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revision 1.1549 by jmc, Thu Dec 15 22:45:47 2011 UTC revision 1.1671 by gforget, Wed Jun 20 23:23:26 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 model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
8      - changes to use model/src/the_main_loop.F rather than the ecco version
9        in ecco type adjoint runs.
10    o model/src:
11      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
12        update output of test experiment bottom_ctrl_5x5.
13    o pkg/generic_advdiff:
14      - implement vertical bi-harmonic diffusion (for now, only for T & S and
15        only explicitly).
16    o verification/bottom_ctrl_5x5/
17      update reference output (results changed quite some time ago,
18      not sure when; but new reference results look ok in terms of grdchk)
19    o verification/1D_ocean_ice_column/
20      For verification purposes, the exact adjoint rather than an approx.
21      should be used (e.g., to comare against F.D. or TLM).
22      removed autodiff_inadmode*_ad.F routines in code_ad/
23      Update results/ accordingly.
24    o pkg/cal:
25      - change cal_getdate.F so that output date is function of input time only
26        (less ambiguous, not mixed up with input iteration number).
27      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
28    o pkg/diagnostics:
29      - implement calendarDumps also for stats-diags
30      - implement calendarDumps also for snap-shot output (negative freq)
31      - for now, ignores calendarDumps if non-zero phase-lag.
32    
33    checkpoint63n (2012/06/04)
34    o model/src:
35      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
36        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
37      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
38        similar to calc_r_star.F); update results of experiment internal_wave and
39        tutorial_global_oce_in_p (affected @ truncation level).
40    o pkg/shelfice:
41      - add parameterisation of advective-diffusive flux into the ice shelf
42        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
43      - simply eps3/3a computation
44    o eesupp:
45     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
46       between tiles, just fill-in edges assuming locally periodic subdomain) and
47       add corresponding exchange subroutines (EXCH0);
48     - new CG-solver version (_EX0) for disconnected-tiles special case.
49    o model/src (CG-solvers):
50     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
51       (similar final residual output and max-Iter number as with standard version);
52     - allows to store and use lowest-residual solution (standard & _SR versions);
53     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
54     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
55    o eesup/src:
56     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
57       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
58    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
59    
60    checkpoint63m (2012/04/27)
61    o pkg/shelfice:
62     - account for partical cells in surface level below ice-shelf for hydrostatic
63       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
64    o ad test experiments:
65     - update and rename to "ad_optfile.local" local AD-optfile specific to a
66       particular adjoint verification experiment (in verification/*/code_ad/)
67    o pkg/seaice & pkg/exf:
68     - Part two of ECCO-CLIVAR code merges.
69       Completes merge of seaice area relax. code.
70       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
71       to be set in EXF_OPTIONS.h since this pkg controls its I/O
72       (and avoids second CPP option in SEAICE_OPTIONS.h)
73     - change default value of costIceStart & costIceEnd to a valid date.
74     - add snowPrecip to HSNOW in seaice_growth
75    o pkg/ptracers:
76     - move ptracers summary and setup check into separated S/R ; add a check for
77       valid PTRACERS_Iter0 value (error+stop or just warning).
78    o pkg/cal (+ pkg/ecco):
79     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
80       as input; and for AD, unless both are not differentiable (e.g., k index)).
81    o model/src:
82     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
83       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
84       temporary set to usingZCoords value (to be changed to F when using shelfice).
85     - hydrostatic pressure: implement partial cell near the surface also for
86       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
87       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
88    o pkg/ctrl/ctrl_init.F:
89     - add a formal parameter to s/r ctrl_init_rec to print
90       xx_$(ctrl_valiable)_file for easier debugging
91     - move call of cal_* routines into the if-block where they are really
92       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
93       to specify a startdate
94    o pkg/seaice:
95     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
96       global_ocean.cs32x15/code versions).
97     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
98       verification experiment global_ocean.cs32x15.seaice and update results.
99    o pkg/exf:
100     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
101       (according to useExfYearlyFields).
102    o pkg/cal:
103     - move calendar setting & summary (previously in cal_readparams.F) into new
104       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
105       length of the simulation is set (after SET_PARMS call); This is an attempt
106       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
107     - For safety: keep a record of pkg/cal parameter settings status
108               to allow to STOP if one pkg/cal S/R is called too early.
109     - add a stop in all basic pkg/cal subroutines if called before setting is done.
