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revision 1.1557 by jmc, Wed Dec 21 17:31:53 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):  o pkg/exf (interpolation):
622    - add a set of run-time param ({inputfield}_interpMethod), one for    - add a set of run-time param ({inputfield}_interpMethod), one for
623      each interpolated input field, to select the interpolation method      each interpolated input field, to select the interpolation method
# Line 11  o pkg/exf (interpolation): Line 625  o pkg/exf (interpolation):
625    - print interpolation parameters to standard output;    - print interpolation parameters to standard output;
626    - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined    - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
627      (to use instead runoff_interpMethod=0 in data.exf).      (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  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.     within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
634     this factor is absolutely required, because the lw exitance (= out-going     this factor is absolutely required, because the lw exitance (= out-going
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