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revision 1.1670 by jmc, Fri Jun 15 22:01:45 2012 UTC revision 1.1727 by jmc, Wed Aug 29 13:49:44 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, exf, ptracers & seaice (AD & TL output):
8      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
9        a) can damage previously written records in any other multi-record files.
10        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
11    o tools/genmake2:
12      - define variable MAKE within Makefile and use it in place of 'make';
13      - update AD_CONFIG.h (if needed) before building any of the executable
14        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
15        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
16      - always print usual warning comment 'this file is automatically generated'
17        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
18    o pkg/cheapaml:
19      - updated to correspond to the code used in accepted paper (Nico Wienders).
20    o pkg/exf:
21        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
22        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
23        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
24    o pkg/exf, autodiff, ctrl, ecco and seaice:
25        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
26    o pkg/ctrl, ecco:
27        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
28        Depending on useAtmWind, one is inactive, and the other is active (see
29        exf_getffields.F/exf_getsurfacefluxes.F).
30    o tools/genmake2:
31      - improve error msg when failing in 2nd test of check_for_broken_Ff
32      - fix option '-makefile' short-name (-mf according to genmake2 -help)
33      - source local config file "genmake_local" just after processing the genmake2
34        command arguments (previously done before processing arg).
35    o pkg/grdchk:
36      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
37        to this routine from cost_final has been dropped in g_cost_final)
38      - improve printed information (more explicit msg, no longer using "print *,"
39         fix fcpertminus printed value).
40  o model/src:  o model/src:
41    - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);    - move call to COST_INIT_VARIA out of packages_init_variables.F directly
42        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
43        this prevents getting cost-funct reset in adinitialise_varia recomputations.
44    o pkg/dic:
45      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
46        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
47    o pkg/grdchk:
48      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
49      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
50    o pkg/autodiff/ctrl/grdchk :
51      - attempt to sort out what works and what does not,
52        with regard to I/O, and to warn/stop accordingly.
53    o pkg/grdchk:
54      - attempt to fix grdchk in the case of useSingleCpuIO.
55      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
56       statements were moved from grdchk_main.F and into
57       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
58      - a global sum is applied to record numbers icvrec/layer
59       out of grdchk_loc so that they be passed to I/O routines.
60    o pkg/smooth:
61      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
62        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
63    o verification/testreport:
64      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
65      - can also use compressed (gzip) reference output file;
66      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
67        to be easier to collect by testreport.
68      - update existing TLM output (half out-of-date by more than 3 yrs).
69      - report NETCDF & LAPACK settings (from genmake2) in output dir.
70      - report run-time in each individual summary (previously only for AD test);
71        for TLM test, add also TAF version.
72      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
73    
74    checkpoint63r (2012/08/15)
75    o tools/genmake2:
76      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
77    o pkg/ecco/ecco_cost_final.F :
78      - fix fc print statements (to stdout and costfunction0000) so
79        that the printed value is always after the global sum.
80    o pkg/seaice/seaice_dynsolver.F :
81      - fix ice strength assymptote at SEAICE_area_max<1
82        (no change for the standard case of SEAICE_area_max=1)
83    o some cleaning:
84      - pkg source files: ensure that all *.F files from each pkg included the
85        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
86        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
87        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
88        includes;
89      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
90      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
91        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
92        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
93      - update option-file CPP_OPTIONS.h of all AD experiments:
94        * no longer include PACKAGES_CONFIG.h ;
95        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
96        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
97          including ECCO_CPPOPTIONS.h).
98    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
99      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
100        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
101        not necessary accurate).
102      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
103        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
104        deliberately break compilation (a remainder that it needs to be customized)
105      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
106      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
107      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
108    o tools/genamke2:
109      - check for lapack.
110    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
111      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
112        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
113        from both packages.
114      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
115      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
116      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
117        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
118    o pkg/cost : add comments to explain special and/or untested setups.
