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revision 1.1593 by gforget, Tue Feb 7 19:12:06 2012 UTC revision 1.1670 by jmc, Fri Jun 15 22:01:45 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      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
9        update output of test experiment bottom_ctrl_5x5.
10    o pkg/generic_advdiff:
11      - implement vertical bi-harmonic diffusion (for now, only for T & S and
12        only explicitly).
13    o verification/bottom_ctrl_5x5/
14      update reference output (results changed quite some time ago,
15      not sure when; but new reference results look ok in terms of grdchk)
16    o verification/1D_ocean_ice_column/
17      For verification purposes, the exact adjoint rather than an approx.
18      should be used (e.g., to comare against F.D. or TLM).
19      removed autodiff_inadmode*_ad.F routines in code_ad/
20      Update results/ accordingly.
21    o pkg/cal:
22      - change cal_getdate.F so that output date is function of input time only
23        (less ambiguous, not mixed up with input iteration number).
24      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
25    o pkg/diagnostics:
26      - implement calendarDumps also for stats-diags
27      - implement calendarDumps also for snap-shot output (negative freq)
28      - for now, ignores calendarDumps if non-zero phase-lag.
29    
30    checkpoint63n (2012/06/04)
31    o model/src:
32      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
33        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
34      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
35        similar to calc_r_star.F); update results of experiment internal_wave and
36        tutorial_global_oce_in_p (affected @ truncation level).
37    o pkg/shelfice:
38      - add parameterisation of advective-diffusive flux into the ice shelf
39        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
40      - simply eps3/3a computation
41    o eesupp:
42     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
43       between tiles, just fill-in edges assuming locally periodic subdomain) and
44       add corresponding exchange subroutines (EXCH0);
45     - new CG-solver version (_EX0) for disconnected-tiles special case.
46    o model/src (CG-solvers):
47     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
48       (similar final residual output and max-Iter number as with standard version);
49     - allows to store and use lowest-residual solution (standard & _SR versions);
50     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
51     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
52    o eesup/src:
53     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
54       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
55    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
56    
57    checkpoint63m (2012/04/27)
58    o pkg/shelfice:
59     - account for partical cells in surface level below ice-shelf for hydrostatic
60       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
61    o ad test experiments:
62     - update and rename to "ad_optfile.local" local AD-optfile specific to a
63       particular adjoint verification experiment (in verification/*/code_ad/)
64    o pkg/seaice & pkg/exf:
65     - Part two of ECCO-CLIVAR code merges.
66       Completes merge of seaice area relax. code.
67       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
68       to be set in EXF_OPTIONS.h since this pkg controls its I/O
69       (and avoids second CPP option in SEAICE_OPTIONS.h)
70     - change default value of costIceStart & costIceEnd to a valid date.
71     - add snowPrecip to HSNOW in seaice_growth
72    o pkg/ptracers:
73     - move ptracers summary and setup check into separated S/R ; add a check for
74       valid PTRACERS_Iter0 value (error+stop or just warning).
75    o pkg/cal (+ pkg/ecco):
76     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
77       as input; and for AD, unless both are not differentiable (e.g., k index)).
78    o model/src:
79     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
80       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
81       temporary set to usingZCoords value (to be changed to F when using shelfice).
82     - hydrostatic pressure: implement partial cell near the surface also for
83       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
84       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
85    o pkg/ctrl/ctrl_init.F:
86     - add a formal parameter to s/r ctrl_init_rec to print
87       xx_$(ctrl_valiable)_file for easier debugging
88     - move call of cal_* routines into the if-block where they are really
89       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
90       to specify a startdate
91    o pkg/seaice:
92     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
93       global_ocean.cs32x15/code versions).
94     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
95       verification experiment global_ocean.cs32x15.seaice and update results.
96    o pkg/exf:
97     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
98       (according to useExfYearlyFields).
99    o pkg/cal:
100     - move calendar setting & summary (previously in cal_readparams.F) into new
101       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
102       length of the simulation is set (after SET_PARMS call); This is an attempt
103       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
104     - For safety: keep a record of pkg/cal parameter settings status
105               to allow to STOP if one pkg/cal S/R is called too early.
106     - add a stop in all basic pkg/cal subroutines if called before setting is done.
