/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1518 by mlosch, Mon Oct 24 16:12:39 2011 UTC revision 1.1682 by jmc, Thu Jul 5 19:38:02 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/autodiff:
8      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
9      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
10        which are now read from new parameter file "data.autodiff" (inAdExact
11        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
12      - add file "data.autodiff" in all verification/*/input_ad/ directories.
13      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
14        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
15    o verification/tutorial_tracer_adjsens/
16      - add extra sub-verification which uses "SOM" advection scheme
17        (2nd Order-Moment Advection Scheme, Prather Limiter) with
18          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
19        and in data:
20          multiDimAdvection=.TRUE.,
21          tempAdvScheme=81,
22          saltAdvScheme=81,
23    
24    checkpoint63o (2012/06/29)
25    o vertical mixing schemes:
26      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
27      - replace computation of density (in Function STATE1, opps_calc.F) by a call
28        to S/R FIND_RHO_SCALAR
29      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
30        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
31        affects output (vermix.ggl90) at truncation level.
32    o testreport:
33      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
34        (nSx,nSy) for the number of threads (from eedata.mth)
35    o model/src:
36      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
37        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
38    o verification/tutorial_tracer_adjsens/
39      - compile with ALLOW_CG2D_NSA
40      - run with nonlinFreeSurf=3
41      - update reference output_adm.txt
42    o tools/genmake2:
43      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
44        refine usePROFILES switching off (only when NetCDF is not available).
45    o verification (atmospheric set-up):
46      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
47    o pkg/profiles : refine profiles and files handling.
48    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
49    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
50      - changes to use model/src/the_main_loop.F rather than the ecco version
51        in ecco type adjoint runs.
52    o model/src:
53      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
54      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
55      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
56    o model/src:
57      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
58        update output of test experiment bottom_ctrl_5x5.
59    o pkg/generic_advdiff:
60      - implement vertical bi-harmonic diffusion (for now, only for T & S and
61        only explicitly).
62    o verification/bottom_ctrl_5x5/
63      update reference output (results changed quite some time ago,
64      not sure when; but new reference results look ok in terms of grdchk)
65    o verification/1D_ocean_ice_column/
66      For verification purposes, the exact adjoint rather than an approx.
67      should be used (e.g., to comare against F.D. or TLM).
68      removed autodiff_inadmode*_ad.F routines in code_ad/
69      Update results/ accordingly.
70    o pkg/cal:
71      - change cal_getdate.F so that output date is function of input time only
72        (less ambiguous, not mixed up with input iteration number).
73      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
74    o pkg/diagnostics:
75      - implement calendarDumps also for stats-diags
76      - implement calendarDumps also for snap-shot output (negative freq)
77      - for now, ignores calendarDumps if non-zero phase-lag.
78    
79    checkpoint63n (2012/06/04)
80    o model/src:
81      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
82        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
83      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
84        similar to calc_r_star.F); update results of experiment internal_wave and
85        tutorial_global_oce_in_p (affected @ truncation level).
86    o pkg/shelfice:
87      - add parameterisation of advective-diffusive flux into the ice shelf
88        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
89      - simply eps3/3a computation
90    o eesupp:
91     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
92       between tiles, just fill-in edges assuming locally periodic subdomain) and
93       add corresponding exchange subroutines (EXCH0);
94     - new CG-solver version (_EX0) for disconnected-tiles special case.
95    o model/src (CG-solvers):
96     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
97       (similar final residual output and max-Iter number as with standard version);
98     - allows to store and use lowest-residual solution (standard & _SR versions);
99     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
100     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
101    o eesup/src:
102     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
103       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
104    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
105    
106    checkpoint63m (2012/04/27)
107    o pkg/shelfice:
108     - account for partical cells in surface level below ice-shelf for hydrostatic
109       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
110    o ad test experiments:
111     - update and rename to "ad_optfile.local" local AD-optfile specific to a
112       particular adjoint verification experiment (in verification/*/code_ad/)
113    o pkg/seaice & pkg/exf:
114     - Part two of ECCO-CLIVAR code merges.