110     - modify cal_getdate.F: stop when nothing was returned;
111       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
112       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
113    
114    checkpoint63l (2012/04/04)
115    o pkg/bbl:
116      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
117        update global_with_exf output.yearly.txt file.
118    o pkg/cal:
119      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
120      - remove 2 unsused and very short (1 line only) functions ;
121      - remove unsused subroutines from AD-Diff list.
122    o model/src:
123      - start to implement clean wait to stop in initialization S/R (config_check.F,
124         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
125    o folowing PRINT_MESSAGE changes:
126      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
127    o pkg/bbl:
128      - modification so it can work with z*
129      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
130      - global_with_exf/input.yearly verification; changes output.yearly.txt
131    o eesupp/src:
132      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
133        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
134      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
135        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
136      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
137      - when using MPI, always set usingMPI=T ; set default accordingly and stop
138        if not consistent.
139      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
140        argument is zero (in case called within single-thread section).
141    o pkg/fizhi:
142        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
143        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
144    o pkg/exch2:
145      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
146        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
147      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
148        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
149        with bad ones coming from a not-yet-updated halo.
150        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
151    o pkg/frazil:
152        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
153        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
154    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
155    o verification/lab_sea
156      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
157      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
158      * nTimeSteps 3 -> 4
159      * changed reference output accordingly
160    o pkg/ctrl:
161      * fix ctrl_get_gen for xx_sst, xx_sss
162    o pkg/fizhi:
163      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
164        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
165      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
166        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
167        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
168    o pkg/gmredi:
169      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
170    o pkg/fizhi:
171      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
172        (old)aces open64 tuv test.
173    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
174    o pkg/mom_vecinv:
175      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
176        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
177        with non-lin free-surf).
178    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
179      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
180      some compilers (gfortran 4.6.0 on MacOS)
181    o momentum:
182      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
183        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
184        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
185    
186    checkpoint63k (2012/03/17)
187    o model/src:
188       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
189         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
190       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
191         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
192    o model/src: solve_*diagonal.F
193       - replace division with multiplication by inverse (similar to original version)
194         update output of AD exp. global_ocean.90x40x15.
195       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
196         to enable the use of the vectorized & differentiable solve_tridiagonal.F
197       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
198         vertical advection (to get solve_tridiagonal tested in AD mode).
199    o pkg/seaice: ECCO-CLIVAR merge:
200      1. seaice AREA relaxation
201         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
202         * runtime flag: SEAICE_tauAreaObsRelax
203      2. modified global mean cost imbalance code: CPP option
204          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
205    o another iteration on solve_*diagonal.F
206       Make choices independent of AUTODIFF
207       Default will be the adjoinable vectorized version.
208       Alternative choices are:
209       * non-adjoinable original version with low memory footprint:
210         #define SOLVE_DIAGONAL_LOWMEMORY
211       * still adjoinable but does not vectorize (k as inner-most loop):
212         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
213    o testreport
214     - add option to use a home made wrapper around "make"
215     - remove MITGCM_IEEE env. variable (no longer active)
216    o pkg/shelfice
217     - improve computation of friction velocity for velocity dependent
218       exchange coefficients: include velocities into SHELFICEBoundaryLayer
219       block to average velocities vertically
220     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
221    o Modify diagonal solvers, now three versions (upon request):
222      #ifndef SOLVE_DIAGONAL_AUTODIFF
223        1. default version (dating back a while ago)
224      #else /* def SOLVE_DIAGONAL_AUTODIFF */
225      # ifdef SOLVE_DIAGONAL_KINNER
226        2. adjoinable version with k-innermost loop (G. Forget)
227      # else
228        3. adjoinable vectorized version of 2.
229      # endif
230      #endif /* SOLVE_DIAGONAL_AUTODIFF */
231      All flags are currently set within routines, but could/should be moved to CPP-options.
232      Array bounds for 1. are as before, for 2.,3. cover the entire domain
233      (could be changed for 1. too).
234    o verification/lab_sea (fwd):
235      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
236        use 7 categories (except hb87), new solve4temp params (except salt_plume),
237        constant salinity (=4) or variable salinity (salt_plume) done through
238        SItracer.
239    o pkg/seaice:
240      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
241      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
242         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
243        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
244        SEAICE_freeze got retired) but already better than previously with
245        SEAICE_freeze=123456.7 deg.C;
246      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
247        (safer multi-threaded setting); always set SEAICEuseEVP;
248      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
249        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
250        stop if multiple specifications for the same coeff; make sure default
251        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
252    o pkg/obcs:
253      - allow to switch to upwind 1rst order advection scheme for the advective
254        flux computation at the open-boundary; disabled for adjoint built.
