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revision 1.1644 by jmc, Tue Apr 3 17:01:48 2012 UTC revision 1.1685 by jmc, Sat Jul 7 01:54:30 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 AD_CONFIG.h file:
8     - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
9     - remove #include "AD_CONFIG.h" from all included OPTIONS files and
10       add it explicitly in each fortran src file where it is needed.
11       motivation: header file AD_CONFIG.h is generated/modified after "make depend"
12       thus introducing potentially wrong dependency; therefore, better to include
13       it only where it's really needed, and after any other included OPTIONS file
14       (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
15       or ALLOW_TANGENTLINEAR_RUN).
16    
17    checkpoint63p (2012/07/06)
18    o pkg/autodiff:
19      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
20      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
21        which are now read from new parameter file "data.autodiff" (inAdExact
22        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
23      - add file "data.autodiff" in all verification/*/input_ad/ directories.
24      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
25        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
26    o verification/tutorial_tracer_adjsens/
27      - add extra sub-verification which uses "SOM" advection scheme
28        (2nd Order-Moment Advection Scheme, Prather Limiter) with
29          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
30        and in data:
31          multiDimAdvection=.TRUE.,
32          tempAdvScheme=81,
33          saltAdvScheme=81,
34    o model/src:
35      - introduce ALLOW_BALANCE_RELAX which allow the removal
36       of the global mean of relaxation terms by setting
37       balanceThetaClimRelax and balanceSaltClimRelax
38      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
39       This case is now treated appropriately in seaice_growth.F
40    o pkg/seaice:
41      - do balanceEmPmR and balanceQnet based on the net fluxes
42        (SItflux) that enter the ocean+ice system rather than QNET
43        and EMPMR. Works best in real fresh water.
44      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
45        out of the diagnotics bloc, and stored in global arrays.
46    
47    checkpoint63o (2012/06/29)
48    o vertical mixing schemes:
49      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
50      - replace computation of density (in Function STATE1, opps_calc.F) by a call
51        to S/R FIND_RHO_SCALAR
52      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
53        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
54        affects output (vermix.ggl90) at truncation level.
55    o testreport:
56      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
57        (nSx,nSy) for the number of threads (from eedata.mth)
58    o model/src:
59      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
60        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
61    o verification/tutorial_tracer_adjsens/
62      - compile with ALLOW_CG2D_NSA
63      - run with nonlinFreeSurf=3
64      - update reference output_adm.txt
65    o tools/genmake2:
66      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
67        refine usePROFILES switching off (only when NetCDF is not available).
68    o verification (atmospheric set-up):
69      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
70    o pkg/profiles : refine profiles and files handling.
71    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
72    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
73      - changes to use model/src/the_main_loop.F rather than the ecco version
74        in ecco type adjoint runs.
75    o model/src:
76      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
77      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
78      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
79    o model/src:
80      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
81        update output of test experiment bottom_ctrl_5x5.
82    o pkg/generic_advdiff:
83      - implement vertical bi-harmonic diffusion (for now, only for T & S and
84        only explicitly).
85    o verification/bottom_ctrl_5x5/
86      update reference output (results changed quite some time ago,
87      not sure when; but new reference results look ok in terms of grdchk)
88    o verification/1D_ocean_ice_column/
89      For verification purposes, the exact adjoint rather than an approx.
90      should be used (e.g., to comare against F.D. or TLM).
91      removed autodiff_inadmode*_ad.F routines in code_ad/
92      Update results/ accordingly.
93    o pkg/cal:
94      - change cal_getdate.F so that output date is function of input time only
95        (less ambiguous, not mixed up with input iteration number).
96      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
97    o pkg/diagnostics:
98      - implement calendarDumps also for stats-diags
99      - implement calendarDumps also for snap-shot output (negative freq)
100      - for now, ignores calendarDumps if non-zero phase-lag.
101    
102    checkpoint63n (2012/06/04)
103    o model/src:
104      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
105        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
106      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
107        similar to calc_r_star.F); update results of experiment internal_wave and
108        tutorial_global_oce_in_p (affected @ truncation level).
