initialisation (normally done in the caller S/R).
350    o pkg/seaice:
351      - final version of turbulent flux params, as agreed at MIT ice meet:
352           SEAICE_mcPheePiston (default is ~ 0.000875)
353           SEAICE_mcPheeTaper (default is 0.)
354           SEAICE_frazilFrac (defualt is 1.)
355           SEAICE_mcPheeStepFunc (default is false)
356      - changes results at trunction error level
357      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
358    o added pkg/frazil:
359      - see frazil_description.tex for details
360      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
361    o pkg/shelfice/shelfice_thermodynamics.F
362      - fix exponents for velocity dependent exchange coefficients: change
363        from 2/3(=0) to 0.66666666666666667
364      - move computation of velocity dependent exchange coefficients into
365        separate loop, so that it applies to both thermodynamics
366      - move some divisions by constants out of loops
367    
368    checkpoint63j (2012/02/16)
369    o pkg/seaice:
370      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
371      - SItracer:  added run time params, and allow coupling to ocn salinity.
372    o pkg/seaice: remove (almost) all divisions by constants within loops
373      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
374      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
375      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
376      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
377    o pkg/seaice :
378      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
379        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
380      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
381      - add permanent SItflux diag that corresponds to TFLUX but includes
382        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
383      - allow activation/testing of a fix for suspected missing term in
384        ocn-ice heat budget (to be confirmed). To test this, you want to
385        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
386        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
387      - no change in results, fwd or ad.
388    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
389      - switch to variable freezing point.
390           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
391      - bug fix : the sublimation term that was missing is now activated.
392           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
393      - bug fix : flooding sign term for SIsal0.NE.0.
394           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
395    o pkg/seaice:
396      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
397        is now the default, and the old default constant freezing point is recovered
398        with SEAICE_tempFrz0    = -1.96,
399             SEAICE_dTempFrz_dS = 0.,
400      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
401      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
402      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
403        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
404      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
405        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
406      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
407        seaice_growth r149 for legacy branch (no results change).
408      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
409        from I. Fenty).
410      - results did not change except for global_ocean.cs32x15, mostly due to the
411        switch to variable freezing point (see above item for detail).
412    o pkg/thsice:
413      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
414        seawater freezing in thsice_calc_thickn (not used).
415    o pkg/seaice: turbulent flux term specification via run time params.
416      - replace CPP switches with run time switches to facilitate testing
417      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
418                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
419      - added runtime parameter : SEAICEturbFluxFormula
420      - move Mcphee constants to SEAICE_PARAMS.h
421      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
422                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
423                 remove seaice_summary call (moved to seaice_init_fixed)
424      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
425        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
426      - seaice_summary.F : add missing report of read turbulent flux term set up
427                           and SITRACER.
428      - seaice_check.F : check range; inform and stop if retired CPPs are used
429                         (incl. SEAICE_AGE).
430      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
431             CPP switch, same computation as before for the different options.
432      - change results at the truncation level.
433    o pkg/seaice:
434      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
435        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
436        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
437      - update verification/*/input*/data.seaice:
438        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
439        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
440        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
441        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
442    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
443      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
444        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
445        difference in results only due to machine truncation.
446      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
447        MaykutPolySatVap; keep MIN_LWDOWN.
448      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
449      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
450        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
451    o pkg/salt_plume:
452      - isolate saltPlumeFlux array exch into a specific S/R called from
453        do_oceanic_phys.F
454      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
455    o verification:
456      - move untested set-up to MITgcm_contrib/verification_other.
457    o pkg/seaice:
458      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
459    o pkg/seaice:
460      - seaice_solve4temp.F (keeping results unchanged):
461        * add 2 future run-time params to select which saturation vapor pressure
462          formula is used and how post-iteration fluxes are set.
463          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
464        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
465          the linearized expression to stay consistent with tsurf finding.
466      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
467        can be < 0.
468    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
469      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
470        conductive heat flux F_c , and add it explicitly when updating tsurf as
471        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
472        so that now F_ia has a consistent meaning through the entire routine.