255    o pkg/ptracers:
256      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
257      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
258      - add parameter to decide when to start a tracer; use internal flag to
259        know which tracer to step-forward; switch this internal flag at the top
260        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
261        for adjoint built.
262    o pkg/seaice:
263      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
264      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
265      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
266    o pkg/ecco:
267      - fix writing of output file DiagnosCost_ClimSalt/Theta
268        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
269    o pkg/seaice:
270      - add missing initialisation of COR_ICE array in dynsolver.F
271      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
272        compiled either way, and is tested in all exps (multidim was only tested
273        in lab_sea ad before).
274      - cosmetic change to prepare for future addition of ITD. no change to results.
275        no defaults change.
276      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
277      - by lack of adequate verification experiments, I further used custom versions
278        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
279        should be correct.
280      - avoid recomputations in ad.
281    o array initialisation in adjoint mode:
282      1) pkg/mom_common/mom_calc_ke.F:
283        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
284        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
285        part this initialisation is gone, resulting in Floating Point Exception
286        (caught by open64 compiler with debug option).
287      2) model/src/convective_weights.F
288        set output convectCount over the full array range (instead of doing
289        an update): this fix a similar issue when called within recomputation (adjoint)
290        which could by-pass the initialisation (normally done in the caller S/R).
291    o pkg/seaice:
292      - final version of turbulent flux params, as agreed at MIT ice meet:
293           SEAICE_mcPheePiston (default is ~ 0.000875)
294           SEAICE_mcPheeTaper (default is 0.)
295           SEAICE_frazilFrac (defualt is 1.)
296           SEAICE_mcPheeStepFunc (default is false)
297      - changes results at trunction error level
298      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
299    o added pkg/frazil:
300      - see frazil_description.tex for details
301      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
302    o pkg/shelfice/shelfice_thermodynamics.F
303      - fix exponents for velocity dependent exchange coefficients: change
304        from 2/3(=0) to 0.66666666666666667
305      - move computation of velocity dependent exchange coefficients into
306        separate loop, so that it applies to both thermodynamics
307      - move some divisions by constants out of loops
308    
309    checkpoint63j (2012/02/16)
310    o pkg/seaice:
311      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
312      - SItracer:  added run time params, and allow coupling to ocn salinity.
313    o pkg/seaice: remove (almost) all divisions by constants within loops
314      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
315      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
316      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
317      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
318    o pkg/seaice :
319      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
320        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
321      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
322      - add permanent SItflux diag that corresponds to TFLUX but includes
323        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
324      - allow activation/testing of a fix for suspected missing term in
325        ocn-ice heat budget (to be confirmed). To test this, you want to
326        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
327        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
328      - no change in results, fwd or ad.
329    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
330      - switch to variable freezing point.
331           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
332      - bug fix : the sublimation term that was missing is now activated.
333           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
334      - bug fix : flooding sign term for SIsal0.NE.0.
335           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
336    o pkg/seaice:
337      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
338        is now the default, and the old default constant freezing point is recovered
339        with SEAICE_tempFrz0    = -1.96,
340             SEAICE_dTempFrz_dS = 0.,
341      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
342      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
343      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
344        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
345      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
346        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
347      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
348        seaice_growth r149 for legacy branch (no results change).
349      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
350        from I. Fenty).
351      - results did not change except for global_ocean.cs32x15, mostly due to the
352        switch to variable freezing point (see above item for detail).
353    o pkg/thsice:
354      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
355        seawater freezing in thsice_calc_thickn (not used).
356    o pkg/seaice: turbulent flux term specification via run time params.
357      - replace CPP switches with run time switches to facilitate testing
358      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
359                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
360      - added runtime parameter : SEAICEturbFluxFormula
361      - move Mcphee constants to SEAICE_PARAMS.h
362      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
363                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
364                 remove seaice_summary call (moved to seaice_init_fixed)
365      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
366        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
367      - seaice_summary.F : add missing report of read turbulent flux term set up
368                           and SITRACER.
369      - seaice_check.F : check range; inform and stop if retired CPPs are used
370                         (incl. SEAICE_AGE).
