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revision 1.1605 by dimitri, Sat Mar 3 16:04:38 2012 UTC revision 1.1679 by jmc, Fri Jun 29 13:51:53 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 :  checkpoint63o (2012/06/29)
8    o vertical mixing schemes:
9      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
10      - replace computation of density (in Function STATE1, opps_calc.F) by a call
11        to S/R FIND_RHO_SCALAR
12      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
13        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
14        affects output (vermix.ggl90) at truncation level.
15    o testreport:
16      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
17        (nSx,nSy) for the number of threads (from eedata.mth)
18    o model/src:
19      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
20        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
21    o verification/tutorial_tracer_adjsens/
22      - compile with ALLOW_CG2D_NSA
23      - run with nonlinFreeSurf=3
24      - update reference output_adm.txt
25    o tools/genmake2:
26      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
27        refine usePROFILES switching off (only when NetCDF is not available).
28    o verification (atmospheric set-up):
29      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
30    o pkg/profiles : refine profiles and files handling.
31    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
32    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
33      - changes to use model/src/the_main_loop.F rather than the ecco version
34        in ecco type adjoint runs.
35    o model/src:
36      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
37      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
38      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
39    o model/src:
40      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
41        update output of test experiment bottom_ctrl_5x5.
42    o pkg/generic_advdiff:
43      - implement vertical bi-harmonic diffusion (for now, only for T & S and
44        only explicitly).
45    o verification/bottom_ctrl_5x5/
46      update reference output (results changed quite some time ago,
47      not sure when; but new reference results look ok in terms of grdchk)
48    o verification/1D_ocean_ice_column/
49      For verification purposes, the exact adjoint rather than an approx.
50      should be used (e.g., to comare against F.D. or TLM).
51      removed autodiff_inadmode*_ad.F routines in code_ad/
52      Update results/ accordingly.
53    o pkg/cal:
54      - change cal_getdate.F so that output date is function of input time only
55        (less ambiguous, not mixed up with input iteration number).
56      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
57    o pkg/diagnostics:
58      - implement calendarDumps also for stats-diags
59      - implement calendarDumps also for snap-shot output (negative freq)
60      - for now, ignores calendarDumps if non-zero phase-lag.
61    
62    checkpoint63n (2012/06/04)
63    o model/src:
64      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
65        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
66      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
67        similar to calc_r_star.F); update results of experiment internal_wave and
68        tutorial_global_oce_in_p (affected @ truncation level).
69    o pkg/shelfice:
70      - add parameterisation of advective-diffusive flux into the ice shelf
71        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
72      - simply eps3/3a computation
73    o eesupp:
74     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
75       between tiles, just fill-in edges assuming locally periodic subdomain) and
76       add corresponding exchange subroutines (EXCH0);
77     - new CG-solver version (_EX0) for disconnected-tiles special case.
78    o model/src (CG-solvers):
79     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
80       (similar final residual output and max-Iter number as with standard version);
81     - allows to store and use lowest-residual solution (standard & _SR versions);
82     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
83     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
84    o eesup/src:
85     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
86       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
87    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
88    
89    checkpoint63m (2012/04/27)
90    o pkg/shelfice:
91     - account for partical cells in surface level below ice-shelf for hydrostatic
92       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
93    o ad test experiments:
94     - update and rename to "ad_optfile.local" local AD-optfile specific to a
95       particular adjoint verification experiment (in verification/*/code_ad/)
96    o pkg/seaice & pkg/exf:
97     - Part two of ECCO-CLIVAR code merges.
98       Completes merge of seaice area relax. code.
99       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
100       to be set in EXF_OPTIONS.h since this pkg controls its I/O
101       (and avoids second CPP option in SEAICE_OPTIONS.h)
102     - change default value of costIceStart & costIceEnd to a valid date.
103     - add snowPrecip to HSNOW in seaice_growth
104    o pkg/ptracers:
105     - move ptracers summary and setup check into separated S/R ; add a check for
106       valid PTRACERS_Iter0 value (error+stop or just warning).
107    o pkg/cal (+ pkg/ecco):
108     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
109       as input; and for AD, unless both are not differentiable (e.g., k index)).
110    o model/src:
111     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
112       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
113       temporary set to usingZCoords value (to be changed to F when using shelfice).
