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revision 1.1540 by jmc, Thu Dec 1 19:33:51 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:
612      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
613      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
614    o pkg/obcs:
615      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
616      tendency for temperature and salinity that is then applied to update
617      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
618      horizontal advection and diffusion contributions on the boundary (in
619      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
620      removing the mask in S/R timestep_tracer. The advantage of this approach is
621      that the updated tracer values include contributions from the surface
622      forcing and vertical diffusion.
623      This modification changes exp4.stevens because of vertical diffusion.
624    o model/src:
625      change non-curvilinear grid setting to also work with exch2 + blank tiles:
626      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
627        face dimensions.
628      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
629        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
630        and INI_SPHERICAL_POLAR_GRID.
631      change test-experiment global_ocean.90x40x15:
632      - split the domain in many more tiles (9x4 tiles of 10x10 each);
633      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
634      - update results of both test (std & dwnslp).
635    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
636       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
637    o model/src:
638      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
639        and fix initialisation when using sigma-coords.
640    o model/src:
641     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
642       to their current value at the beginning of forward_step.F": add a new run-time
643       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
644     - set doResetHFactors=T in the following test exp:
645        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
646        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
647        and tutorial_global_oce_in_p (nonLinFS in p)
648    o pkg/ecco
649      - added IES cost term
650    o verification/advect_xz
651      - scale down the depth by 1/100 (from 200 km to just 2.km)
652      - add secondary test using divergent flow, r-star and implicit vertical advection.
653      - add note (check_conserve_TS.txt) and matlab script to check global
654        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
655    o pkg/rbcs:
656      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
657    o pkg/obcs (Stevens BCs):
658      - fix various problems in the phase speed computations of the Stevens
659        boundary conditions:
660        - sign error for western and southern boundaries,
661        - time tendencies were underestimated by factor of dTracerLev and some just
662          zero (for multidim advection schemes) -> now estimate time tendencies
663          from difference between previous (n) time level and the one before (n-1);
664          this requires storing a field per tracer per boundary, also in the pickup
665          files.
666        - replace deltaTmom in cflMer/Zon computation with dTracerLev
667        - set default phase velocity to cflMer/Zon
668      - update verification experiment exp4.stevens
669  o pkg/generic_advdiff (implicit_r):  o pkg/generic_advdiff (implicit_r):
670    - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf    - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
671      (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);      (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
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