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revision 1.1618 by mlosch, Mon Mar 12 16:51:37 2012 UTC revision 1.1691 by jmc, Tue Jul 17 01:15:26 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 verification/tutorial_tracer_adjsens:
8       improve parameter consistencyi (and get rid of warnings):
9       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
10       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
11       - use staggerTimeStep (for stability) in som81; use default rotation period.
12    o pkg/exch2:
13      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
14        reset to 0 = 1 long line in X)
15    o pkg/mdsio:
16      - fix reading of dimensions from meta file for large-size domain
17    o model/src:
18      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
19      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
20        Cubed-Sphere Exch with CS-corners inside the domain;
21        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
22        globalArea and to set hasWetCSCorners.
23      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
24        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
25      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
26        useCDscheme and useCubedSphereExchange).
27    o pkg/seaice/seaice_growth.F :
28      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
29        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
30        when the previous code was not correct.
31      - in all cases diagnoze the boundary condition mismatch to SIaaflux
32      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
33        that term to QNET (essentially to set the melt/freeze water to 0degC).
34        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
35    o verification/global_ocean.cs32x15/input.seaice :
36      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
37      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
38      - update results (output.seaice.txt) accordingly.
39    o verification/lab_sea/input/data.seaice :
40      - remove SEAICEheatConsFix, which is now be tested
41        in global_ocean.cs32x15. The presently coded fix
42        is only consistent with real fresh water + nlfs.
43      - update results (output.txt) accordingly.
44    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
45    o AD_CONFIG.h file:
46      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
47      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
48        add it explicitly in each fortran src file where it is needed.
49        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
50        thus introducing potentially wrong dependency; therefore, better to include
51        it only where it's really needed, and after any other included OPTIONS file
52        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
53        or ALLOW_TANGENTLINEAR_RUN).
54    
55    checkpoint63p (2012/07/06)
56    o pkg/autodiff:
57      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
58      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
59        which are now read from new parameter file "data.autodiff" (inAdExact
60        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
61      - add file "data.autodiff" in all verification/*/input_ad/ directories.
62      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
63        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
64    o verification/tutorial_tracer_adjsens/
65      - add extra sub-verification which uses "SOM" advection scheme
66        (2nd Order-Moment Advection Scheme, Prather Limiter) with
67          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
68        and in data:
69          multiDimAdvection=.TRUE.,
70          tempAdvScheme=81,
71          saltAdvScheme=81,
72    o model/src:
73      - introduce ALLOW_BALANCE_RELAX which allow the removal
74       of the global mean of relaxation terms by setting
75       balanceThetaClimRelax and balanceSaltClimRelax
76      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
77       This case is now treated appropriately in seaice_growth.F
78    o pkg/seaice:
79      - do balanceEmPmR and balanceQnet based on the net fluxes
80        (SItflux) that enter the ocean+ice system rather than QNET
81        and EMPMR. Works best in real fresh water.
82      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
83        out of the diagnotics bloc, and stored in global arrays.
84    
85    checkpoint63o (2012/06/29)
86    o vertical mixing schemes:
87      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
88      - replace computation of density (in Function STATE1, opps_calc.F) by a call
89        to S/R FIND_RHO_SCALAR
90      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
91        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
92        affects output (vermix.ggl90) at truncation level.
93    o testreport:
94      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
95        (nSx,nSy) for the number of threads (from eedata.mth)
96    o model/src:
97      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
98        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
99    o verification/tutorial_tracer_adjsens/
100      - compile with ALLOW_CG2D_NSA
101      - run with nonlinFreeSurf=3
102      - update reference output_adm.txt
103    o tools/genmake2:
104      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
105        refine usePROFILES switching off (only when NetCDF is not available).
106    o verification (atmospheric set-up):
107      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
108    o pkg/profiles : refine profiles and files handling.
109    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
110    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
111      - changes to use model/src/the_main_loop.F rather than the ecco version
112        in ecco type adjoint runs.
113    o model/src:
114      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
115      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
116      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
117    o model/src:
118      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
119        update output of test experiment bottom_ctrl_5x5.
120    o pkg/generic_advdiff:
121      - implement vertical bi-harmonic diffusion (for now, only for T & S and
122        only explicitly).
123    o verification/bottom_ctrl_5x5/
124      update reference output (results changed quite some time ago,
125      not sure when; but new reference results look ok in terms of grdchk)
126    o verification/1D_ocean_ice_column/
127      For verification purposes, the exact adjoint rather than an approx.
128      should be used (e.g., to comare against F.D. or TLM).
129      removed autodiff_inadmode*_ad.F routines in code_ad/
130      Update results/ accordingly.
131    o pkg/cal:
132      - change cal_getdate.F so that output date is function of input time only
133        (less ambiguous, not mixed up with input iteration number).
134      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
135    o pkg/diagnostics:
136      - implement calendarDumps also for stats-diags
137      - implement calendarDumps also for snap-shot output (negative freq)
138      - for now, ignores calendarDumps if non-zero phase-lag.
139    
140    checkpoint63n (2012/06/04)
141    o model/src:
142      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
143        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
144      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
145        similar to calc_r_star.F); update results of experiment internal_wave and
146        tutorial_global_oce_in_p (affected @ truncation level).
147    o pkg/shelfice:
148      - add parameterisation of advective-diffusive flux into the ice shelf
149        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
150      - simply eps3/3a computation
151    o eesupp:
152     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
153       between tiles, just fill-in edges assuming locally periodic subdomain) and
154       add corresponding exchange subroutines (EXCH0);
155     - new CG-solver version (_EX0) for disconnected-tiles special case.