114     - hydrostatic pressure: implement partial cell near the surface also for
115       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
116       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
117    o pkg/ctrl/ctrl_init.F:
118     - add a formal parameter to s/r ctrl_init_rec to print
119       xx_$(ctrl_valiable)_file for easier debugging
120     - move call of cal_* routines into the if-block where they are really
121       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
122       to specify a startdate
123    o pkg/seaice:
124     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
125       global_ocean.cs32x15/code versions).
126     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
127       verification experiment global_ocean.cs32x15.seaice and update results.
128    o pkg/exf:
129     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
130       (according to useExfYearlyFields).
131    o pkg/cal:
132     - move calendar setting & summary (previously in cal_readparams.F) into new
133       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
134       length of the simulation is set (after SET_PARMS call); This is an attempt
135       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
136     - For safety: keep a record of pkg/cal parameter settings status
137               to allow to STOP if one pkg/cal S/R is called too early.
138     - add a stop in all basic pkg/cal subroutines if called before setting is done.
139     - modify cal_getdate.F: stop when nothing was returned;
140       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
141       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
142    
143    checkpoint63l (2012/04/04)
144    o pkg/bbl:
145      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
146        update global_with_exf output.yearly.txt file.
147    o pkg/cal:
148      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
149      - remove 2 unsused and very short (1 line only) functions ;
150      - remove unsused subroutines from AD-Diff list.
151    o model/src:
152      - start to implement clean wait to stop in initialization S/R (config_check.F,
153         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
154    o folowing PRINT_MESSAGE changes:
155      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
156    o pkg/bbl:
157      - modification so it can work with z*
158      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
159      - global_with_exf/input.yearly verification; changes output.yearly.txt
160    o eesupp/src:
161      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
162        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
163      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
164        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
165      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
166      - when using MPI, always set usingMPI=T ; set default accordingly and stop
167        if not consistent.
168      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
169        argument is zero (in case called within single-thread section).
170    o pkg/fizhi:
171        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
172        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
173    o pkg/exch2:
174      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
175        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
176      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
177        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
178        with bad ones coming from a not-yet-updated halo.
179        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
180    o pkg/frazil:
181        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
182        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
183    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
184    o verification/lab_sea
185      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
186      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
187      * nTimeSteps 3 -> 4
188      * changed reference output accordingly
189    o pkg/ctrl:
190      * fix ctrl_get_gen for xx_sst, xx_sss
191    o pkg/fizhi:
192      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
193        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
194      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
195        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
196        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
197    o pkg/gmredi:
198      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
199    o pkg/fizhi:
200      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
201        (old)aces open64 tuv test.
202    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
203    o pkg/mom_vecinv:
204      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
205        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
206        with non-lin free-surf).
207    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
208      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
209      some compilers (gfortran 4.6.0 on MacOS)
210    o momentum:
211      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
212        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
213        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
214    
215    checkpoint63k (2012/03/17)
216    o model/src:
217       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
218         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
219       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
220         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
221    o model/src: solve_*diagonal.F
222       - replace division with multiplication by inverse (similar to original version)
223         update output of AD exp. global_ocean.90x40x15.
224       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
225         to enable the use of the vectorized & differentiable solve_tridiagonal.F
226       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
227         vertical advection (to get solve_tridiagonal tested in AD mode).
228    o pkg/seaice: ECCO-CLIVAR merge:
229      1. seaice AREA relaxation
230         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
231         * runtime flag: SEAICE_tauAreaObsRelax
232      2. modified global mean cost imbalance code: CPP option
233          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
234    o another iteration on solve_*diagonal.F
235       Make choices independent of AUTODIFF
236       Default will be the adjoinable vectorized version.
237       Alternative choices are:
238       * non-adjoinable original version with low memory footprint:
239         #define SOLVE_DIAGONAL_LOWMEMORY
240       * still adjoinable but does not vectorize (k as inner-most loop):
241         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
242    o testreport
243     - add option to use a home made wrapper around "make"
244     - remove MITGCM_IEEE env. variable (no longer active)
245    o pkg/shelfice
246     - improve computation of friction velocity for velocity dependent
247       exchange coefficients: include velocities into SHELFICEBoundaryLayer
248       block to average velocities vertically
249     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
250    o Modify diagonal solvers, now three versions (upon request):
251      #ifndef SOLVE_DIAGONAL_AUTODIFF
252        1. default version (dating back a while ago)
253      #else /* def SOLVE_DIAGONAL_AUTODIFF */
254      # ifdef SOLVE_DIAGONAL_KINNER
255        2. adjoinable version with k-innermost loop (G. Forget)
256      # else
257        3. adjoinable vectorized version of 2.