119    o pkg/exf:
120      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
121        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
122    o verification/*/code_ad:
123      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
124      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
125      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
126        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
127    o pkg/seaice :
128      - added possibility to change ice strength/PRESS0 relationship to
129        HEFF, according to the following run time parameters
130        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
131        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
132        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
133    o pkg/ggl90 :
134      - added run time flag mxlSurfFlag to include the code that ensure
135        mixing between first and second level (previously included as a comment)
136    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
137      - add test of newly added dumpAdByRec=T option where
138        we write all records to one file per variable.
139    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
140      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
141        to check that this code is ok with taf and compiles in adjoint.
142    o pkg/autodiff :
143      - added run time param dumpAdByRec : ad dump format switch.
144        If true then write all records to one file per variable.
145        Else write one file per record (remains the default).
146      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
147    o pkg/seaice:
148     - Added SEAICEuseTILT run time switch : if set to
149       false then omit the tilt term in seaice dynamics.
150     - Fix free drift calculation.
151    o pkg/shelfice:
152      When initializing SHELFICEDragQuadratic, set default to be
153      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
154      but retain option to set it independently
155      (inconsistenty spotted by Veronique Dansereau)
156    o eesupp/inc:
157      - in EEPARAMS.h, add real-type constant for some frequently used simple number
158         (0,1,2,1/2), with name explicitly referring to RS/RL type.
159    o model/src:
160      - move balancing of relaxation terms to new S/R balance_relax.F.
161    o pkg/autodiff:
162      re-write active I/O high-level (control) S/R:
163      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
164      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
165      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
166        MDS_READ/WRITE_FIELD); change loops to multi-threads.
167      - update and merge active_file_control_slice.flow into active_file_control.flow
168      - update the calls in lower level S/R (active_file.F, active_file_g.F and
169        active_file_ad.F) keeping the argument list and function unchanged.
170      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
171        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
172      - new low-level active I/O routines, one for each type (RL/RS), for active var
173        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
174        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
175        right type.
176    o autodiff and RS=real*4:
177      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
178        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
179      - change argument type of 3-D mask argument to _RS to match type in the call
180        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
181    o pkg/thsice:
182      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
183      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
184        fresh-water flux: uniform correction or proportional to local precip.
185    o pkg/ctrl:
186      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
187      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
188                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
189      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
190    
191    checkpoint63q (2012/07/30)
192    o pkg/autodiff:
193      note about monitor and snap-shot of ad-variables:
194      a) need to apply ADEXCH before monitor or output of ad-vars to include
195       overlap contributions (was done for adjDump but missing for monitor).
196      b) since ADEXCH implies adding overlap values to interior array, machine
197       truncation error is expected when adding an ADEXCH call in the middle of
198       the time-stepping (although mathematically identical).
199      modifs:
200      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
201        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
202      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
203        apply ADEXCH before monitor or snap-shot of ad-variables:
204           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
205      - implement new method (copy+adexch) for snap-shot and monitor of main model
206        ad-vars (initially not used by default -> output unchanged).
207      - change default (set to 2) to use new method and update few output_adm.txt
208        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
209        and both tutorial_tracer_adjsens tests).
210      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
211        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
212    o pkg/ctrl:
213      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
214      generic control variables via
215      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
216      Only required customization should be S/R ctrl_map_ini_genarr.F
217      (routine in repository contains example)
218    o pkg/exf:
219      - fix and refine checking of surface-relaxation setting when using EXF
220    o verification (adjoint exp):
221      - reduce length of simulation by half for experiment global_ocean.cs32x15
222        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
223    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
224      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
225        of KE that can occur with aggressive optimization
226      + put quadratic bottom drag calculation in separated loops (only done if
227        using bottomDragQuadratic)
228    o model/src: CG2D_NSA
229      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
230         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
231      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
232         change cg2d residual target to be expressed in Wunits (=> do not normalise
233         RHS ; this fix global_max Pb with TAF); update output.
234    o verification/tutorial_tracer_adjsens:
235       improve parameter consistency (and get rid of warnings):
236       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
237       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
238       - use staggerTimeStep (for stability) in som81; use default rotation period.