156    o model/src (CG-solvers):
157     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
158       (similar final residual output and max-Iter number as with standard version);
159     - allows to store and use lowest-residual solution (standard & _SR versions);
160     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
161     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
162    o eesup/src:
163     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
164       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
165    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
166    
167    checkpoint63m (2012/04/27)
168    o pkg/shelfice:
169     - account for partical cells in surface level below ice-shelf for hydrostatic
170       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
171    o ad test experiments:
172     - update and rename to "ad_optfile.local" local AD-optfile specific to a
173       particular adjoint verification experiment (in verification/*/code_ad/)
174    o pkg/seaice & pkg/exf:
175     - Part two of ECCO-CLIVAR code merges.
176       Completes merge of seaice area relax. code.
177       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
178       to be set in EXF_OPTIONS.h since this pkg controls its I/O
179       (and avoids second CPP option in SEAICE_OPTIONS.h)
180     - change default value of costIceStart & costIceEnd to a valid date.
181     - add snowPrecip to HSNOW in seaice_growth
182    o pkg/ptracers:
183     - move ptracers summary and setup check into separated S/R ; add a check for
184       valid PTRACERS_Iter0 value (error+stop or just warning).
185    o pkg/cal (+ pkg/ecco):
186     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
187       as input; and for AD, unless both are not differentiable (e.g., k index)).
188    o model/src:
189     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
190       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
191       temporary set to usingZCoords value (to be changed to F when using shelfice).
192     - hydrostatic pressure: implement partial cell near the surface also for
193       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
194       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
195    o pkg/ctrl/ctrl_init.F:
196     - add a formal parameter to s/r ctrl_init_rec to print
197       xx_$(ctrl_valiable)_file for easier debugging
198     - move call of cal_* routines into the if-block where they are really
199       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
200       to specify a startdate
201    o pkg/seaice:
202     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
203       global_ocean.cs32x15/code versions).
204     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
205       verification experiment global_ocean.cs32x15.seaice and update results.
206    o pkg/exf:
207     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
208       (according to useExfYearlyFields).
209    o pkg/cal:
210     - move calendar setting & summary (previously in cal_readparams.F) into new
211       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
212       length of the simulation is set (after SET_PARMS call); This is an attempt
213       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
214     - For safety: keep a record of pkg/cal parameter settings status
215               to allow to STOP if one pkg/cal S/R is called too early.
216     - add a stop in all basic pkg/cal subroutines if called before setting is done.
217     - modify cal_getdate.F: stop when nothing was returned;
218       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
219       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
220    
221    checkpoint63l (2012/04/04)
222    o pkg/bbl:
223      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
224        update global_with_exf output.yearly.txt file.
225    o pkg/cal:
226      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
227      - remove 2 unsused and very short (1 line only) functions ;
228      - remove unsused subroutines from AD-Diff list.
229    o model/src:
230      - start to implement clean wait to stop in initialization S/R (config_check.F,
231         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
232    o folowing PRINT_MESSAGE changes:
233      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
234    o pkg/bbl:
235      - modification so it can work with z*
236      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
237      - global_with_exf/input.yearly verification; changes output.yearly.txt
238    o eesupp/src:
239      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
240        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
241      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
242        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
243      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
244      - when using MPI, always set usingMPI=T ; set default accordingly and stop
245        if not consistent.
246      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
247        argument is zero (in case called within single-thread section).
248    o pkg/fizhi:
249        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
250        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
251    o pkg/exch2:
252      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
253        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
254      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
255        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
256        with bad ones coming from a not-yet-updated halo.
257        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
258    o pkg/frazil:
259        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
260        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
261    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
262    o verification/lab_sea
263      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
264      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
265      * nTimeSteps 3 -> 4
266      * changed reference output accordingly
267    o pkg/ctrl:
268      * fix ctrl_get_gen for xx_sst, xx_sss
269    o pkg/fizhi:
270      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
271        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
272      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
273        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
274        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
275    o pkg/gmredi:
276      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
277    o pkg/fizhi:
278      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
279        (old)aces open64 tuv test.
280    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
281    o pkg/mom_vecinv:
282      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
283        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
284        with non-lin free-surf).
285    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
286      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
287      some compilers (gfortran 4.6.0 on MacOS)
288    o momentum:
289      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
290        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
291        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
292    
293    checkpoint63k (2012/03/17)
294    o model/src:
295       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
296         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
297       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
298         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
299    o model/src: solve_*diagonal.F
300       - replace division with multiplication by inverse (similar to original version)
301         update output of AD exp. global_ocean.90x40x15.
302       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
303         to enable the use of the vectorized & differentiable solve_tridiagonal.F
304       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
305         vertical advection (to get solve_tridiagonal tested in AD mode).
306    o pkg/seaice: ECCO-CLIVAR merge:
307      1. seaice AREA relaxation
308         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
309         * runtime flag: SEAICE_tauAreaObsRelax
310      2. modified global mean cost imbalance code: CPP option
311          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
312    o another iteration on solve_*diagonal.F
313       Make choices independent of AUTODIFF
314       Default will be the adjoinable vectorized version.
315       Alternative choices are:
316       * non-adjoinable original version with low memory footprint:
317         #define SOLVE_DIAGONAL_LOWMEMORY
318       * still adjoinable but does not vectorize (k as inner-most loop):
319         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
320    o testreport
321     - add option to use a home made wrapper around "make"
322     - remove MITGCM_IEEE env. variable (no longer active)
323  o pkg/shelfice  o pkg/shelfice
324   - improve computation of friction velocity for velocity dependent   - improve computation of friction velocity for velocity dependent
325     exchange coefficients: include velocities into SHELFICEBoundaryLayer     exchange coefficients: include velocities into SHELFICEBoundaryLayer

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