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revision 1.1638 by jmc, Tue Mar 27 15:53:56 2012 UTC revision 1.1681 by jmc, Wed Jul 4 20:39:21 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/autodiff:
8      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
9      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
10        which are now read from new parameter file "data.autodiff" (inAdExact
11        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
12      - add file "data.autodiff" in all verification/*/input_ad/ directories.
13    o verification/tutorial_tracer_adjsens/
14      - add extra sub-verification which uses "SOM" advection scheme
15        (2nd Order-Moment Advection Scheme, Prather Limiter) with
16          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
17        and in data:
18          multiDimAdvection=.TRUE.,
19          tempAdvScheme=81,
20          saltAdvScheme=81,
21    
22    checkpoint63o (2012/06/29)
23    o vertical mixing schemes:
24      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
25      - replace computation of density (in Function STATE1, opps_calc.F) by a call
26        to S/R FIND_RHO_SCALAR
27      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
28        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
29        affects output (vermix.ggl90) at truncation level.
30    o testreport:
31      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
32        (nSx,nSy) for the number of threads (from eedata.mth)
33    o model/src:
34      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
35        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
36    o verification/tutorial_tracer_adjsens/
37      - compile with ALLOW_CG2D_NSA
38      - run with nonlinFreeSurf=3
39      - update reference output_adm.txt
40    o tools/genmake2:
41      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
42        refine usePROFILES switching off (only when NetCDF is not available).
43    o verification (atmospheric set-up):
44      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
45    o pkg/profiles : refine profiles and files handling.
46    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
47    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
48      - changes to use model/src/the_main_loop.F rather than the ecco version
49        in ecco type adjoint runs.
50    o model/src:
51      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
52      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
53      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
54    o model/src:
55      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
56        update output of test experiment bottom_ctrl_5x5.
57    o pkg/generic_advdiff:
58      - implement vertical bi-harmonic diffusion (for now, only for T & S and
59        only explicitly).
60    o verification/bottom_ctrl_5x5/
61      update reference output (results changed quite some time ago,
62      not sure when; but new reference results look ok in terms of grdchk)
63    o verification/1D_ocean_ice_column/
64      For verification purposes, the exact adjoint rather than an approx.
65      should be used (e.g., to comare against F.D. or TLM).
66      removed autodiff_inadmode*_ad.F routines in code_ad/
67      Update results/ accordingly.
68    o pkg/cal:
69      - change cal_getdate.F so that output date is function of input time only
70        (less ambiguous, not mixed up with input iteration number).
71      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
72    o pkg/diagnostics:
73      - implement calendarDumps also for stats-diags
74      - implement calendarDumps also for snap-shot output (negative freq)
75      - for now, ignores calendarDumps if non-zero phase-lag.
76    
77    checkpoint63n (2012/06/04)
78    o model/src:
79      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
80        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
81      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
82        similar to calc_r_star.F); update results of experiment internal_wave and
83        tutorial_global_oce_in_p (affected @ truncation level).
84    o pkg/shelfice:
85      - add parameterisation of advective-diffusive flux into the ice shelf
86        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
87      - simply eps3/3a computation
88    o eesupp:
89     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
90       between tiles, just fill-in edges assuming locally periodic subdomain) and
91       add corresponding exchange subroutines (EXCH0);
92     - new CG-solver version (_EX0) for disconnected-tiles special case.
93    o model/src (CG-solvers):
94     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
95       (similar final residual output and max-Iter number as with standard version);
96     - allows to store and use lowest-residual solution (standard & _SR versions);
97     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
98     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
99    o eesup/src:
100     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
101       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
102    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
103    
104    checkpoint63m (2012/04/27)
105    o pkg/shelfice:
106     - account for partical cells in surface level below ice-shelf for hydrostatic
107       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
108    o ad test experiments:
109     - update and rename to "ad_optfile.local" local AD-optfile specific to a
110       particular adjoint verification experiment (in verification/*/code_ad/)
111    o pkg/seaice & pkg/exf:
112     - Part two of ECCO-CLIVAR code merges.
113       Completes merge of seaice area relax. code.
114       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
115       to be set in EXF_OPTIONS.h since this pkg controls its I/O
116       (and avoids second CPP option in SEAICE_OPTIONS.h)
117     - change default value of costIceStart & costIceEnd to a valid date.
118     - add snowPrecip to HSNOW in seaice_growth
119    o pkg/ptracers:
120     - move ptracers summary and setup check into separated S/R ; add a check for
121       valid PTRACERS_Iter0 value (error+stop or just warning).
122    o pkg/cal (+ pkg/ecco):
123     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
124       as input; and for AD, unless both are not differentiable (e.g., k index)).
125    o model/src:
126     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
127       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
128       temporary set to usingZCoords value (to be changed to F when using shelfice).
129     - hydrostatic pressure: implement partial cell near the surface also for
130       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
131       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
132    o pkg/ctrl/ctrl_init.F:
133     - add a formal parameter to s/r ctrl_init_rec to print
134       xx_$(ctrl_valiable)_file for easier debugging
135     - move call of cal_* routines into the if-block where they are really
136       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
137       to specify a startdate
138    o pkg/seaice:
139     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
140       global_ocean.cs32x15/code versions).
141     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
142       verification experiment global_ocean.cs32x15.seaice and update results.
143    o pkg/exf:
144     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
145       (according to useExfYearlyFields).
146    o pkg/cal:
147     - move calendar setting & summary (previously in cal_readparams.F) into new
148       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
149       length of the simulation is set (after SET_PARMS call); This is an attempt
150       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
151     - For safety: keep a record of pkg/cal parameter settings status
152               to allow to STOP if one pkg/cal S/R is called too early.
153     - add a stop in all basic pkg/cal subroutines if called before setting is done.
154     - modify cal_getdate.F: stop when nothing was returned;
155       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
156       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
157    
158    checkpoint63l (2012/04/04)
159    o pkg/bbl:
160      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
161        update global_with_exf output.yearly.txt file.
162    o pkg/cal:
163      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
164      - remove 2 unsused and very short (1 line only) functions ;
165      - remove unsused subroutines from AD-Diff list.
166    o model/src:
167      - start to implement clean wait to stop in initialization S/R (config_check.F,
168         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
169    o folowing PRINT_MESSAGE changes:
170      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
171    o pkg/bbl:
172      - modification so it can work with z*
173      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
174      - global_with_exf/input.yearly verification; changes output.yearly.txt
175    o eesupp/src:
176      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
177        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
178      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
179        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
180      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
181      - when using MPI, always set usingMPI=T ; set default accordingly and stop
182        if not consistent.
183      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
184        argument is zero (in case called within single-thread section).
185  o pkg/fizhi:  o pkg/fizhi:
186      clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored      clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
187      in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.      in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
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