115       Completes merge of seaice area relax. code.
116       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
117       to be set in EXF_OPTIONS.h since this pkg controls its I/O
118       (and avoids second CPP option in SEAICE_OPTIONS.h)
119     - change default value of costIceStart & costIceEnd to a valid date.
120     - add snowPrecip to HSNOW in seaice_growth
121    o pkg/ptracers:
122     - move ptracers summary and setup check into separated S/R ; add a check for
123       valid PTRACERS_Iter0 value (error+stop or just warning).
124    o pkg/cal (+ pkg/ecco):
125     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
126       as input; and for AD, unless both are not differentiable (e.g., k index)).
127    o model/src:
128     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
129       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
130       temporary set to usingZCoords value (to be changed to F when using shelfice).
131     - hydrostatic pressure: implement partial cell near the surface also for
132       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
133       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
134    o pkg/ctrl/ctrl_init.F:
135     - add a formal parameter to s/r ctrl_init_rec to print
136       xx_$(ctrl_valiable)_file for easier debugging
137     - move call of cal_* routines into the if-block where they are really
138       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
139       to specify a startdate
140    o pkg/seaice:
141     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
142       global_ocean.cs32x15/code versions).
143     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
144       verification experiment global_ocean.cs32x15.seaice and update results.
145    o pkg/exf:
146     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
147       (according to useExfYearlyFields).
148    o pkg/cal:
149     - move calendar setting & summary (previously in cal_readparams.F) into new
150       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
151       length of the simulation is set (after SET_PARMS call); This is an attempt
152       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
153     - For safety: keep a record of pkg/cal parameter settings status
154               to allow to STOP if one pkg/cal S/R is called too early.
155     - add a stop in all basic pkg/cal subroutines if called before setting is done.
156     - modify cal_getdate.F: stop when nothing was returned;
157       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
158       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
159    
160    checkpoint63l (2012/04/04)
161    o pkg/bbl:
162      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
163        update global_with_exf output.yearly.txt file.
164    o pkg/cal:
165      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
166      - remove 2 unsused and very short (1 line only) functions ;
167      - remove unsused subroutines from AD-Diff list.
168    o model/src:
169      - start to implement clean wait to stop in initialization S/R (config_check.F,
170         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
171    o folowing PRINT_MESSAGE changes:
172      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
173    o pkg/bbl:
174      - modification so it can work with z*
175      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
176      - global_with_exf/input.yearly verification; changes output.yearly.txt
177    o eesupp/src:
178      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
179        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
180      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
181        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
182      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
183      - when using MPI, always set usingMPI=T ; set default accordingly and stop
184        if not consistent.
185      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
186        argument is zero (in case called within single-thread section).
187    o pkg/fizhi:
188        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
189        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
190    o pkg/exch2:
191      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
192        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
193      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
194        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
195        with bad ones coming from a not-yet-updated halo.
196        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
197    o pkg/frazil:
198        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
199        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
200    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
201    o verification/lab_sea
202      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
203      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
204      * nTimeSteps 3 -> 4
205      * changed reference output accordingly
206    o pkg/ctrl:
207      * fix ctrl_get_gen for xx_sst, xx_sss
208    o pkg/fizhi:
209      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
210        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
211      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
212        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
213        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
214    o pkg/gmredi:
215      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
216    o pkg/fizhi:
217      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
218        (old)aces open64 tuv test.
219    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
220    o pkg/mom_vecinv:
221      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
222        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
223        with non-lin free-surf).
224    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
225      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
226      some compilers (gfortran 4.6.0 on MacOS)
227    o momentum:
228      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
229        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
230        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
231    
232    checkpoint63k (2012/03/17)
233    o model/src:
234       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
235         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
236       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
237         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
238    o model/src: solve_*diagonal.F
239       - replace division with multiplication by inverse (similar to original version)
240         update output of AD exp. global_ocean.90x40x15.