473        This causes differences at truncation level: update output of fwd exp.
474        global_ocean.cs32x15.seaice.
475    o pkg/seaice:
476      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
477        of arrays, sign/direction of fluxes; no effect on results.
478      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
479        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
480        note: this should have been done before changing celsius2K default.
481      - to keep results unchanged, add back old value of celsius2K in verification
482        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
483      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
484        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
485        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
486        freezing temp is consistent with value in seaice_growth.F ; this causes
487        differences at machine truncation level: update lab_sea AD output (3/4).
488    o pkg/seaice:
489      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
490        and climsst/sss even when using seaice (to prevent calculation that might
491        use SST on land); does not affect any verification exp.
492      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
493        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
494    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
495      over land (non-legacy code)
496    o vectorize salt_plume package:
497      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
498      - this code computes plumebk everywhere (also over land), thus requires
499        code to avoid divisions by zero and catch the case of kLev=Nr.
500      - efficiency of salt_plume_frac is still sub-optimal
501    o tools (genmake2):
502      - fix makefile NAME specification (option: -makefile NAME) by adding
503        "-f $MAKEFILE" in few places where it was missing including makedepend
504        command (contribution from Paul).
505    
506    checkpoint63i (2012/01/24)
507    o model/src:
508      - add factorized versions of some EOS code to find_rho.F,
509        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
510    o model/src:
511      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
512      - change default celsius2K from 273.16 to 273.15
513      - to keep results unchanged, add back old value of celsius2K in verification
514        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
515         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
516    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
517      to make TAF generate vectorizable code
518    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
519       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
520       have flags that do this more efficiently.
521    o pkg/diagnostics/diagstats_calc.F
522      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
523    o pkg/obcs (with exch2):
524      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
525        and remove code (in obcs_readparms.F) which was based on EXCH of indices
526        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
527    o pkg/exf and seaice exp:
528      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
529        so that switching off area & heff advection flags does not affect results.
530      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
531      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
532        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
533        results of verification experiments: 1D_ocean_ice_column(fwd),
534        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
535        and offline_exf_seaice (all 4).
536    o pkg/seaice:
537      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
538        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
539      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
540        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
541        not multi-dim advection;
542      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
543        SHORTWAVE_HEATING #undef.
544    o optim: make Makefile more robust (?)
545    o pkg/obcs:
546      * fix treatment of obcs_read_pickup for TAF
547    o pkg/shelfice:
548      * add missing initialisation of num_shifwflx
549      * new adjoint verification exp. for isomip
550      * change Prandtl and Schmidt numbers from generic formulations
551        (in terms of model diffus. and visc.) to separate runtime
552        parameters, with Holland and Jenkins (1999) default values.
553    o pkg/exf (interpolation):
554      - extended input field (2 rows) near the N & S poles:
555        * fill in with the symetric value (when even Nb of data in longitude)
556        * add average value at the poles only for scalar quantities ; for vector
557          component interpolation, skip the averaging and keep duplicated values,
558          unless the 2 components have same location (uvInterp=T) in which case
559          interpolate the 2 components together using S/R EXF_INTERP_UV.
560      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
561        together: this allows to account properly for local orientation when
562        averaging at N & S pole.
563      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
564        exf-interpolation near N & S poles. Undef by default.
565      - add debug check/print on 1rst iter if debugLevel >=2.
566    o pkg/exf:
567      - change masking flags definition (no longer "parameter"), put them in
568        common block and set them in S/R EXF_INIT_FIXED.
569      - change recognized masking flag from s,u,v to c,w,s since the mask
570        to use (maskC,W,S) depends on position on model grid and has little to
571        do with scalar/vector difference; fix masking if using P-coordinates.
572      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
573        and update results of exp. global_with_exf (x2).
574      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
575    o pkg/obcs
576      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
577    o pkg/exf (interpolation):
578      - assume periodicity in X only if input field cover full longitude range.
579      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
580        and should vectorise).
581      - fix input lat of the 2 added row (in case we provide N.pole data).
