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revision 1.1588 by jmc, Thu Feb 2 19:22:02 2012 UTC revision 1.1653 by heimbach, Thu Apr 19 16:09:58 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 pkg/seaice & pkg/exf:
8       Part two of ECCO-CLIVAR code merges.
9       Completes merge of seaice area relax. code.
10       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
11       to be set in EXF_OPTIONS.h since this pkg controls its I/O
12       (and avoids second CPP option in SEAICE_OPTIONS.h)
13    o pkg/ptracers:
14     - move ptracers summary and setup check into separated S/R ; add a check for
15       valid PTRACERS_Iter0 value (error+stop or just warning).
16    o pkg/cal (+ pkg/ecco):
17     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
18       as input; and for AD, unless both are not differentiable (e.g., k index)).
19    o model/src:
20     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
21       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
22       temporary set to usingZCoords value (to be changed to F when using shelfice).
23     - hydrostatic pressure: implement partial cell near the surface also for
24       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
25       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
26    o pkg/ctrl/ctrl_init.F:
27     - add a formal parameter to s/r ctrl_init_rec to print
28       xx_$(ctrl_valiable)_file for easier debugging
29     - move call of cal_* routines into the if-block where they are really
30       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
31       to specify a startdate
32    o pkg/seaice:
33     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
34       global_ocean.cs32x15/code versions).
35     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
36       verification experiment global_ocean.cs32x15.seaice and update results.
37    o pkg/exf:
38     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
39       (according to useExfYearlyFields).
40    o pkg/cal:
41     - move calendar setting & summary (previously in cal_readparams.F) into new
42       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
43       length of the simulation is set (after SET_PARMS call); This is an attempt
44       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
45     - For safety: keep a record of pkg/cal parameter settings status
46               to allow to STOP if one pkg/cal S/R is called too early.
47     - add a stop in all basic pkg/cal subroutines if called before setting is done.
48     - modify cal_getdate.F: stop when nothing was returned;
49       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
50       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
51    
52    checkpoint63l (2012/04/04)
53    o pkg/bbl:
54      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
55        update global_with_exf output.yearly.txt file.
56    o pkg/cal:
57      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
58      - remove 2 unsused and very short (1 line only) functions ;
59      - remove unsused subroutines from AD-Diff list.
60    o model/src:
61      - start to implement clean wait to stop in initialization S/R (config_check.F,
62         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
63    o folowing PRINT_MESSAGE changes:
64      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
65    o pkg/bbl:
66      - modification so it can work with z*
67      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
68      - global_with_exf/input.yearly verification; changes output.yearly.txt
69    o eesupp/src:
70      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
71        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
72      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
73        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
74      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
75      - when using MPI, always set usingMPI=T ; set default accordingly and stop
76        if not consistent.
77      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
78        argument is zero (in case called within single-thread section).
79    o pkg/fizhi:
80        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
81        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
82    o pkg/exch2:
83      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
84        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
85      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
86        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
87        with bad ones coming from a not-yet-updated halo.
88        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
89    o pkg/frazil:
90        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
91        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
92    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
93    o verification/lab_sea
94      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
95      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
96      * nTimeSteps 3 -> 4
97      * changed reference output accordingly
98    o pkg/ctrl:
99      * fix ctrl_get_gen for xx_sst, xx_sss
100    o pkg/fizhi:
101      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
102        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
103      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
104        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
105        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
106    o pkg/gmredi:
107      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
108    o pkg/fizhi:
109      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
110        (old)aces open64 tuv test.
111    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
112    o pkg/mom_vecinv:
113      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
114        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
115        with non-lin free-surf).
116    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
117      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
118      some compilers (gfortran 4.6.0 on MacOS)
119    o momentum:
120      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
121        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
122        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
123    
124    checkpoint63k (2012/03/17)
125    o model/src:
126       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
127         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
128       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
129         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
130    o model/src: solve_*diagonal.F
131       - replace division with multiplication by inverse (similar to original version)
132         update output of AD exp. global_ocean.90x40x15.
133       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
134         to enable the use of the vectorized & differentiable solve_tridiagonal.F
135       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
136         vertical advection (to get solve_tridiagonal tested in AD mode).
137    o pkg/seaice: ECCO-CLIVAR merge:
138      1. seaice AREA relaxation
139         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
140         * runtime flag: SEAICE_tauAreaObsRelax
141      2. modified global mean cost imbalance code: CPP option
142          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
143    o another iteration on solve_*diagonal.F
144       Make choices independent of AUTODIFF
145       Default will be the adjoinable vectorized version.
146       Alternative choices are:
147       * non-adjoinable original version with low memory footprint:
148         #define SOLVE_DIAGONAL_LOWMEMORY
149       * still adjoinable but does not vectorize (k as inner-most loop):
150         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
151    o testreport
152     - add option to use a home made wrapper around "make"
153     - remove MITGCM_IEEE env. variable (no longer active)
154    o pkg/shelfice
155     - improve computation of friction velocity for velocity dependent
156       exchange coefficients: include velocities into SHELFICEBoundaryLayer
157       block to average velocities vertically
158     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
159    o Modify diagonal solvers, now three versions (upon request):
160      #ifndef SOLVE_DIAGONAL_AUTODIFF
161        1. default version (dating back a while ago)
162      #else /* def SOLVE_DIAGONAL_AUTODIFF */
163      # ifdef SOLVE_DIAGONAL_KINNER
164        2. adjoinable version with k-innermost loop (G. Forget)
165      # else
166        3. adjoinable vectorized version of 2.
167      # endif
168      #endif /* SOLVE_DIAGONAL_AUTODIFF */
169      All flags are currently set within routines, but could/should be moved to CPP-options.
170      Array bounds for 1. are as before, for 2.,3. cover the entire domain
171      (could be changed for 1. too).
