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revision 1.1588 by jmc, Thu Feb 2 19:22:02 2012 UTC revision 1.1663 by jmc, Fri Jun 1 18:49:32 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:
8      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
9        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
10      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
11        similar to calc_r_star.F); update results of experiment internal_wave and
12        tutorial_global_oce_in_p (affected @ truncation level).
13    o pkg/shelfice:
14      - add parameterisation of advective-diffusive flux into the ice shelf
15        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
16      - simply eps3/3a computation
17    o eesupp:
18     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
19       between tiles, just fill-in edges assuming locally periodic subdomain) and
20       add corresponding exchange subroutines (EXCH0);
21     - new CG-solver version (_EX0) for disconnected-tiles special case.
22    o model/src (CG-solvers):
23     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
24       (similar final residual output and max-Iter number as with standard version);
25     - allows to store and use lowest-residual solution (standard & _SR versions);
26     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
27     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
28    o eesup/src:
29     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
30       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
31    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
32    
33    checkpoint63m (2012/04/27)
34    o pkg/shelfice:
35     - account for partical cells in surface level below ice-shelf for hydrostatic
36       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
37    o ad test experiments:
38     - update and rename to "ad_optfile.local" local AD-optfile specific to a
39       particular adjoint verification experiment (in verification/*/code_ad/)
40    o pkg/seaice & pkg/exf:
41     - Part two of ECCO-CLIVAR code merges.
42       Completes merge of seaice area relax. code.
43       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
44       to be set in EXF_OPTIONS.h since this pkg controls its I/O
45       (and avoids second CPP option in SEAICE_OPTIONS.h)
46     - change default value of costIceStart & costIceEnd to a valid date.
47     - add snowPrecip to HSNOW in seaice_growth
48    o pkg/ptracers:
49     - move ptracers summary and setup check into separated S/R ; add a check for
50       valid PTRACERS_Iter0 value (error+stop or just warning).
51    o pkg/cal (+ pkg/ecco):
52     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
53       as input; and for AD, unless both are not differentiable (e.g., k index)).
54    o model/src:
55     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
56       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
57       temporary set to usingZCoords value (to be changed to F when using shelfice).
58     - hydrostatic pressure: implement partial cell near the surface also for
59       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
60       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
61    o pkg/ctrl/ctrl_init.F:
62     - add a formal parameter to s/r ctrl_init_rec to print
63       xx_$(ctrl_valiable)_file for easier debugging
64     - move call of cal_* routines into the if-block where they are really
65       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
66       to specify a startdate
67    o pkg/seaice:
68     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
69       global_ocean.cs32x15/code versions).
70     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
71       verification experiment global_ocean.cs32x15.seaice and update results.
72    o pkg/exf:
73     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
74       (according to useExfYearlyFields).
75    o pkg/cal:
76     - move calendar setting & summary (previously in cal_readparams.F) into new
77       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
78       length of the simulation is set (after SET_PARMS call); This is an attempt
79       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
80     - For safety: keep a record of pkg/cal parameter settings status
81               to allow to STOP if one pkg/cal S/R is called too early.
82     - add a stop in all basic pkg/cal subroutines if called before setting is done.
83     - modify cal_getdate.F: stop when nothing was returned;
84       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
85       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
86    
87    checkpoint63l (2012/04/04)
88    o pkg/bbl:
89      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
90        update global_with_exf output.yearly.txt file.
91    o pkg/cal:
92      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
93      - remove 2 unsused and very short (1 line only) functions ;
94      - remove unsused subroutines from AD-Diff list.
95    o model/src:
96      - start to implement clean wait to stop in initialization S/R (config_check.F,
97         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
98    o folowing PRINT_MESSAGE changes:
99      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
100    o pkg/bbl:
101      - modification so it can work with z*
102      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
103      - global_with_exf/input.yearly verification; changes output.yearly.txt
104    o eesupp/src:
105      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
106        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
107      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
108        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
109      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
110      - when using MPI, always set usingMPI=T ; set default accordingly and stop
111        if not consistent.
112      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
113        argument is zero (in case called within single-thread section).
114    o pkg/fizhi:
115        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
116        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
117    o pkg/exch2:
118      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
119        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
120      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
121        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
122        with bad ones coming from a not-yet-updated halo.