582    
583    checkpoint63h (2011/12/30)
584    o pkg/seaice:
585      - change declaration of UVM from _RL to _RS in order to get B-grid
586        uIce,vIce monitor when _RS = real*4
587    o pkg/offline:
588      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
589      - compute vertical velocity if not read from file (switch on exactConserv
590        & staggerTimeStep);
591      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
592    o verification:
593      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
594        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
595        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
596      - update output of exp. global_ocean.cs32x15.viscA4 after changing
597        grid-file angles (used here for coriolis-3d);
598      - remove (or gzip) few files not needed to run fizhi-cs experiments.
599    o pkg/exf (vector interpolation):
600      - rotate vector component toward local grid-axis orientation using grid-angles
601        (stored in GRID.h) instead of locally computed rotation angle; keep old code
602        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
603    o pkg/seaice:
604      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
605        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
606    o pkg/PKG_OPTIONS.h files:
607      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
608        outside of the #ifdef ALLOW_THISPKG / #endif block.
609      - update verification/*/code/PKG_OPTIONS.h files.
610    o add a verification experiment (offline_exf_seaice/input.seaice) that test
611      the B-grid LSOR solver
612    o pkg/seaice: sort out emissivity and long wave radiation step 2:
613      - add emissivity for snow and ice as new run-time parameters
614        (unfortunately) that default to the corresponding exf values; this
615        changes results in most verification experiments so that for backward
616        compatibility these parameter have to be set explicitly to inconsistent
617        values (ugly);
618      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
619        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
620        until we agree how to handle this bug properly
621    o pkg/exf (interpolation):
622      - add a set of run-time param ({inputfield}_interpMethod), one for
623        each interpolated input field, to select the interpolation method
624        with a value of zero switching off the interpolation;
625      - print interpolation parameters to standard output;
626      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
627        (to use instead runoff_interpMethod=0 in data.exf).
628      - simplify default setting of interpolation parameters (for all fields,
629        set position to match model grid cell-center position, leading to trivial
630        interpolation in case of regular Lat-Lon grid) and fix for the case of
631        non-uniform delY.
632    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
633       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
634       this factor is absolutely required, because the lw exitance (= out-going
635       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
636       where the reflectivity rho = 1-emissivity for conservation reasons. Once
637       this is established, we can remove the CPP-Flag (if we want to).
638    o pkg/seaice:
639      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
640        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
641      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
642        what the name implies (and not emissivity*BoltzmannConstant), this means
643        the old default value of 5.5e-8 now means
644        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
645        S/R exf_readparms
646      - FV-discretization of the B-grid LSOR solver, turn on with
647        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
648        of the calling routine dynsolver, so that B and C-grid code look a
649        little more alike.
650      - fix index bugs in ostres.F (B-grid code)
651    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
652    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
653      default for SEAICE_emissivity, if useEXF; requires setting a wrong
654      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
655      backward compatiblity
656    o model/src: use sigmaR in calc_ivdc
657    
658    checkpoint63g (2011/12/16)
659    o pkg/seaice/seaice_growth.F:
660      fix heat conservation of the coupled ocean-seaice system.
661      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
662      solid vs liquid water treatment is resolved via QNET.
663    o pkg/seaice/seaice_growth.F:
664      add missing term for sublimation in saltFlux, which was breaking conservation.
665    o pkg/seaice/seaice_model.F:
666      Remove this patholigical case treatment in evolution branch,
667      where it is un-necessary and breaks conservation.
668      Update global_ocean.cs32x15/results accordingly for
669      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
670    o model/src:
671      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
672      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
673    o pkg/obcs:
674      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
675      tendency for temperature and salinity that is then applied to update
676      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
677      horizontal advection and diffusion contributions on the boundary (in
678      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
679      removing the mask in S/R timestep_tracer. The advantage of this approach is
680      that the updated tracer values include contributions from the surface
681      forcing and vertical diffusion.
682      This modification changes exp4.stevens because of vertical diffusion.
683    o model/src:
684      change non-curvilinear grid setting to also work with exch2 + blank tiles:
685      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
686        face dimensions.
687      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
688        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
689        and INI_SPHERICAL_POLAR_GRID.