239    o pkg/exch2:
240      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
241        reset to 0 = 1 long line in X)
242    o pkg/mdsio:
243      - fix reading of dimensions from meta file for large-size domain
244    o model/src:
245      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
246      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
247        Cubed-Sphere Exch with CS-corners inside the domain;
248        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
249        globalArea and to set hasWetCSCorners.
250      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
251        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
252      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
253        useCDscheme and useCubedSphereExchange).
254    o pkg/seaice/seaice_growth.F :
255      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
256        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
257        when the previous code was not correct.
258      - in all cases diagnoze the boundary condition mismatch to SIaaflux
259      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
260        that term to QNET (essentially to set the melt/freeze water to 0degC).
261        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
262    o verification/global_ocean.cs32x15/input.seaice :
263      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
264      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
265      - update results (output.seaice.txt) accordingly.
266    o verification/lab_sea/input/data.seaice :
267      - remove SEAICEheatConsFix, which is now be tested
268        in global_ocean.cs32x15. The presently coded fix
269        is only consistent with real fresh water + nlfs.
270      - update results (output.txt) accordingly.
271    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
272    o AD_CONFIG.h file:
273      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
274      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
275        add it explicitly in each fortran src file where it is needed.
276        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
277        thus introducing potentially wrong dependency; therefore, better to include
278        it only where it's really needed, and after any other included OPTIONS file
279        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
280        or ALLOW_TANGENTLINEAR_RUN).
281    
282    checkpoint63p (2012/07/06)
283    o pkg/autodiff:
284      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
285      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
286        which are now read from new parameter file "data.autodiff" (inAdExact
287        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
288      - add file "data.autodiff" in all verification/*/input_ad/ directories.
289      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
290        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
291    o verification/tutorial_tracer_adjsens/
292      - add extra sub-verification which uses "SOM" advection scheme
293        (2nd Order-Moment Advection Scheme, Prather Limiter) with
294          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
295        and in data:
296          multiDimAdvection=.TRUE.,
297          tempAdvScheme=81,
298          saltAdvScheme=81,
299    o model/src:
300      - introduce ALLOW_BALANCE_RELAX which allow the removal
301       of the global mean of relaxation terms by setting
302       balanceThetaClimRelax and balanceSaltClimRelax
303      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
304       This case is now treated appropriately in seaice_growth.F
305    o pkg/seaice:
306      - do balanceEmPmR and balanceQnet based on the net fluxes
307        (SItflux) that enter the ocean+ice system rather than QNET
308        and EMPMR. Works best in real fresh water.
309      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
310        out of the diagnotics bloc, and stored in global arrays.
311    
312    checkpoint63o (2012/06/29)
313    o vertical mixing schemes:
314      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
315      - replace computation of density (in Function STATE1, opps_calc.F) by a call
316        to S/R FIND_RHO_SCALAR
317      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
318        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
319        affects output (vermix.ggl90) at truncation level.
320    o testreport:
321      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
322        (nSx,nSy) for the number of threads (from eedata.mth)
323    o model/src:
324      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
325        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
326    o verification/tutorial_tracer_adjsens/
327      - compile with ALLOW_CG2D_NSA
328      - run with nonlinFreeSurf=3
329      - update reference output_adm.txt
330    o tools/genmake2:
331      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
332        refine usePROFILES switching off (only when NetCDF is not available).
333    o verification (atmospheric set-up):
334      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
335    o pkg/profiles : refine profiles and files handling.
336    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
337    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
338      - changes to use model/src/the_main_loop.F rather than the ecco version
339        in ecco type adjoint runs.
340    o model/src:
341      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
342      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
343      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
344    o model/src:
345      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
346      update output of test experiment bottom_ctrl_5x5.      update output of test experiment bottom_ctrl_5x5.
347  o pkg/generic_advdiff:  o pkg/generic_advdiff:
348    - 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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