241       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
242         to enable the use of the vectorized & differentiable solve_tridiagonal.F
243       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
244         vertical advection (to get solve_tridiagonal tested in AD mode).
245    o pkg/seaice: ECCO-CLIVAR merge:
246      1. seaice AREA relaxation
247         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
248         * runtime flag: SEAICE_tauAreaObsRelax
249      2. modified global mean cost imbalance code: CPP option
250          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
251    o another iteration on solve_*diagonal.F
252       Make choices independent of AUTODIFF
253       Default will be the adjoinable vectorized version.
254       Alternative choices are:
255       * non-adjoinable original version with low memory footprint:
256         #define SOLVE_DIAGONAL_LOWMEMORY
257       * still adjoinable but does not vectorize (k as inner-most loop):
258         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
259    o testreport
260     - add option to use a home made wrapper around "make"
261     - remove MITGCM_IEEE env. variable (no longer active)
262    o pkg/shelfice
263     - improve computation of friction velocity for velocity dependent
264       exchange coefficients: include velocities into SHELFICEBoundaryLayer
265       block to average velocities vertically
266     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
267    o Modify diagonal solvers, now three versions (upon request):
268      #ifndef SOLVE_DIAGONAL_AUTODIFF
269        1. default version (dating back a while ago)
270      #else /* def SOLVE_DIAGONAL_AUTODIFF */
271      # ifdef SOLVE_DIAGONAL_KINNER
272        2. adjoinable version with k-innermost loop (G. Forget)
273      # else
274        3. adjoinable vectorized version of 2.
275      # endif
276      #endif /* SOLVE_DIAGONAL_AUTODIFF */
277      All flags are currently set within routines, but could/should be moved to CPP-options.
278      Array bounds for 1. are as before, for 2.,3. cover the entire domain
279      (could be changed for 1. too).
280    o verification/lab_sea (fwd):
281      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
282        use 7 categories (except hb87), new solve4temp params (except salt_plume),
283        constant salinity (=4) or variable salinity (salt_plume) done through
284        SItracer.
285    o pkg/seaice:
286      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
287      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
288         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
289        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
290        SEAICE_freeze got retired) but already better than previously with
291        SEAICE_freeze=123456.7 deg.C;
292      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
293        (safer multi-threaded setting); always set SEAICEuseEVP;
294      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
295        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
296        stop if multiple specifications for the same coeff; make sure default
297        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
298    o pkg/obcs:
299      - allow to switch to upwind 1rst order advection scheme for the advective
300        flux computation at the open-boundary; disabled for adjoint built.
301    o pkg/ptracers:
302      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
303      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
304      - add parameter to decide when to start a tracer; use internal flag to
305        know which tracer to step-forward; switch this internal flag at the top
306        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
307        for adjoint built.
308    o pkg/seaice:
309      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
310      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
311      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
312    o pkg/ecco:
313      - fix writing of output file DiagnosCost_ClimSalt/Theta
314        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
315    o pkg/seaice:
316      - add missing initialisation of COR_ICE array in dynsolver.F
317      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
318        compiled either way, and is tested in all exps (multidim was only tested
319        in lab_sea ad before).
320      - cosmetic change to prepare for future addition of ITD. no change to results.
321        no defaults change.
322      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
323      - by lack of adequate verification experiments, I further used custom versions
324        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
325        should be correct.
326      - avoid recomputations in ad.
327    o array initialisation in adjoint mode:
328      1) pkg/mom_common/mom_calc_ke.F:
329        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
330        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
331        part this initialisation is gone, resulting in Floating Point Exception
332        (caught by open64 compiler with debug option).
333      2) model/src/convective_weights.F
334        set output convectCount over the full array range (instead of doing
335        an update): this fix a similar issue when called within recomputation (adjoint)
336        which could by-pass the initialisation (normally done in the caller S/R).