690      change test-experiment global_ocean.90x40x15:
691      - split the domain in many more tiles (9x4 tiles of 10x10 each);
692      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
693      - update results of both test (std & dwnslp).
694    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
695       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
696    o model/src:
697      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
698        and fix initialisation when using sigma-coords.
699    o model/src:
700     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
701       to their current value at the beginning of forward_step.F": add a new run-time
702       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
703     - set doResetHFactors=T in the following test exp:
704        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
705        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
706        and tutorial_global_oce_in_p (nonLinFS in p)
707    o pkg/ecco
708      - added IES cost term
709    o verification/advect_xz
710      - scale down the depth by 1/100 (from 200 km to just 2.km)
711      - add secondary test using divergent flow, r-star and implicit vertical advection.
712      - add note (check_conserve_TS.txt) and matlab script to check global
713        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
714    o pkg/rbcs:
715      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
716    o pkg/obcs (Stevens BCs):
717      - fix various problems in the phase speed computations of the Stevens
718        boundary conditions:
719        - sign error for western and southern boundaries,
720        - time tendencies were underestimated by factor of dTracerLev and some just
721          zero (for multidim advection schemes) -> now estimate time tendencies
722          from difference between previous (n) time level and the one before (n-1);
723          this requires storing a field per tracer per boundary, also in the pickup
724          files.
725        - replace deltaTmom in cflMer/Zon computation with dTracerLev
726        - set default phase velocity to cflMer/Zon
727      - update verification experiment exp4.stevens
728    o pkg/generic_advdiff (implicit_r):
729      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
730        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
731      - fix implicit vertical diffusion or advection with NonLin FreeSurf
732        (was using current recip_hFacC instead of future recip_hFacC): set future
733        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
734        solver S/R ;
735      - fill diagnostics of vertical advective fluxes (computed from tendency)
736        when using implicit vert. advection;
737      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
738         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
739         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
740         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
741    o pkg/diagnostics:
742      - add diags for T & S tendency which goes through Adams-Bashforth.
743    
744    checkpoint63f (2011/11/30)
745    o pkg/obcs/obcs_calc_stevens.F:
746      - join some loops to reduce number of if-statements
747      - fix a bug in code for northern and southern boundaries.
748    o pkg/seaice/seaice_init_varia.F
749      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
750        caused zero ice-velocities for the B-grid code
751    o pkg/seaice/seaice_init_fixed.F
752      - fix a bug in the initialisation of the second metric terms
753        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
754      - this affects all seaice configurations with useCurviLinearGrid = .true.
755        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
756        = .true. (default)
757      - the only verification experiment affected is global_ocean.cs32x15:
758        icedyn, seaice, and seaice_dynmix (AD)
759    o pkg/thsice/thsice_diagnostics_state.F
760      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
761        not contain garbage that can lead to surprises in diagstats_calc.F
762    o model/src:
763      - move bi,bj loops inside INTEGR_CONTINUITY ;
764      - call INTEGR_CONTINUITY directly from forward_step.F
765        (previously called from momentum_correction_step.F)
766      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
767        forward_step.F and pkg/ecco/the_main_loop.F
768    o model/src/do_oceanic_phys.F:
769      - reset addMass to zero only if useICEFRONT ;
770      - separated k-loop for rhoInSitu calculation ;
771      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
772        and at constant T,S (= WdRHOdP);
773      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
774        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
775        transport of locally-referenced potential density);
776        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
777    o gluemnc:
778      - replace ncrcat with ncks when adding variables to *.glob.nc
779      - change the way variables without record dimensions are handled so that
780        files that have variables with and without record variables can be glued:
781        add a record dimension with a new unique name to be able to differentiate
782        between variable with and without a-prior record dimensions. Remove
783        this record dimension before adding the variable to the *.glob.nc file.
784        This procedure automatically works also for grid.*.nc files that do not
785        have any record dimension.
786    o verification/cpl_aim+ocn:
787      - generate new reference output on baudelaire (gfortran, mpich2) (previously
788        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
789    o pkg/obcs/obcs_calc_stevens.F:
790      - add code for northern and southern boundaries.