107     - modify cal_getdate.F: stop when nothing was returned;
108       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
109       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
110    
111    checkpoint63l (2012/04/04)
112    o pkg/bbl:
113      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
114        update global_with_exf output.yearly.txt file.
115    o pkg/cal:
116      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
117      - remove 2 unsused and very short (1 line only) functions ;
118      - remove unsused subroutines from AD-Diff list.
119    o model/src:
120      - start to implement clean wait to stop in initialization S/R (config_check.F,
121         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
122    o folowing PRINT_MESSAGE changes:
123      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
124    o pkg/bbl:
125      - modification so it can work with z*
126      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
127      - global_with_exf/input.yearly verification; changes output.yearly.txt
128    o eesupp/src:
129      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
130        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
131      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
132        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
133      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
134      - when using MPI, always set usingMPI=T ; set default accordingly and stop
135        if not consistent.
136      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
137        argument is zero (in case called within single-thread section).
138    o pkg/fizhi:
139        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
140        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
141    o pkg/exch2:
142      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
143        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
144      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
145        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
146        with bad ones coming from a not-yet-updated halo.
147        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
148    o pkg/frazil:
149        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
150        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
151    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
152    o verification/lab_sea
153      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
154      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
155      * nTimeSteps 3 -> 4
156      * changed reference output accordingly
157    o pkg/ctrl:
158      * fix ctrl_get_gen for xx_sst, xx_sss
159    o pkg/fizhi:
160      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
161        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
162      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
163        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
164        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
165    o pkg/gmredi:
166      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
167    o pkg/fizhi:
168      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
169        (old)aces open64 tuv test.
170    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
171    o pkg/mom_vecinv:
172      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
173        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
174        with non-lin free-surf).
175    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
176      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
177      some compilers (gfortran 4.6.0 on MacOS)
178    o momentum:
179      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
180        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
181        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
182    
183    checkpoint63k (2012/03/17)
184    o model/src:
185       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
186         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
187       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
188         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
189    o model/src: solve_*diagonal.F
190       - replace division with multiplication by inverse (similar to original version)
191         update output of AD exp. global_ocean.90x40x15.
192       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
193         to enable the use of the vectorized & differentiable solve_tridiagonal.F
194       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
195         vertical advection (to get solve_tridiagonal tested in AD mode).
196    o pkg/seaice: ECCO-CLIVAR merge:
197      1. seaice AREA relaxation
198         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
199         * runtime flag: SEAICE_tauAreaObsRelax
200      2. modified global mean cost imbalance code: CPP option
201          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
202    o another iteration on solve_*diagonal.F
203       Make choices independent of AUTODIFF
204       Default will be the adjoinable vectorized version.
205       Alternative choices are:
206       * non-adjoinable original version with low memory footprint:
207         #define SOLVE_DIAGONAL_LOWMEMORY
208       * still adjoinable but does not vectorize (k as inner-most loop):
209         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
210    o testreport
211     - add option to use a home made wrapper around "make"
212     - remove MITGCM_IEEE env. variable (no longer active)
213    o pkg/shelfice
214     - improve computation of friction velocity for velocity dependent
215       exchange coefficients: include velocities into SHELFICEBoundaryLayer
216       block to average velocities vertically
217     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
218    o Modify diagonal solvers, now three versions (upon request):
219      #ifndef SOLVE_DIAGONAL_AUTODIFF
220        1. default version (dating back a while ago)
221      #else /* def SOLVE_DIAGONAL_AUTODIFF */
222      # ifdef SOLVE_DIAGONAL_KINNER
223        2. adjoinable version with k-innermost loop (G. Forget)
224      # else
225        3. adjoinable vectorized version of 2.
226      # endif
227      #endif /* SOLVE_DIAGONAL_AUTODIFF */
228      All flags are currently set within routines, but could/should be moved to CPP-options.
229      Array bounds for 1. are as before, for 2.,3. cover the entire domain
230      (could be changed for 1. too).
231    o verification/lab_sea (fwd):
232      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
233        use 7 categories (except hb87), new solve4temp params (except salt_plume),
234        constant salinity (=4) or variable salinity (salt_plume) done through
235        SItracer.
236    o pkg/seaice:
237      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
238      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
239         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
240        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
241        SEAICE_freeze got retired) but already better than previously with
242        SEAICE_freeze=123456.7 deg.C;
243      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
244        (safer multi-threaded setting); always set SEAICEuseEVP;
245      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
246        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
247        stop if multiple specifications for the same coeff; make sure default
248        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
249    o pkg/obcs:
250      - allow to switch to upwind 1rst order advection scheme for the advective
251        flux computation at the open-boundary; disabled for adjoint built.