337    o pkg/seaice:
338      - final version of turbulent flux params, as agreed at MIT ice meet:
339           SEAICE_mcPheePiston (default is ~ 0.000875)
340           SEAICE_mcPheeTaper (default is 0.)
341           SEAICE_frazilFrac (defualt is 1.)
342           SEAICE_mcPheeStepFunc (default is false)
343      - changes results at trunction error level
344      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
345    o added pkg/frazil:
346      - see frazil_description.tex for details
347      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
348    o pkg/shelfice/shelfice_thermodynamics.F
349      - fix exponents for velocity dependent exchange coefficients: change
350        from 2/3(=0) to 0.66666666666666667
351      - move computation of velocity dependent exchange coefficients into
352        separate loop, so that it applies to both thermodynamics
353      - move some divisions by constants out of loops
354    
355    checkpoint63j (2012/02/16)
356    o pkg/seaice:
357      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
358      - SItracer:  added run time params, and allow coupling to ocn salinity.
359    o pkg/seaice: remove (almost) all divisions by constants within loops
360      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
361      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
362      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
363      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
364    o pkg/seaice :
365      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
366        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
367      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
368      - add permanent SItflux diag that corresponds to TFLUX but includes
369        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
370      - allow activation/testing of a fix for suspected missing term in
371        ocn-ice heat budget (to be confirmed). To test this, you want to
372        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
373        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
374      - no change in results, fwd or ad.
375    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
376      - switch to variable freezing point.
377           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
378      - bug fix : the sublimation term that was missing is now activated.
379           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
380      - bug fix : flooding sign term for SIsal0.NE.0.
381           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
382    o pkg/seaice:
383      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
384        is now the default, and the old default constant freezing point is recovered
385        with SEAICE_tempFrz0    = -1.96,
386             SEAICE_dTempFrz_dS = 0.,
387      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
388      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
389      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
390        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
391      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
392        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
393      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
394        seaice_growth r149 for legacy branch (no results change).
395      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
396        from I. Fenty).
397      - results did not change except for global_ocean.cs32x15, mostly due to the
398        switch to variable freezing point (see above item for detail).
399    o pkg/thsice:
400      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
401        seawater freezing in thsice_calc_thickn (not used).
402    o pkg/seaice: turbulent flux term specification via run time params.
403      - replace CPP switches with run time switches to facilitate testing
404      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
405                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
406      - added runtime parameter : SEAICEturbFluxFormula
407      - move Mcphee constants to SEAICE_PARAMS.h
408      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
409                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
410                 remove seaice_summary call (moved to seaice_init_fixed)
411      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
412        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
413      - seaice_summary.F : add missing report of read turbulent flux term set up
414                           and SITRACER.
415      - seaice_check.F : check range; inform and stop if retired CPPs are used
416                         (incl. SEAICE_AGE).
417      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
418             CPP switch, same computation as before for the different options.
419      - change results at the truncation level.
420    o pkg/seaice:
421      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
422        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
423        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
424      - update verification/*/input*/data.seaice:
425        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
426        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
427        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
428        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
429    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
430      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
431        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
432        difference in results only due to machine truncation.
433      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
434        MaykutPolySatVap; keep MIN_LWDOWN.
435      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
436      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
437        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
438    o pkg/salt_plume:
439      - isolate saltPlumeFlux array exch into a specific S/R called from
440        do_oceanic_phys.F
441      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
442    o verification:
443      - move untested set-up to MITgcm_contrib/verification_other.
444    o pkg/seaice:
445      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
446    o pkg/seaice:
447      - seaice_solve4temp.F (keeping results unchanged):
448        * add 2 future run-time params to select which saturation vapor pressure
449          formula is used and how post-iteration fluxes are set.
450          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
451        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
452          the linearized expression to stay consistent with tsurf finding.
453      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
454        can be < 0.