791      - reorder some loops to save some operations and so that drFBar can be scalar
792    o model/src:
793      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
794        truncation) and add diagnostics for Adams-Bashforth tendency increment.
795      - update test-exp. AD output:
796        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
797      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
798        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
799        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
800        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
801        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
802        tutorial_plume_on_slope.
803    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
804      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
805      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
806      does not even come with an F77 compiler anymore, this should not be
807      a limitation
808    
809    checkpoint63e (2011/11/06)
810    o pkg/seaice adjoint of LSR:
811      - substantially rework STORE dirs.
812      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
813        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
814        and only perform SOLV_MAX_FIXED adjoint iters.
815        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
816        always goes to same record, meaning that the last forward field will be
817        the one used in the adjoint - an approximation.
818      - now produces non-zero LSR-related gradients, and acceptable gradients for
819        An's zonal (x-z) test case (to be checked in)
820      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
821        (but these are screwed up by the thermodynamics in the first place);
822        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
823        output_adm.txt also reflects changes to seaice_lsr
824      - global_ocean.cs32x15:
825        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
826          (output_adm.seaice.txt was updated)
827        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
828          (output_adm.seaice_dynmix.txt)
829    o test-exp. exp4+stevens:
830      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
831    o pkg/seaice (lsr solver):
832      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
833        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
834      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
835      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
836        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
837      - compute (with new S/R) and print initial (+ free-driff sol. if available)
838        and final residual of linearised system.
839    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
840      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
841    o pkg/obcs: Stevens BCs (still only for east and west)
842      - fix Stevens BCs by using intermediate velocities of previous
843        time step as "baroclinic" contribution rather velocity of one grid cell
844        inside the boundaries; more consistent but makes the entire treatment
845        more complicated, requires new pickup files and two new S/Rs:
846        obcs_copy_uv_n and obcs_save_uv_n
847        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
848        (undefined by default)
849      - silently move computation of some grid factors into separate loops to
850        save some recomputations
851      - add a hack for non-linear free surface
852      - add a verification experiment to exp4 that tests this code
853    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
854    
855    checkpoint63d (2011/10/25)
856    o pkg/obcs + seaice-dynamics:
857      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
858        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
859        values (consistent with an implicit method).
860      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
861        return to older implementation (same results as before); note that none of
862        the "experimental" OBCS_SEAICE options are implemented in the new version.
863      - switch test exp. seaice_obcs to use new version (update output).
864    o pkg/seaice:
865      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
866      - add parenthesis in Water-Ice drag calculations (evp & lsr);
867      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
868        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
869      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
870        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
871    o pkg/layers:
872      - Include potential density as new coordinate (Thanks to David Munday)
873    o pkg/dic:
874      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
875        carbonate computation/output to CALC_PCO2_APPROX
876    o pkg/generic_advdiff
877      - make TAF generate code that vectorizes:
878        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
879    o model/src:
880      - improve vectorization also for adjoint code of
881        solve_tridiagonal and solve_pentadiagonal. As this requires up to
882        5 new 3D-fields, this code is only turned on for the combination of
883        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
884        for singular matrix check (only for TARGET_NEC_SX).
885      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
886        ALLOW_AUTODIFF. This flag now needs to be set outside of
887        solve_tri/pentadiagonal.F
888    o pkg/exf:
889      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
890        optional namelist EXF_NML_OBCS).
891      - add many debug-print (to trace down where pkg/cal error msg comes from)
892    o pkg/mom_vecinv/mom_vi_hdissip.F
893      - rearrange loops so that vectorization is improved and in particular
894        the adjoint routine vectorizes. The code is a little longer now, but I
895        think easier to read.
896        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
897    o pkg/seaice:
898      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
899    o pkg/exch2:
900      - alternative code (without tile x tile matrix) for cumulated (global) sum;
901        used as default; keep using matrix version in adjustment.cs-32x32x1.