123        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
124    o pkg/frazil:
125        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
126        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
127    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
128    o verification/lab_sea
129      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
130      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
131      * nTimeSteps 3 -> 4
132      * changed reference output accordingly
133    o pkg/ctrl:
134      * fix ctrl_get_gen for xx_sst, xx_sss
135    o pkg/fizhi:
136      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
137        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
138      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
139        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
140        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
141    o pkg/gmredi:
142      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
143    o pkg/fizhi:
144      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
145        (old)aces open64 tuv test.
146    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
147    o pkg/mom_vecinv:
148      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
149        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
150        with non-lin free-surf).
151    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
152      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
153      some compilers (gfortran 4.6.0 on MacOS)
154    o momentum:
155      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
156        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
157        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
158    
159    checkpoint63k (2012/03/17)
160    o model/src:
161       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
162         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
163       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
164         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
165    o model/src: solve_*diagonal.F
166       - replace division with multiplication by inverse (similar to original version)
167         update output of AD exp. global_ocean.90x40x15.
168       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
169         to enable the use of the vectorized & differentiable solve_tridiagonal.F
170       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
171         vertical advection (to get solve_tridiagonal tested in AD mode).
172    o pkg/seaice: ECCO-CLIVAR merge:
173      1. seaice AREA relaxation
174         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
175         * runtime flag: SEAICE_tauAreaObsRelax
176      2. modified global mean cost imbalance code: CPP option
177          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
178    o another iteration on solve_*diagonal.F
179       Make choices independent of AUTODIFF
180       Default will be the adjoinable vectorized version.
181       Alternative choices are:
182       * non-adjoinable original version with low memory footprint:
183         #define SOLVE_DIAGONAL_LOWMEMORY
184       * still adjoinable but does not vectorize (k as inner-most loop):
185         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
186    o testreport
187     - add option to use a home made wrapper around "make"
188     - remove MITGCM_IEEE env. variable (no longer active)
189    o pkg/shelfice
190     - improve computation of friction velocity for velocity dependent
191       exchange coefficients: include velocities into SHELFICEBoundaryLayer
192       block to average velocities vertically
193     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
194    o Modify diagonal solvers, now three versions (upon request):
195      #ifndef SOLVE_DIAGONAL_AUTODIFF
196        1. default version (dating back a while ago)
197      #else /* def SOLVE_DIAGONAL_AUTODIFF */
198      # ifdef SOLVE_DIAGONAL_KINNER
199        2. adjoinable version with k-innermost loop (G. Forget)
200      # else
201        3. adjoinable vectorized version of 2.
202      # endif
203      #endif /* SOLVE_DIAGONAL_AUTODIFF */
204      All flags are currently set within routines, but could/should be moved to CPP-options.
205      Array bounds for 1. are as before, for 2.,3. cover the entire domain
206      (could be changed for 1. too).
207    o verification/lab_sea (fwd):
208      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
209        use 7 categories (except hb87), new solve4temp params (except salt_plume),
210        constant salinity (=4) or variable salinity (salt_plume) done through
211        SItracer.
212    o pkg/seaice:
213      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
214      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
215         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
216        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
217        SEAICE_freeze got retired) but already better than previously with
218        SEAICE_freeze=123456.7 deg.C;
219      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
220        (safer multi-threaded setting); always set SEAICEuseEVP;
221      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
222        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
223        stop if multiple specifications for the same coeff; make sure default
224        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
225    o pkg/obcs:
226      - allow to switch to upwind 1rst order advection scheme for the advective
227        flux computation at the open-boundary; disabled for adjoint built.
228    o pkg/ptracers:
229      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
230      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
231      - add parameter to decide when to start a tracer; use internal flag to
232        know which tracer to step-forward; switch this internal flag at the top
233        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
234        for adjoint built.
235    o pkg/seaice:
236      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
237      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
238      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
239    o pkg/ecco:
240      - fix writing of output file DiagnosCost_ClimSalt/Theta
241        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
242    o pkg/seaice:
243      - add missing initialisation of COR_ICE array in dynsolver.F
244      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
245        compiled either way, and is tested in all exps (multidim was only tested
246        in lab_sea ad before).
247      - cosmetic change to prepare for future addition of ITD. no change to results.
248        no defaults change.
249      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
250      - by lack of adequate verification experiments, I further used custom versions
251        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
252        should be correct.