455    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
456      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
457        conductive heat flux F_c , and add it explicitly when updating tsurf as
458        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
459        so that now F_ia has a consistent meaning through the entire routine.
460        This causes differences at truncation level: update output of fwd exp.
461        global_ocean.cs32x15.seaice.
462    o pkg/seaice:
463      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
464        of arrays, sign/direction of fluxes; no effect on results.
465      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
466        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
467        note: this should have been done before changing celsius2K default.
468      - to keep results unchanged, add back old value of celsius2K in verification
469        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
470      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
471        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
472        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
473        freezing temp is consistent with value in seaice_growth.F ; this causes
474        differences at machine truncation level: update lab_sea AD output (3/4).
475    o pkg/seaice:
476      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
477        and climsst/sss even when using seaice (to prevent calculation that might
478        use SST on land); does not affect any verification exp.
479      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
480        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
481    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
482      over land (non-legacy code)
483    o vectorize salt_plume package:
484      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
485      - this code computes plumebk everywhere (also over land), thus requires
486        code to avoid divisions by zero and catch the case of kLev=Nr.
487      - efficiency of salt_plume_frac is still sub-optimal
488    o tools (genmake2):
489      - fix makefile NAME specification (option: -makefile NAME) by adding
490        "-f $MAKEFILE" in few places where it was missing including makedepend
491        command (contribution from Paul).
492    
493    checkpoint63i (2012/01/24)
494    o model/src:
495      - add factorized versions of some EOS code to find_rho.F,
496        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
497    o model/src:
498      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
499      - change default celsius2K from 273.16 to 273.15
500      - to keep results unchanged, add back old value of celsius2K in verification
501        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
502         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
503    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
504      to make TAF generate vectorizable code
505    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
506       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
507       have flags that do this more efficiently.
508    o pkg/diagnostics/diagstats_calc.F
509      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
510    o pkg/obcs (with exch2):
511      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
512        and remove code (in obcs_readparms.F) which was based on EXCH of indices
513        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
514    o pkg/exf and seaice exp:
515      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
516        so that switching off area & heff advection flags does not affect results.
517      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
518      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
519        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
520        results of verification experiments: 1D_ocean_ice_column(fwd),
521        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
522        and offline_exf_seaice (all 4).
523    o pkg/seaice:
524      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
525        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
526      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
527        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
528        not multi-dim advection;
529      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
530        SHORTWAVE_HEATING #undef.
531    o optim: make Makefile more robust (?)
532    o pkg/obcs:
533      * fix treatment of obcs_read_pickup for TAF
534    o pkg/shelfice:
535      * add missing initialisation of num_shifwflx
536      * new adjoint verification exp. for isomip
537      * change Prandtl and Schmidt numbers from generic formulations
538        (in terms of model diffus. and visc.) to separate runtime
539        parameters, with Holland and Jenkins (1999) default values.
540    o pkg/exf (interpolation):
541      - extended input field (2 rows) near the N & S poles:
542        * fill in with the symetric value (when even Nb of data in longitude)
543        * add average value at the poles only for scalar quantities ; for vector
544          component interpolation, skip the averaging and keep duplicated values,
545          unless the 2 components have same location (uvInterp=T) in which case
546          interpolate the 2 components together using S/R EXF_INTERP_UV.
547      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
548        together: this allows to account properly for local orientation when
549        averaging at N & S pole.
550      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
551        exf-interpolation near N & S poles. Undef by default.
552      - add debug check/print on 1rst iter if debugLevel >=2.
553    o pkg/exf:
554      - change masking flags definition (no longer "parameter"), put them in
555        common block and set them in S/R EXF_INIT_FIXED.
556      - change recognized masking flag from s,u,v to c,w,s since the mask
557        to use (maskC,W,S) depends on position on model grid and has little to
558        do with scalar/vector difference; fix masking if using P-coordinates.
559      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
560        and update results of exp. global_with_exf (x2).