172    o verification/lab_sea (fwd):
173      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
174        use 7 categories (except hb87), new solve4temp params (except salt_plume),
175        constant salinity (=4) or variable salinity (salt_plume) done through
176        SItracer.
177    o pkg/seaice:
178      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
179      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
180         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
181        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
182        SEAICE_freeze got retired) but already better than previously with
183        SEAICE_freeze=123456.7 deg.C;
184      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
185        (safer multi-threaded setting); always set SEAICEuseEVP;
186      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
187        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
188        stop if multiple specifications for the same coeff; make sure default
189        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
190    o pkg/obcs:
191      - allow to switch to upwind 1rst order advection scheme for the advective
192        flux computation at the open-boundary; disabled for adjoint built.
193    o pkg/ptracers:
194      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
195      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
196      - add parameter to decide when to start a tracer; use internal flag to
197        know which tracer to step-forward; switch this internal flag at the top
198        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
199        for adjoint built.
200    o pkg/seaice:
201      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
202      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
203      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
204    o pkg/ecco:
205      - fix writing of output file DiagnosCost_ClimSalt/Theta
206        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
207    o pkg/seaice:
208      - add missing initialisation of COR_ICE array in dynsolver.F
209      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
210        compiled either way, and is tested in all exps (multidim was only tested
211        in lab_sea ad before).
212      - cosmetic change to prepare for future addition of ITD. no change to results.
213        no defaults change.
214      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
215      - by lack of adequate verification experiments, I further used custom versions
216        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
217        should be correct.
218      - avoid recomputations in ad.
219    o array initialisation in adjoint mode:
220      1) pkg/mom_common/mom_calc_ke.F:
221        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
222        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
223        part this initialisation is gone, resulting in Floating Point Exception
224        (caught by open64 compiler with debug option).
225      2) model/src/convective_weights.F
226        set output convectCount over the full array range (instead of doing
227        an update): this fix a similar issue when called within recomputation (adjoint)
228        which could by-pass the initialisation (normally done in the caller S/R).
229    o pkg/seaice:
230      - final version of turbulent flux params, as agreed at MIT ice meet:
231           SEAICE_mcPheePiston (default is ~ 0.000875)
232           SEAICE_mcPheeTaper (default is 0.)
233           SEAICE_frazilFrac (defualt is 1.)
234           SEAICE_mcPheeStepFunc (default is false)
235      - changes results at trunction error level
236      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
237    o added pkg/frazil:
238      - see frazil_description.tex for details
239      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
240    o pkg/shelfice/shelfice_thermodynamics.F
241      - fix exponents for velocity dependent exchange coefficients: change
242        from 2/3(=0) to 0.66666666666666667
243      - move computation of velocity dependent exchange coefficients into
244        separate loop, so that it applies to both thermodynamics
245      - move some divisions by constants out of loops
246    
247    checkpoint63j (2012/02/16)
248    o pkg/seaice:
249      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
250      - SItracer:  added run time params, and allow coupling to ocn salinity.
251    o pkg/seaice: remove (almost) all divisions by constants within loops
252      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
253      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
254      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
255      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
256    o pkg/seaice :
257      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
258        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
259      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
260      - add permanent SItflux diag that corresponds to TFLUX but includes
261        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
262      - allow activation/testing of a fix for suspected missing term in
263        ocn-ice heat budget (to be confirmed). To test this, you want to
264        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
265        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
266      - no change in results, fwd or ad.
267    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
268      - switch to variable freezing point.
269           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
270      - bug fix : the sublimation term that was missing is now activated.
271           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
272      - bug fix : flooding sign term for SIsal0.NE.0.
273           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
274    o pkg/seaice:
275      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
276        is now the default, and the old default constant freezing point is recovered
277        with SEAICE_tempFrz0    = -1.96,
278             SEAICE_dTempFrz_dS = 0.,
279      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
280      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
281      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
282        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
283      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
284        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
285      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
286        seaice_growth r149 for legacy branch (no results change).
287      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
288        from I. Fenty).
289      - results did not change except for global_ocean.cs32x15, mostly due to the
290        switch to variable freezing point (see above item for detail).
291    o pkg/thsice:
292      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
293        seawater freezing in thsice_calc_thickn (not used).
294    o pkg/seaice: turbulent flux term specification via run time params.
295      - replace CPP switches with run time switches to facilitate testing
296      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
297                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
298      - added runtime parameter : SEAICEturbFluxFormula
299      - move Mcphee constants to SEAICE_PARAMS.h
300      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
301                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
302                 remove seaice_summary call (moved to seaice_init_fixed)
303      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
304        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
305      - seaice_summary.F : add missing report of read turbulent flux term set up
306                           and SITRACER.
307      - seaice_check.F : check range; inform and stop if retired CPPs are used
308                         (incl. SEAICE_AGE).
309      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
310             CPP switch, same computation as before for the different options.
311      - change results at the truncation level.
312    o pkg/seaice:
313      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
314        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
315        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
316      - update verification/*/input*/data.seaice:
317        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
318        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
319        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
320        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
321    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
322      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
323        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
324        difference in results only due to machine truncation.
325      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
326        MaykutPolySatVap; keep MIN_LWDOWN.
327      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
328      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
329        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
330    o pkg/salt_plume:
331      - isolate saltPlumeFlux array exch into a specific S/R called from
332        do_oceanic_phys.F
333      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
334    o verification:
335      - move untested set-up to MITgcm_contrib/verification_other.
336    o pkg/seaice:
337      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
338  o pkg/seaice:  o pkg/seaice:
339    - seaice_solve4temp.F (keeping results unchanged):    - seaice_solve4temp.F (keeping results unchanged):
340      * 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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