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revision 1.1670 by jmc, Fri Jun 15 22:01:45 2012 UTC revision 1.1699 by jmc, Mon Jul 30 16:13:19 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63q (2012/07/30)
8    o pkg/autodiff:
9      note about monitor and snap-shot of ad-variables:
10      a) need to apply ADEXCH before monitor or output of ad-vars to include
11       overlap contributions (was done for adjDump but missing for monitor).
12      b) since ADEXCH implies adding overlap values to interior array, machine
13       truncation error is expected when adding an ADEXCH call in the middle of
14       the time-stepping (although mathematically identical).
15      modifs:
16      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
17        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
18      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
19        apply ADEXCH before monitor or snap-shot of ad-variables:
20           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
21      - implement new method (copy+adexch) for snap-shot and monitor of main model
22        ad-vars (initially not used by default -> output unchanged).
23      - change default (set to 2) to use new method and update few output_adm.txt
24        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
25        and both tutorial_tracer_adjsens tests).
26      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
27        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
28    o pkg/ctrl:
29      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
30      generic control variables via
31      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
32      Only required customization should be S/R ctrl_map_ini_genarr.F
33      (routine in repository contains example)
34    o pkg/exf:
35      - fix and refine checking of surface-relaxation setting when using EXF
36    o verification (adjoint exp):
37      - reduce length of simulation by half for experiment global_ocean.cs32x15
38        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
39    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
40      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
41        of KE that can occur with aggressive optimization
42      + put quadratic bottom drag calculation in separated loops (only done if
43        using bottomDragQuadratic)
44    o model/src: CG2D_NSA
45      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
46         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
47      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
48         change cg2d residual target to be expressed in Wunits (=> do not normalise
49         RHS ; this fix global_max Pb with TAF); update output.
50    o verification/tutorial_tracer_adjsens:
51       improve parameter consistency (and get rid of warnings):
52       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
53       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
54       - use staggerTimeStep (for stability) in som81; use default rotation period.
55    o pkg/exch2:
56      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
57        reset to 0 = 1 long line in X)
58    o pkg/mdsio:
59      - fix reading of dimensions from meta file for large-size domain
60  o model/src:  o model/src:
61    - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);    - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
62      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
63        Cubed-Sphere Exch with CS-corners inside the domain;
64        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
65        globalArea and to set hasWetCSCorners.
66      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
67        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
68      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
69        useCDscheme and useCubedSphereExchange).
70    o pkg/seaice/seaice_growth.F :
71      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
72        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
73        when the previous code was not correct.
74      - in all cases diagnoze the boundary condition mismatch to SIaaflux
75      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
76        that term to QNET (essentially to set the melt/freeze water to 0degC).
77        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
78    o verification/global_ocean.cs32x15/input.seaice :
79      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
80      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
81      - update results (output.seaice.txt) accordingly.
82    o verification/lab_sea/input/data.seaice :
83      - remove SEAICEheatConsFix, which is now be tested
84        in global_ocean.cs32x15. The presently coded fix
85        is only consistent with real fresh water + nlfs.
86      - update results (output.txt) accordingly.
87    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
88    o AD_CONFIG.h file:
89      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
90      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
91        add it explicitly in each fortran src file where it is needed.
92        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
93        thus introducing potentially wrong dependency; therefore, better to include
94        it only where it's really needed, and after any other included OPTIONS file
95        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
96        or ALLOW_TANGENTLINEAR_RUN).
97    
98    checkpoint63p (2012/07/06)
99    o pkg/autodiff:
100      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
101      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
102        which are now read from new parameter file "data.autodiff" (inAdExact
103        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
104      - add file "data.autodiff" in all verification/*/input_ad/ directories.
105      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
106        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
107    o verification/tutorial_tracer_adjsens/
108      - add extra sub-verification which uses "SOM" advection scheme
109        (2nd Order-Moment Advection Scheme, Prather Limiter) with
110          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
111        and in data:
112          multiDimAdvection=.TRUE.,
113          tempAdvScheme=81,
114          saltAdvScheme=81,
115    o model/src:
116      - introduce ALLOW_BALANCE_RELAX which allow the removal
117       of the global mean of relaxation terms by setting
118       balanceThetaClimRelax and balanceSaltClimRelax
119      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
120       This case is now treated appropriately in seaice_growth.F
121    o pkg/seaice:
122      - do balanceEmPmR and balanceQnet based on the net fluxes
123        (SItflux) that enter the ocean+ice system rather than QNET
124        and EMPMR. Works best in real fresh water.
125      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
126        out of the diagnotics bloc, and stored in global arrays.
127    
128    checkpoint63o (2012/06/29)
129    o vertical mixing schemes:
130      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
131      - replace computation of density (in Function STATE1, opps_calc.F) by a call
132        to S/R FIND_RHO_SCALAR
133      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
134        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
135        affects output (vermix.ggl90) at truncation level.
136    o testreport:
137      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
138        (nSx,nSy) for the number of threads (from eedata.mth)
139    o model/src:
140      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
141        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
142    o verification/tutorial_tracer_adjsens/
143      - compile with ALLOW_CG2D_NSA
144      - run with nonlinFreeSurf=3
145      - update reference output_adm.txt
146    o tools/genmake2:
147      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
148        refine usePROFILES switching off (only when NetCDF is not available).
149    o verification (atmospheric set-up):
150      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
151    o pkg/profiles : refine profiles and files handling.
152    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
153    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
154      - changes to use model/src/the_main_loop.F rather than the ecco version
155        in ecco type adjoint runs.
156    o model/src:
157      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
158      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
159      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
160    o model/src:
161      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
162      update output of test experiment bottom_ctrl_5x5.      update output of test experiment bottom_ctrl_5x5.
163  o pkg/generic_advdiff:  o pkg/generic_advdiff:
164    - implement vertical bi-harmonic diffusion (for now, only for T & S and    - implement vertical bi-harmonic diffusion (for now, only for T & S and
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