561      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
562    o pkg/obcs
563      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
564    o pkg/exf (interpolation):
565      - assume periodicity in X only if input field cover full longitude range.
566      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
567        and should vectorise).
568      - fix input lat of the 2 added row (in case we provide N.pole data).
569    
570    checkpoint63h (2011/12/30)
571    o pkg/seaice:
572      - change declaration of UVM from _RL to _RS in order to get B-grid
573        uIce,vIce monitor when _RS = real*4
574    o pkg/offline:
575      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
576      - compute vertical velocity if not read from file (switch on exactConserv
577        & staggerTimeStep);
578      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
579    o verification:
580      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
581        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
582        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
583      - update output of exp. global_ocean.cs32x15.viscA4 after changing
584        grid-file angles (used here for coriolis-3d);
585      - remove (or gzip) few files not needed to run fizhi-cs experiments.
586    o pkg/exf (vector interpolation):
587      - rotate vector component toward local grid-axis orientation using grid-angles
588        (stored in GRID.h) instead of locally computed rotation angle; keep old code
589        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
590    o pkg/seaice:
591      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
592        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
593    o pkg/PKG_OPTIONS.h files:
594      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
595        outside of the #ifdef ALLOW_THISPKG / #endif block.
596      - update verification/*/code/PKG_OPTIONS.h files.
597    o add a verification experiment (offline_exf_seaice/input.seaice) that test
598      the B-grid LSOR solver
599    o pkg/seaice: sort out emissivity and long wave radiation step 2:
600      - add emissivity for snow and ice as new run-time parameters
601        (unfortunately) that default to the corresponding exf values; this
602        changes results in most verification experiments so that for backward
603        compatibility these parameter have to be set explicitly to inconsistent
604        values (ugly);
605      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
606        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
607        until we agree how to handle this bug properly
608    o pkg/exf (interpolation):
609      - add a set of run-time param ({inputfield}_interpMethod), one for
610        each interpolated input field, to select the interpolation method
611        with a value of zero switching off the interpolation;
612      - print interpolation parameters to standard output;
613      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
614        (to use instead runoff_interpMethod=0 in data.exf).
615      - simplify default setting of interpolation parameters (for all fields,
616        set position to match model grid cell-center position, leading to trivial
617        interpolation in case of regular Lat-Lon grid) and fix for the case of
618        non-uniform delY.
619    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
620       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
621       this factor is absolutely required, because the lw exitance (= out-going
622       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
623       where the reflectivity rho = 1-emissivity for conservation reasons. Once
624       this is established, we can remove the CPP-Flag (if we want to).
625    o pkg/seaice:
626      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
627        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
628      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
629        what the name implies (and not emissivity*BoltzmannConstant), this means
630        the old default value of 5.5e-8 now means
631        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
632        S/R exf_readparms
633      - FV-discretization of the B-grid LSOR solver, turn on with
634        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
635        of the calling routine dynsolver, so that B and C-grid code look a
636        little more alike.
637      - fix index bugs in ostres.F (B-grid code)
638    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
639    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
640      default for SEAICE_emissivity, if useEXF; requires setting a wrong
641      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
642      backward compatiblity
643    o model/src: use sigmaR in calc_ivdc
644    
645    checkpoint63g (2011/12/16)
646    o pkg/seaice/seaice_growth.F:
647      fix heat conservation of the coupled ocean-seaice system.
648      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
649      solid vs liquid water treatment is resolved via QNET.
650    o pkg/seaice/seaice_growth.F:
651      add missing term for sublimation in saltFlux, which was breaking conservation.
652    o pkg/seaice/seaice_model.F:
653      Remove this patholigical case treatment in evolution branch,
654      where it is un-necessary and breaks conservation.