902    o tools/build_options:
903      - after merging some MPI and/or multi-threads specific optfiles so that
904        the modified default optfile support both built (using genmake2 -mpi
905        for the MPI built, using genmake2 -omp for OpenMP built),
906        move now obsolete optfiles to tools/build_options/unsupported/
907       (add copy of email sent to support list in doc/optfiles_changes.txt)
908    
909    checkpoint63c (2011/09/28)
910    o pkg/ebm:
911      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
912        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
913    o pkg/seaice (SItracer pickup)
914    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
915      To be done:
916      - thorough testing of missing fields in S/R seaice_read_pickup
917      - thorough matching between generic tracers and specific fields used
918        (e.g. volume-weighted age, area-weighted age, salinity, ...)
919    o pkg/grdchk:
920      - all procs calculate and print finite-difference gradient (for testreport)
921      - change description output used by testreport;
922      - AD testing: also compare and report Finite-difference gradient;
923        => update all output_adm*.txt
924    o test exp. global_ocean_ebm:
925      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
926        and turn on exactConserve; update (fwd) output.
927    o pkg/seaice (LSR):
928      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
929      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
930        * identical results with non-CS topology (but save up to half of EXCH calls)
931        * no much changes in cs-32 verification tests since no ice at face edges
932         (differences due to convergence criteria, since nb of iterations changed)
933        * expect some differences on lat-lon-cap grid.
934        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
935    o pkg/exch2:
936      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
937        many tiles); until alternative coding is added, just add a stop.
938    o pkg/kpp:
939      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
940        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
941    o optfiles:
942      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
943        into corresponding standard one, which now support different build:
944        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
945      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
946    o pkg/obcs (seaice):
947      - add missing EXCH for uIce,vIce after applying OBCS;
948      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
949        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
950        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
951      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
952      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
953        and eedata.mth for MPI and mutlti-threaded testing.
954    o pkg/flt:
955      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
956      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
957      - fix pickup and trajectories + profiles output with multi-threads;
958      - add parameter to select group of fields to write along trajectory and
959        profile (default unchanged);
960      - only call PORT_RAND* function when flt_noise <> 0;
961      - add multi-threaded test for verification exp. flt_example.
962    o eesupp/src:
963      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
964      - USE_OMP_THREADING: check that number of threads (from eedata) matches
965        actual number (from env.var. setting).
966    o pkg/ebm:
967      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
968      - add multi-threaded test for verification exp. global_ocean_ebm
969    
970    checkpoint63b (2011/08/29)
971    o pkg/ebm:
972      - fix sign of runoff;
973      - update directly forcing fields (Qnet,EmPmR) to use standard
974        external_forcing_surf.F (remove ebm_forcing_surf.F);
975      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
976      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
977        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
978      - update global_ocean_ebm parameters file data and update output (fwd+ad).
979    o verification/matrix_example:
980      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
981        MPI and mutlti-threaded testing.
982    o pkg/matrix:
983      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
984      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
985      - fix for multi-threaded (remove DATA statement);
986      - use standard DIFFERENT_MULTIPLE function;
987      - add MATRIX_OPTIONS.h
988    o verification/matrix_example:
989       To allow to split the domain in several tiles, change the domain size
990        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
991        Western side) of land points.
992    o (*_)write_pickup:
993      - fix few bugs in mypackage_read/write_pickup.F
994      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
995        array of length 1 (was caught by compiler syntax-check).
996    o pkg/diagnostics (velocity potential solver):
997      - fix initialisation of main diagonal matrix (for overlap values)
998    o tools/build_options:
999      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1000        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1001      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1002        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1003        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1004        and use "-devel" testreport option for standard testing on baudelaire.
1005    o pkg/grdchk:
1006      - Assume that all gradient-check position are within the same tile
1007        corresponding to global indices (iGloTile,jGloTile) and that
1008        positions (i,j indices or nbeg) are local to this tile;
1009      - set tile local-indices and proc. number according to tile global-indices;
1010      - remove grdchkwhichproc from namelist (retired param);
1011      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1012      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1013    o adding package bbl (Bottom Boundary Layer)
1014      description in MITgcm/pkg/bbl/bbl_description.tex
1015      example/test experiment in MITgcm_contrib/bbl
1016    o adjoint verifications
1017      - changed 5 experiments to multi-tiles
1018        * global_ocean.90x40x15
1019        * obcs_ctrl
1020        * offline_exf_seaice
1021        * tutorial_dic_adjoffline
1022        * tutorial_tracer_adjsens
1023        changed reference output for those that crossed tile boundaries
1024        (changed choices of gradient check positions)
1025      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1026      - temporary bug fix in grdchk_loc.F for obcs
1027    o genmake2 & testreport
1028      - add target "obj" (just for OBJFILES files) to Makefile;
1029      - add option to specify FEXTRAFLAGS on command line.
