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revision 1.1686 by gforget, Tue Jul 10 15:47:30 2012 UTC revision 1.1714 by jmc, Mon Aug 13 13:14:49 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 some cleaning:
8      - pkg source files: ensure that all *.F files from each pkg included the
9        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
10        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
11        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
12        includes;
13      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
14      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
15        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
16        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
17      - update option-file CPP_OPTIONS.h of all AD experiments:
18        * no longer include PACKAGES_CONFIG.h ;
19        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
20        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
21          including ECCO_CPPOPTIONS.h).
22    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
23      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
24        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
25        not necessary accurate).
26      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
27        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
28        deliberately break compilation (a remainder that it needs to be customized)
29      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
30      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
31      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
32    o tools/genamke2:
33      - check for lapack.
34    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
35      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
36        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
37        from both packages.
38      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
39      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
40      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
41        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
42    o pkg/cost : add comments to explain special and/or untested setups.
43    o pkg/exf:
44      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
45        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
46    o verification/*/code_ad:
47      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
48      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
49      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
50        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
51    o pkg/seaice :
52      - added possibility to change ice strength/PRESS0 relationship to
53        HEFF, according to the following run time parameters
54        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
55        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
56        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
57    o pkg/ggl90 :
58      - added run time flag mxlSurfFlag to include the code that ensure
59        mixing between first and second level (previously included as a comment)
60    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
61      - add test of newly added dumpAdByRec=T option where
62        we write all records to one file per variable.
63    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
64      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
65        to check that this code is ok with taf and compiles in adjoint.
66    o pkg/autodiff :
67      - added run time param dumpAdByRec : ad dump format switch.
68        If true then write all records to one file per variable.
69        Else write one file per record (remains the default).
70      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
71    o pkg/seaice:
72     - Added SEAICEuseTILT run time switch : if set to
73       false then omit the tilt term in seaice dynamics.
74     - Fix free drift calculation.
75    o pkg/shelfice:
76      When initializing SHELFICEDragQuadratic, set default to be
77      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
78      but retain option to set it independently
79      (inconsistenty spotted by Veronique Dansereau)
80    o eesupp/inc:
81      - in EEPARAMS.h, add real-type constant for some frequently used simple number
82         (0,1,2,1/2), with name explicitly referring to RS/RL type.
83    o model/src:
84      - move balancing of relaxation terms to new S/R balance_relax.F.
85    o pkg/autodiff:
86      re-write active I/O high-level (control) S/R:
87      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
88      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
89      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
90        MDS_READ/WRITE_FIELD); change loops to multi-threads.
91      - update and merge active_file_control_slice.flow into active_file_control.flow
92      - update the calls in lower level S/R (active_file.F, active_file_g.F and
93        active_file_ad.F) keeping the argument list and function unchanged.
94      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
95        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
96      - new low-level active I/O routines, one for each type (RL/RS), for active var
97        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
98        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
99        right type.
100    o autodiff and RS=real*4:
101      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
102        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
103      - change argument type of 3-D mask argument to _RS to match type in the call
104        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
105    o pkg/thsice:
106      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
107      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
108        fresh-water flux: uniform correction or proportional to local precip.
109    o pkg/ctrl:
110      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
111      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
112                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
113      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
114    
115    checkpoint63q (2012/07/30)
116    o pkg/autodiff:
117      note about monitor and snap-shot of ad-variables:
118      a) need to apply ADEXCH before monitor or output of ad-vars to include
119       overlap contributions (was done for adjDump but missing for monitor).
120      b) since ADEXCH implies adding overlap values to interior array, machine
121       truncation error is expected when adding an ADEXCH call in the middle of
122       the time-stepping (although mathematically identical).
123      modifs:
124      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
125        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
126      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
127        apply ADEXCH before monitor or snap-shot of ad-variables:
128           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
129      - implement new method (copy+adexch) for snap-shot and monitor of main model
130        ad-vars (initially not used by default -> output unchanged).
131      - change default (set to 2) to use new method and update few output_adm.txt
132        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
133        and both tutorial_tracer_adjsens tests).
134      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
135        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
136    o pkg/ctrl:
137      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
138      generic control variables via
139      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
140      Only required customization should be S/R ctrl_map_ini_genarr.F
141      (routine in repository contains example)
142    o pkg/exf:
143      - fix and refine checking of surface-relaxation setting when using EXF
144    o verification (adjoint exp):
145      - reduce length of simulation by half for experiment global_ocean.cs32x15
146        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
147    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
148      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
149        of KE that can occur with aggressive optimization
150      + put quadratic bottom drag calculation in separated loops (only done if
151        using bottomDragQuadratic)
152    o model/src: CG2D_NSA
153      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
154         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
155      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
156         change cg2d residual target to be expressed in Wunits (=> do not normalise
157         RHS ; this fix global_max Pb with TAF); update output.
158    o verification/tutorial_tracer_adjsens:
159       improve parameter consistency (and get rid of warnings):
160       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
161       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
162       - use staggerTimeStep (for stability) in som81; use default rotation period.
163    o pkg/exch2:
164      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
165        reset to 0 = 1 long line in X)
166    o pkg/mdsio:
167      - fix reading of dimensions from meta file for large-size domain
168    o model/src:
169      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
170      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
171        Cubed-Sphere Exch with CS-corners inside the domain;
172        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
173        globalArea and to set hasWetCSCorners.
174      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
175        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
176      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
177        useCDscheme and useCubedSphereExchange).
178    o pkg/seaice/seaice_growth.F :
179      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
180        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
181        when the previous code was not correct.
182      - in all cases diagnoze the boundary condition mismatch to SIaaflux
183      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
184        that term to QNET (essentially to set the melt/freeze water to 0degC).
185        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
186    o verification/global_ocean.cs32x15/input.seaice :
187      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
188      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
189      - update results (output.seaice.txt) accordingly.
190    o verification/lab_sea/input/data.seaice :
191      - remove SEAICEheatConsFix, which is now be tested
192        in global_ocean.cs32x15. The presently coded fix
193        is only consistent with real fresh water + nlfs.
194      - update results (output.txt) accordingly.
195  o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).  o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
196  o AD_CONFIG.h file:  o AD_CONFIG.h file:
197   - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;    - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
198   - remove #include "AD_CONFIG.h" from all included OPTIONS files and    - remove #include "AD_CONFIG.h" from all included OPTIONS files and
199     add it explicitly in each fortran src file where it is needed.      add it explicitly in each fortran src file where it is needed.
200     motivation: header file AD_CONFIG.h is generated/modified after "make depend"      motivation: header file AD_CONFIG.h is generated/modified after "make depend"
201     thus introducing potentially wrong dependency; therefore, better to include      thus introducing potentially wrong dependency; therefore, better to include
202     it only where it's really needed, and after any other included OPTIONS file      it only where it's really needed, and after any other included OPTIONS file
203     (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN      (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
204     or ALLOW_TANGENTLINEAR_RUN).      or ALLOW_TANGENTLINEAR_RUN).
205    
206  checkpoint63p (2012/07/06)  checkpoint63p (2012/07/06)
207  o pkg/autodiff:  o pkg/autodiff:
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