655      Update global_ocean.cs32x15/results accordingly for
656      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
657    o model/src:
658      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
659      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
660    o pkg/obcs:
661      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
662      tendency for temperature and salinity that is then applied to update
663      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
664      horizontal advection and diffusion contributions on the boundary (in
665      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
666      removing the mask in S/R timestep_tracer. The advantage of this approach is
667      that the updated tracer values include contributions from the surface
668      forcing and vertical diffusion.
669      This modification changes exp4.stevens because of vertical diffusion.
670    o model/src:
671      change non-curvilinear grid setting to also work with exch2 + blank tiles:
672      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
673        face dimensions.
674      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
675        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
676        and INI_SPHERICAL_POLAR_GRID.
677      change test-experiment global_ocean.90x40x15:
678      - split the domain in many more tiles (9x4 tiles of 10x10 each);
679      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
680      - update results of both test (std & dwnslp).
681    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
682       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
683    o model/src:
684      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
685        and fix initialisation when using sigma-coords.
686    o model/src:
687     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
688       to their current value at the beginning of forward_step.F": add a new run-time
689       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
690     - set doResetHFactors=T in the following test exp:
691        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
692        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
693        and tutorial_global_oce_in_p (nonLinFS in p)
694    o pkg/ecco
695      - added IES cost term
696    o verification/advect_xz
697      - scale down the depth by 1/100 (from 200 km to just 2.km)
698      - add secondary test using divergent flow, r-star and implicit vertical advection.
699      - add note (check_conserve_TS.txt) and matlab script to check global
700        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
701    o pkg/rbcs:
702      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
703    o pkg/obcs (Stevens BCs):
704      - fix various problems in the phase speed computations of the Stevens
705        boundary conditions:
706        - sign error for western and southern boundaries,
707        - time tendencies were underestimated by factor of dTracerLev and some just
708          zero (for multidim advection schemes) -> now estimate time tendencies
709          from difference between previous (n) time level and the one before (n-1);
710          this requires storing a field per tracer per boundary, also in the pickup
711          files.
712        - replace deltaTmom in cflMer/Zon computation with dTracerLev
713        - set default phase velocity to cflMer/Zon
714      - update verification experiment exp4.stevens
715    o pkg/generic_advdiff (implicit_r):
716      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
717        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
718      - fix implicit vertical diffusion or advection with NonLin FreeSurf
719        (was using current recip_hFacC instead of future recip_hFacC): set future
720        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
721        solver S/R ;
722      - fill diagnostics of vertical advective fluxes (computed from tendency)
723        when using implicit vert. advection;
724      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
725         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
726         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
727         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
728    o pkg/diagnostics:
729      - add diags for T & S tendency which goes through Adams-Bashforth.
730    
731    checkpoint63f (2011/11/30)
732    o pkg/obcs/obcs_calc_stevens.F:
733      - join some loops to reduce number of if-statements
734      - fix a bug in code for northern and southern boundaries.
735    o pkg/seaice/seaice_init_varia.F
736      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
737        caused zero ice-velocities for the B-grid code
738    o pkg/seaice/seaice_init_fixed.F
739      - fix a bug in the initialisation of the second metric terms
740        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
741      - this affects all seaice configurations with useCurviLinearGrid = .true.
742        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
743        = .true. (default)
744      - the only verification experiment affected is global_ocean.cs32x15:
745        icedyn, seaice, and seaice_dynmix (AD)
746    o pkg/thsice/thsice_diagnostics_state.F
747      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
748        not contain garbage that can lead to surprises in diagstats_calc.F
749    o model/src:
750      - move bi,bj loops inside INTEGR_CONTINUITY ;
751      - call INTEGR_CONTINUITY directly from forward_step.F
752        (previously called from momentum_correction_step.F)
753      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
754        forward_step.F and pkg/ecco/the_main_loop.F
755    o model/src/do_oceanic_phys.F:
756      - reset addMass to zero only if useICEFRONT ;
757      - separated k-loop for rhoInSitu calculation ;
758      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
759        and at constant T,S (= WdRHOdP);
760      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
761        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
762        transport of locally-referenced potential density);
763        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
764    o gluemnc:
765      - replace ncrcat with ncks when adding variables to *.glob.nc
766      - change the way variables without record dimensions are handled so that
767        files that have variables with and without record variables can be glued:
768        add a record dimension with a new unique name to be able to differentiate
769        between variable with and without a-prior record dimensions. Remove
770        this record dimension before adding the variable to the *.glob.nc file.