1030    o pkg/mypackage:
1031      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1032    
1033    checkpoint63a (2011/08/02)
1034    o pkg/diagnostics (velocity potential):
1035      - fix velocity-potential calculation when using OBCS: balance net inflow
1036        at each level (new S/R OBCS_DIAG_BALANCE).
1037      - fix some of the problems with OBCS in stream-function calculation.
1038    o pkg/exf/exf_readparms.F
1039      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1040        EXF_NML_OBCS) more consistent, so that you need not have these lists
1041        in data.exf when they are not used.
1042    o optim/optim_readdata.F:
1043      - add some output about obcs variables that might help debugging
1044      - add a check about nvarlength
1045    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1046    o pkg/diagnostics (velocity potential):
1047      - fix mask for OBCS (still problems in stream-function with OBCS);
1048      - add specific parameter (default = main code CG2D params) for solver;
1049      - in case of poor convergence, use solution corresponding to lowest residual.
1050    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1051      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1052      and should be avoided where possible.
1053    o model/src (rStar):
1054      - include r* effect on reference-state (PhiRef) in totPhiHyd
1055        (so that it's really the potential anomaly at the cell center);
1056        affect solution only if z* with full pressure in EOS.
1057      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1058        update output (because of z* in totPhiHyd and viscA4 changes);
1059      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1060        @ constant r) until interpolation at constant r is implemented.
1061    o pkg/diagnostics
1062      - fix RCENTER diagnostics in case cell center is not at interface middle
1063    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1064      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1065      that THETA and SALT are "conservative temperature" and "absolute
1066      salinity"
1067    o pkg/ctrl
1068      - fix computation of endrec in s/r ctrl_init_rec
1069      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1070    o pkg/seaice/seaice_growth.F
1071      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1072        remove then obsolete STORE directives
1073      - fix STORE directives for tice and tices, so that only the
1074        appropriate part of the fields are stored (and not the entire
1075        field); update global_ocean.cs32x15.seaice AD output.
1076      - cosmetic changes: adjust CPP flags and indentation for better
1077        legibilty
1078    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1079      Chris Wilson)
1080    o pkg/gmredi:
1081       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1082       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1083    
1084    checkpoint63  (2011/07/11)
1085    o pkg/exch2:
1086     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1087     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1088       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1089       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1090    o pkg/diagnostics:
1091     - deal with pairs of post-processed diags which are computed together; in
1092       particular, re-order list of diags within 1 file to save 2nd computation.
1093     - add S/R to compute velocity stream-function (called after velocity-potential
1094       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1095     - add parameter to select grid-point location where PsiVEL == 0.
1096    o eesupp/src:
1097       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1098       (specific S/R needed with exch2 topology - for now, just print an error msg)
1099  o pkg/shelfice  o pkg/shelfice
1100   - Implement friction velocity-dependent transfer coefficients following   - Implement friction velocity-dependent transfer coefficients following
1101     Holland and Jenkins, JPO, 1999     Holland and Jenkins, JPO, 1999
# Line 27  o pkg/seaice/seaice_growth.F: Line 1119  o pkg/seaice/seaice_growth.F:
1119      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1120      non-legacy seaice_solve4temp.      non-legacy seaice_solve4temp.
1121    - add diagnostic of the residual sublimation freshwater flux (the freshwater    - add diagnostic of the residual sublimation freshwater flux (the freshwater
1122      flux taken from the ocean if the total actual latent heat fluxes exceed      flux taken from the ocean if the total actual latent heat fluxes exceed
1123      the maximum)      the maximum)
1124    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1125     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
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