258      # endif
259      #endif /* SOLVE_DIAGONAL_AUTODIFF */
260      All flags are currently set within routines, but could/should be moved to CPP-options.
261      Array bounds for 1. are as before, for 2.,3. cover the entire domain
262      (could be changed for 1. too).
263    o verification/lab_sea (fwd):
264      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
265        use 7 categories (except hb87), new solve4temp params (except salt_plume),
266        constant salinity (=4) or variable salinity (salt_plume) done through
267        SItracer.
268    o pkg/seaice:
269      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
270      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
271         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
272        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
273        SEAICE_freeze got retired) but already better than previously with
274        SEAICE_freeze=123456.7 deg.C;
275      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
276        (safer multi-threaded setting); always set SEAICEuseEVP;
277      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
278        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
279        stop if multiple specifications for the same coeff; make sure default
280        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
281    o pkg/obcs:
282      - allow to switch to upwind 1rst order advection scheme for the advective
283        flux computation at the open-boundary; disabled for adjoint built.
284    o pkg/ptracers:
285      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
286      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
287      - add parameter to decide when to start a tracer; use internal flag to
288        know which tracer to step-forward; switch this internal flag at the top
289        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
290        for adjoint built.
291    o pkg/seaice:
292      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
293      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
294      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
295    o pkg/ecco:
296      - fix writing of output file DiagnosCost_ClimSalt/Theta
297        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
298    o pkg/seaice:
299      - add missing initialisation of COR_ICE array in dynsolver.F
300      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
301        compiled either way, and is tested in all exps (multidim was only tested
302        in lab_sea ad before).
303      - cosmetic change to prepare for future addition of ITD. no change to results.
304        no defaults change.
305      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
306      - by lack of adequate verification experiments, I further used custom versions
307        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
308        should be correct.
309      - avoid recomputations in ad.
310    o array initialisation in adjoint mode:
311      1) pkg/mom_common/mom_calc_ke.F:
312        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
313        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
314        part this initialisation is gone, resulting in Floating Point Exception
315        (caught by open64 compiler with debug option).
316      2) model/src/convective_weights.F
317        set output convectCount over the full array range (instead of doing
318        an update): this fix a similar issue when called within recomputation (adjoint)
319        which could by-pass the initialisation (normally done in the caller S/R).
320    o pkg/seaice:
321    - final version of turbulent flux params, as agreed at MIT ice meet:    - final version of turbulent flux params, as agreed at MIT ice meet:
322         SEAICE_mcPheePiston (default is ~ 0.000875)         SEAICE_mcPheePiston (default is ~ 0.000875)
323         SEAICE_mcPheeTaper (default is 0.)         SEAICE_mcPheeTaper (default is 0.)
# Line 12  o pkg/seaice : Line 325  o pkg/seaice :
325         SEAICE_mcPheeStepFunc (default is false)         SEAICE_mcPheeStepFunc (default is false)
326    - changes results at trunction error level    - changes results at trunction error level
327    - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo    - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
328  o added pkg/frazil - see frazil_description.tex for details  o added pkg/frazil:
329      - see frazil_description.tex for details
330      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
331  o pkg/shelfice/shelfice_thermodynamics.F  o pkg/shelfice/shelfice_thermodynamics.F
332    - fix exponents for velocity dependent exchange coefficients: change    - fix exponents for velocity dependent exchange coefficients: change
333      from 2/3(=0) to 0.66666666666666667      from 2/3(=0) to 0.66666666666666667
334    - move computation of velocity dependent exchange coefficients into    - move computation of velocity dependent exchange coefficients into
335      separate loop, so that it applies to both thermodynamics      separate loop, so that it applies to both thermodynamics
336    - move some divisions by constants out of loops    - move some divisions by constants out of loops
337    
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