771        This procedure automatically works also for grid.*.nc files that do not
772        have any record dimension.
773    o verification/cpl_aim+ocn:
774      - generate new reference output on baudelaire (gfortran, mpich2) (previously
775        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
776    o pkg/obcs/obcs_calc_stevens.F:
777      - add code for northern and southern boundaries.
778      - reorder some loops to save some operations and so that drFBar can be scalar
779    o model/src:
780      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
781        truncation) and add diagnostics for Adams-Bashforth tendency increment.
782      - update test-exp. AD output:
783        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
784      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
785        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
786        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
787        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
788        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
789        tutorial_plume_on_slope.
790    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
791      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
792      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
793      does not even come with an F77 compiler anymore, this should not be
794      a limitation
795    
796    checkpoint63e (2011/11/06)
797    o pkg/seaice adjoint of LSR:
798      - substantially rework STORE dirs.
799      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
800        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
801        and only perform SOLV_MAX_FIXED adjoint iters.
802        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
803        always goes to same record, meaning that the last forward field will be
804        the one used in the adjoint - an approximation.
805      - now produces non-zero LSR-related gradients, and acceptable gradients for
806        An's zonal (x-z) test case (to be checked in)
807      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
808        (but these are screwed up by the thermodynamics in the first place);
809        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
810        output_adm.txt also reflects changes to seaice_lsr
811      - global_ocean.cs32x15:
812        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
813          (output_adm.seaice.txt was updated)
814        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
815          (output_adm.seaice_dynmix.txt)
816    o test-exp. exp4+stevens:
817      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
818    o pkg/seaice (lsr solver):
819      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
820        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
821      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
822      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
823        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
824      - compute (with new S/R) and print initial (+ free-driff sol. if available)
825        and final residual of linearised system.
826    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
827      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
828    o pkg/obcs: Stevens BCs (still only for east and west)
829      - fix Stevens BCs by using intermediate velocities of previous
830        time step as "baroclinic" contribution rather velocity of one grid cell
831        inside the boundaries; more consistent but makes the entire treatment
832        more complicated, requires new pickup files and two new S/Rs:
833        obcs_copy_uv_n and obcs_save_uv_n
834        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
835        (undefined by default)
836      - silently move computation of some grid factors into separate loops to
837        save some recomputations
838      - add a hack for non-linear free surface
839      - add a verification experiment to exp4 that tests this code
840    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
841    
842    checkpoint63d (2011/10/25)
843  o pkg/obcs + seaice-dynamics:  o pkg/obcs + seaice-dynamics:
844    - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before    - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
845      solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB      solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
# Line 25  o pkg/dic: Line 861  o pkg/dic:
861    - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add    - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
862      carbonate computation/output to CALC_PCO2_APPROX      carbonate computation/output to CALC_PCO2_APPROX
863  o pkg/generic_advdiff  o pkg/generic_advdiff
864    - make TAF generate code that vectorizes:    - make TAF generate code that vectorizes:
865      gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F      gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
866  o model/src:  o model/src:
867    - improve vectorization also for adjoint code of    - improve vectorization also for adjoint code of
868      solve_tridiagonal and solve_pentadiagonal. As this requires up to      solve_tridiagonal and solve_pentadiagonal. As this requires up to
869      5 new 3D-fields, this code is only turned on for the combination of      5 new 3D-fields, this code is only turned on for the combination of
870      ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message      ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
Legend:
Removed from v.1.1518  
changed lines
  Added in v.1.1682
  ViewVC Help
Powered by ViewVC 1.1.22