253      - avoid recomputations in ad.
254    o array initialisation in adjoint mode:
255      1) pkg/mom_common/mom_calc_ke.F:
256        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
257        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
258        part this initialisation is gone, resulting in Floating Point Exception
259        (caught by open64 compiler with debug option).
260      2) model/src/convective_weights.F
261        set output convectCount over the full array range (instead of doing
262        an update): this fix a similar issue when called within recomputation (adjoint)
263        which could by-pass the initialisation (normally done in the caller S/R).
264    o pkg/seaice:
265      - final version of turbulent flux params, as agreed at MIT ice meet:
266           SEAICE_mcPheePiston (default is ~ 0.000875)
267           SEAICE_mcPheeTaper (default is 0.)
268           SEAICE_frazilFrac (defualt is 1.)
269           SEAICE_mcPheeStepFunc (default is false)
270      - changes results at trunction error level
271      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
272    o added pkg/frazil:
273      - see frazil_description.tex for details
274      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
275    o pkg/shelfice/shelfice_thermodynamics.F
276      - fix exponents for velocity dependent exchange coefficients: change
277        from 2/3(=0) to 0.66666666666666667
278      - move computation of velocity dependent exchange coefficients into
279        separate loop, so that it applies to both thermodynamics
280      - move some divisions by constants out of loops
281    
282    checkpoint63j (2012/02/16)
283    o pkg/seaice:
284      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
285      - SItracer:  added run time params, and allow coupling to ocn salinity.
286    o pkg/seaice: remove (almost) all divisions by constants within loops
287      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
288      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
289      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
290      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
291    o pkg/seaice :
292      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
293        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
294      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
295      - add permanent SItflux diag that corresponds to TFLUX but includes
296        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
297      - allow activation/testing of a fix for suspected missing term in
298        ocn-ice heat budget (to be confirmed). To test this, you want to
299        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
300        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
301      - no change in results, fwd or ad.
302    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
303      - switch to variable freezing point.
304           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
305      - bug fix : the sublimation term that was missing is now activated.
306           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
307      - bug fix : flooding sign term for SIsal0.NE.0.
308           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
309    o pkg/seaice:
310      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
311        is now the default, and the old default constant freezing point is recovered
312        with SEAICE_tempFrz0    = -1.96,
313             SEAICE_dTempFrz_dS = 0.,
314      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
315      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
316      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
317        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
318      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
319        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
320      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
321        seaice_growth r149 for legacy branch (no results change).
322      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
323        from I. Fenty).
324      - results did not change except for global_ocean.cs32x15, mostly due to the
325        switch to variable freezing point (see above item for detail).
326    o pkg/thsice:
327      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
328        seawater freezing in thsice_calc_thickn (not used).
329    o pkg/seaice: turbulent flux term specification via run time params.
330      - replace CPP switches with run time switches to facilitate testing
331      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
332                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
333      - added runtime parameter : SEAICEturbFluxFormula
334      - move Mcphee constants to SEAICE_PARAMS.h
335      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
336                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
337                 remove seaice_summary call (moved to seaice_init_fixed)
338      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
339        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
340      - seaice_summary.F : add missing report of read turbulent flux term set up
341                           and SITRACER.
342      - seaice_check.F : check range; inform and stop if retired CPPs are used
343                         (incl. SEAICE_AGE).
344      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
345             CPP switch, same computation as before for the different options.
346      - change results at the truncation level.
347    o pkg/seaice:
348      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
349        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
350        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
351      - update verification/*/input*/data.seaice:
352        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
353        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
354        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
355        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
356    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
357      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
358        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
359        difference in results only due to machine truncation.
360      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
361        MaykutPolySatVap; keep MIN_LWDOWN.
362      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
363      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
364        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
365    o pkg/salt_plume:
366      - isolate saltPlumeFlux array exch into a specific S/R called from
367        do_oceanic_phys.F
368      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
369    o verification:
370      - move untested set-up to MITgcm_contrib/verification_other.
371    o pkg/seaice:
372      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
373  o pkg/seaice:  o pkg/seaice:
374    - seaice_solve4temp.F (keeping results unchanged):    - seaice_solve4temp.F (keeping results unchanged):
375      * add 2 future run-time params to select which saturation vapor pressure      * add 2 future run-time params to select which saturation vapor pressure
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