252    o pkg/ptracers:
253      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
254      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
255      - add parameter to decide when to start a tracer; use internal flag to
256        know which tracer to step-forward; switch this internal flag at the top
257        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
258        for adjoint built.
259    o pkg/seaice:
260      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
261      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
262      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
263    o pkg/ecco:
264      - fix writing of output file DiagnosCost_ClimSalt/Theta
265        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
266    o pkg/seaice:
267      - add missing initialisation of COR_ICE array in dynsolver.F
268      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
269        compiled either way, and is tested in all exps (multidim was only tested
270        in lab_sea ad before).
271      - cosmetic change to prepare for future addition of ITD. no change to results.
272        no defaults change.
273      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
274      - by lack of adequate verification experiments, I further used custom versions
275        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
276        should be correct.
277      - avoid recomputations in ad.
278    o array initialisation in adjoint mode:
279      1) pkg/mom_common/mom_calc_ke.F:
280        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
281        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
282        part this initialisation is gone, resulting in Floating Point Exception
283        (caught by open64 compiler with debug option).
284      2) model/src/convective_weights.F
285        set output convectCount over the full array range (instead of doing
286        an update): this fix a similar issue when called within recomputation (adjoint)
287        which could by-pass the initialisation (normally done in the caller S/R).
288    o pkg/seaice:
289      - final version of turbulent flux params, as agreed at MIT ice meet:
290           SEAICE_mcPheePiston (default is ~ 0.000875)
291           SEAICE_mcPheeTaper (default is 0.)
292           SEAICE_frazilFrac (defualt is 1.)
293           SEAICE_mcPheeStepFunc (default is false)
294      - changes results at trunction error level
295      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
296    o added pkg/frazil:
297      - see frazil_description.tex for details
298      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
299    o pkg/shelfice/shelfice_thermodynamics.F
300      - fix exponents for velocity dependent exchange coefficients: change
301        from 2/3(=0) to 0.66666666666666667
302      - move computation of velocity dependent exchange coefficients into
303        separate loop, so that it applies to both thermodynamics
304      - move some divisions by constants out of loops
305    
306    checkpoint63j (2012/02/16)
307    o pkg/seaice:
308      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
309      - SItracer:  added run time params, and allow coupling to ocn salinity.
310    o pkg/seaice: remove (almost) all divisions by constants within loops
311      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
312      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
313      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
314      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
315    o pkg/seaice :
316      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
317        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
318      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
319      - add permanent SItflux diag that corresponds to TFLUX but includes
320        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
321      - allow activation/testing of a fix for suspected missing term in
322        ocn-ice heat budget (to be confirmed). To test this, you want to
323        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
324        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
325      - no change in results, fwd or ad.
326    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
327      - switch to variable freezing point.
328           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
329      - bug fix : the sublimation term that was missing is now activated.
330           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
331      - bug fix : flooding sign term for SIsal0.NE.0.
332           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
333    o pkg/seaice:
334      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
335        is now the default, and the old default constant freezing point is recovered
336        with SEAICE_tempFrz0    = -1.96,
337             SEAICE_dTempFrz_dS = 0.,
338      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
339      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
340      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
341        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
342      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
343        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
344      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
345        seaice_growth r149 for legacy branch (no results change).
346      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
347        from I. Fenty).
348      - results did not change except for global_ocean.cs32x15, mostly due to the
349        switch to variable freezing point (see above item for detail).
350    o pkg/thsice:
351      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
352        seawater freezing in thsice_calc_thickn (not used).
353  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
354    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
355    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
356                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
357    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
358    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
359    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
360     SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
361     seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
362    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
363     SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
364    - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).    - seaice_summary.F : add missing report of read turbulent flux term set up
365    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
366    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_check.F : check range; inform and stop if retired CPPs are used
367          CPP switch, same computation as before for the different options.                       (incl. SEAICE_AGE).
368      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
369             CPP switch, same computation as before for the different options.
370    - change results at the truncation level.    - change results at the truncation level.
371  o pkg/seaice:  o pkg/seaice:
372    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:

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