371      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
372             CPP switch, same computation as before for the different options.
373      - change results at the truncation level.
374    o pkg/seaice:
375      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
376        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
377        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
378      - update verification/*/input*/data.seaice:
379        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
380        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
381        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
382        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
383    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
384      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
385        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
386        difference in results only due to machine truncation.
387      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
388        MaykutPolySatVap; keep MIN_LWDOWN.
389      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
390      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
391        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
392    o pkg/salt_plume:
393      - isolate saltPlumeFlux array exch into a specific S/R called from
394        do_oceanic_phys.F
395      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
396    o verification:
397      - move untested set-up to MITgcm_contrib/verification_other.
398    o pkg/seaice:
399      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
400    o pkg/seaice:
401      - seaice_solve4temp.F (keeping results unchanged):
402        * add 2 future run-time params to select which saturation vapor pressure
403          formula is used and how post-iteration fluxes are set.
404          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
405        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
406          the linearized expression to stay consistent with tsurf finding.
407      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
408        can be < 0.
409    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
410      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
411        conductive heat flux F_c , and add it explicitly when updating tsurf as
412        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
413        so that now F_ia has a consistent meaning through the entire routine.
414        This causes differences at truncation level: update output of fwd exp.
415        global_ocean.cs32x15.seaice.
416    o pkg/seaice:
417      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
418        of arrays, sign/direction of fluxes; no effect on results.
419      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
420        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
421        note: this should have been done before changing celsius2K default.
422      - to keep results unchanged, add back old value of celsius2K in verification
423        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
424      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
425        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
426        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
427        freezing temp is consistent with value in seaice_growth.F ; this causes
428        differences at machine truncation level: update lab_sea AD output (3/4).
429    o pkg/seaice:
430      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
431        and climsst/sss even when using seaice (to prevent calculation that might
432        use SST on land); does not affect any verification exp.
433      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
434        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
435    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
436      over land (non-legacy code)
437    o vectorize salt_plume package:
438      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
439      - this code computes plumebk everywhere (also over land), thus requires
440        code to avoid divisions by zero and catch the case of kLev=Nr.
441      - efficiency of salt_plume_frac is still sub-optimal
442    o tools (genmake2):
443      - fix makefile NAME specification (option: -makefile NAME) by adding
444        "-f $MAKEFILE" in few places where it was missing including makedepend
445        command (contribution from Paul).
446    
447    checkpoint63i (2012/01/24)
448    o model/src:
449      - add factorized versions of some EOS code to find_rho.F,
450        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
451    o model/src:
452      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
453      - change default celsius2K from 273.16 to 273.15
454      - to keep results unchanged, add back old value of celsius2K in verification
455        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
456         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
457    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
458      to make TAF generate vectorizable code
459    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
460       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
461       have flags that do this more efficiently.
462    o pkg/diagnostics/diagstats_calc.F
463      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
464    o pkg/obcs (with exch2):
465      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
466        and remove code (in obcs_readparms.F) which was based on EXCH of indices
467        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
468    o pkg/exf and seaice exp:
469      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
470        so that switching off area & heff advection flags does not affect results.
471      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
472      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
473        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
474        results of verification experiments: 1D_ocean_ice_column(fwd),
475        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
476        and offline_exf_seaice (all 4).
477    o pkg/seaice:
478      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
479        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
480      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
481        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
482        not multi-dim advection;
483      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
484        SHORTWAVE_HEATING #undef.
485    o optim: make Makefile more robust (?)
486    o pkg/obcs:
487      * fix treatment of obcs_read_pickup for TAF
488    o pkg/shelfice:
489      * add missing initialisation of num_shifwflx
490      * new adjoint verification exp. for isomip
491      * change Prandtl and Schmidt numbers from generic formulations
492        (in terms of model diffus. and visc.) to separate runtime
493        parameters, with Holland and Jenkins (1999) default values.
494    o pkg/exf (interpolation):
495      - extended input field (2 rows) near the N & S poles:
496        * fill in with the symetric value (when even Nb of data in longitude)
497        * add average value at the poles only for scalar quantities ; for vector
498          component interpolation, skip the averaging and keep duplicated values,
499          unless the 2 components have same location (uvInterp=T) in which case
500          interpolate the 2 components together using S/R EXF_INTERP_UV.
501      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
502        together: this allows to account properly for local orientation when
503        averaging at N & S pole.