109    o pkg/shelfice:
110      - add parameterisation of advective-diffusive flux into the ice shelf
111        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
112      - simply eps3/3a computation
113    o eesupp:
114     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
115       between tiles, just fill-in edges assuming locally periodic subdomain) and
116       add corresponding exchange subroutines (EXCH0);
117     - new CG-solver version (_EX0) for disconnected-tiles special case.
118    o model/src (CG-solvers):
119     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
120       (similar final residual output and max-Iter number as with standard version);
121     - allows to store and use lowest-residual solution (standard & _SR versions);
122     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
123     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
124    o eesup/src:
125     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
126       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
127    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
128    
129    checkpoint63m (2012/04/27)
130    o pkg/shelfice:
131     - account for partical cells in surface level below ice-shelf for hydrostatic
132       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
133    o ad test experiments:
134     - update and rename to "ad_optfile.local" local AD-optfile specific to a
135       particular adjoint verification experiment (in verification/*/code_ad/)
136    o pkg/seaice & pkg/exf:
137     - Part two of ECCO-CLIVAR code merges.
138       Completes merge of seaice area relax. code.
139       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
140       to be set in EXF_OPTIONS.h since this pkg controls its I/O
141       (and avoids second CPP option in SEAICE_OPTIONS.h)
142     - change default value of costIceStart & costIceEnd to a valid date.
143     - add snowPrecip to HSNOW in seaice_growth
144    o pkg/ptracers:
145     - move ptracers summary and setup check into separated S/R ; add a check for
146       valid PTRACERS_Iter0 value (error+stop or just warning).
147    o pkg/cal (+ pkg/ecco):
148     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
149       as input; and for AD, unless both are not differentiable (e.g., k index)).
150    o model/src:
151     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
152       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
153       temporary set to usingZCoords value (to be changed to F when using shelfice).
154     - hydrostatic pressure: implement partial cell near the surface also for
155       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
156       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
157    o pkg/ctrl/ctrl_init.F:
158     - add a formal parameter to s/r ctrl_init_rec to print
159       xx_$(ctrl_valiable)_file for easier debugging
160     - move call of cal_* routines into the if-block where they are really
161       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
162       to specify a startdate
163    o pkg/seaice:
164     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
165       global_ocean.cs32x15/code versions).
166     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
167       verification experiment global_ocean.cs32x15.seaice and update results.
168    o pkg/exf:
169     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
170       (according to useExfYearlyFields).
171    o pkg/cal:
172     - move calendar setting & summary (previously in cal_readparams.F) into new
173       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
174       length of the simulation is set (after SET_PARMS call); This is an attempt
175       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
176     - For safety: keep a record of pkg/cal parameter settings status
177               to allow to STOP if one pkg/cal S/R is called too early.
178     - add a stop in all basic pkg/cal subroutines if called before setting is done.
179     - modify cal_getdate.F: stop when nothing was returned;
180       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
181       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
182    
183    checkpoint63l (2012/04/04)
184  o pkg/bbl:  o pkg/bbl:
185    - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);    - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
186      update global_with_exf output.yearly.txt file.      update global_with_exf output.yearly.txt file.
# Line 13  o pkg/cal: Line 190  o pkg/cal:
190    - remove unsused subroutines from AD-Diff list.    - remove unsused subroutines from AD-Diff list.
191  o model/src:  o model/src:
192    - start to implement clean wait to stop in initialization S/R (config_check.F,    - start to implement clean wait to stop in initialization S/R (config_check.F,
193       packages_check.F and pkg/obcs/obcs_check.F + pkg/mypackage)       packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
194  o folowing PRINT_MESSAGE changes:  o folowing PRINT_MESSAGE changes:
195    - remove reminder multiple print to the same file (STDOUT) when multi-threads.    - remove reminder multiple print to the same file (STDOUT) when multi-threads.
196  o pkg/bbl:  o pkg/bbl:
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