504      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
505        exf-interpolation near N & S poles. Undef by default.
506      - add debug check/print on 1rst iter if debugLevel >=2.
507    o pkg/exf:
508      - change masking flags definition (no longer "parameter"), put them in
509        common block and set them in S/R EXF_INIT_FIXED.
510      - change recognized masking flag from s,u,v to c,w,s since the mask
511        to use (maskC,W,S) depends on position on model grid and has little to
512        do with scalar/vector difference; fix masking if using P-coordinates.
513      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
514        and update results of exp. global_with_exf (x2).
515      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
516    o pkg/obcs
517      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
518    o pkg/exf (interpolation):
519      - assume periodicity in X only if input field cover full longitude range.
520      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
521        and should vectorise).
522      - fix input lat of the 2 added row (in case we provide N.pole data).
523    
524    checkpoint63h (2011/12/30)
525    o pkg/seaice:
526      - change declaration of UVM from _RL to _RS in order to get B-grid
527        uIce,vIce monitor when _RS = real*4
528    o pkg/offline:
529      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
530      - compute vertical velocity if not read from file (switch on exactConserv
531        & staggerTimeStep);
532      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
533    o verification:
534      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
535        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
536        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
537      - update output of exp. global_ocean.cs32x15.viscA4 after changing
538        grid-file angles (used here for coriolis-3d);
539      - remove (or gzip) few files not needed to run fizhi-cs experiments.
540    o pkg/exf (vector interpolation):
541      - rotate vector component toward local grid-axis orientation using grid-angles
542        (stored in GRID.h) instead of locally computed rotation angle; keep old code
543        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
544    o pkg/seaice:
545      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
546        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
547    o pkg/PKG_OPTIONS.h files:
548      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
549        outside of the #ifdef ALLOW_THISPKG / #endif block.
550      - update verification/*/code/PKG_OPTIONS.h files.
551    o add a verification experiment (offline_exf_seaice/input.seaice) that test
552      the B-grid LSOR solver
553    o pkg/seaice: sort out emissivity and long wave radiation step 2:
554      - add emissivity for snow and ice as new run-time parameters
555        (unfortunately) that default to the corresponding exf values; this
556        changes results in most verification experiments so that for backward
557        compatibility these parameter have to be set explicitly to inconsistent
558        values (ugly);
559      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
560        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
561        until we agree how to handle this bug properly
562    o pkg/exf (interpolation):
563      - add a set of run-time param ({inputfield}_interpMethod), one for
564        each interpolated input field, to select the interpolation method
565        with a value of zero switching off the interpolation;
566      - print interpolation parameters to standard output;
567      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
568        (to use instead runoff_interpMethod=0 in data.exf).
569      - simplify default setting of interpolation parameters (for all fields,
570        set position to match model grid cell-center position, leading to trivial
571        interpolation in case of regular Lat-Lon grid) and fix for the case of
572        non-uniform delY.
573    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
574       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
575       this factor is absolutely required, because the lw exitance (= out-going
576       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
577       where the reflectivity rho = 1-emissivity for conservation reasons. Once
578       this is established, we can remove the CPP-Flag (if we want to).
579    o pkg/seaice:
580      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
581        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
582      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
583        what the name implies (and not emissivity*BoltzmannConstant), this means
584        the old default value of 5.5e-8 now means
585        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
586        S/R exf_readparms
587      - FV-discretization of the B-grid LSOR solver, turn on with
588        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
589        of the calling routine dynsolver, so that B and C-grid code look a
590        little more alike.
591      - fix index bugs in ostres.F (B-grid code)
592    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
593    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
594      default for SEAICE_emissivity, if useEXF; requires setting a wrong
595      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
596      backward compatiblity
597    o model/src: use sigmaR in calc_ivdc
598    
599    checkpoint63g (2011/12/16)
600    o pkg/seaice/seaice_growth.F:
601      fix heat conservation of the coupled ocean-seaice system.
602      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
603      solid vs liquid water treatment is resolved via QNET.
604    o pkg/seaice/seaice_growth.F:
605      add missing term for sublimation in saltFlux, which was breaking conservation.
606    o pkg/seaice/seaice_model.F:
607      Remove this patholigical case treatment in evolution branch,
608      where it is un-necessary and breaks conservation.
609      Update global_ocean.cs32x15/results accordingly for
610      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
611  o model/src:  o model/src:
612    useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in    useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
613    external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.    external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
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