/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1670 by jmc, Fri Jun 15 22:01:45 2012 UTC revision 1.1723 by jmc, Fri Aug 24 18:58:43 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/grdchk:
8      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
9        to this routine from cost_final has been dropped in g_cost_final)
10      - improve printed information (more explicit msg, no longer using "print *,"
11         fix fcpertminus printed value).
12  o model/src:  o model/src:
13    - 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
14        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
15        this prevents getting cost-funct reset in adinitialise_varia recomputations.
16    o pkg/dic:
17      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
18        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
19    o pkg/grdchk:
20      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
21      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
22    o pkg/autodiff/ctrl/grdchk :
23      - attempt to sort out what works and what does not,
24        with regard to I/O, and to warn/stop accordingly.
25    o pkg/grdchk:
26      - attempt to fix grdchk in the case of useSingleCpuIO.
27      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
28       statements were moved from grdchk_main.F and into
29       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
30      - a global sum is applied to record numbers icvrec/layer
31       out of grdchk_loc so that they be passed to I/O routines.
32    o pkg/smooth:
33      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
34        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
35    o verification/testreport:
36      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
37      - can also use compressed (gzip) reference output file;
38      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
39        to be easier to collect by testreport.
40      - update existing TLM output (half out-of-date by more than 3 yrs).
41      - report NETCDF & LAPACK settings (from genmake2) in output dir.
42      - report run-time in each individual summary (previously only for AD test);
43        for TLM test, add also TAF version.
44      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
45    
46    checkpoint63r (2012/08/15)
47    o tools/genmake2:
48      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
49    o pkg/ecco/ecco_cost_final.F :
50      - fix fc print statements (to stdout and costfunction0000) so
51        that the printed value is always after the global sum.
52    o pkg/seaice/seaice_dynsolver.F :
53      - fix ice strength assymptote at SEAICE_area_max<1
54        (no change for the standard case of SEAICE_area_max=1)
55    o some cleaning:
56      - pkg source files: ensure that all *.F files from each pkg included the
57        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
58        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
59        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
60        includes;
61      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
62      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
63        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
64        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
65      - update option-file CPP_OPTIONS.h of all AD experiments:
66        * no longer include PACKAGES_CONFIG.h ;
67        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
68        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
69          including ECCO_CPPOPTIONS.h).
70    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
71      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
72        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
73        not necessary accurate).
74      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
75        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
76        deliberately break compilation (a remainder that it needs to be customized)
77      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
78      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
79      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
80    o tools/genamke2:
81      - check for lapack.
82    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
83      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
84        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
85        from both packages.
86      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
87      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
88      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
89        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
90    o pkg/cost : add comments to explain special and/or untested setups.
91    o pkg/exf:
92      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
93        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
94    o verification/*/code_ad:
95      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
96      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
97      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
98        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
99    o pkg/seaice :
100      - added possibility to change ice strength/PRESS0 relationship to
101        HEFF, according to the following run time parameters
102        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
103        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
104        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
105    o pkg/ggl90 :
106      - added run time flag mxlSurfFlag to include the code that ensure
107        mixing between first and second level (previously included as a comment)
108    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
109      - add test of newly added dumpAdByRec=T option where
110        we write all records to one file per variable.
111    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
112      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
113        to check that this code is ok with taf and compiles in adjoint.
114    o pkg/autodiff :
115      - added run time param dumpAdByRec : ad dump format switch.
116        If true then write all records to one file per variable.
117        Else write one file per record (remains the default).
118      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
119    o pkg/seaice:
120     - Added SEAICEuseTILT run time switch : if set to
121       false then omit the tilt term in seaice dynamics.
122     - Fix free drift calculation.
123    o pkg/shelfice:
124      When initializing SHELFICEDragQuadratic, set default to be
125      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
126      but retain option to set it independently
127      (inconsistenty spotted by Veronique Dansereau)
128    o eesupp/inc:
129      - in EEPARAMS.h, add real-type constant for some frequently used simple number
130         (0,1,2,1/2), with name explicitly referring to RS/RL type.
131    o model/src:
132      - move balancing of relaxation terms to new S/R balance_relax.F.
133    o pkg/autodiff:
134      re-write active I/O high-level (control) S/R:
135      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
136      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
137      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
138        MDS_READ/WRITE_FIELD); change loops to multi-threads.
139      - update and merge active_file_control_slice.flow into active_file_control.flow
140      - update the calls in lower level S/R (active_file.F, active_file_g.F and
141        active_file_ad.F) keeping the argument list and function unchanged.
142      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
143        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
144      - new low-level active I/O routines, one for each type (RL/RS), for active var
145        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
146        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
147        right type.
148    o autodiff and RS=real*4:
149      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
150        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
151      - change argument type of 3-D mask argument to _RS to match type in the call
152        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
153    o pkg/thsice:
154      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
155      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
156        fresh-water flux: uniform correction or proportional to local precip.
157    o pkg/ctrl:
158      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
159      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
160                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
161      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
162    
163    checkpoint63q (2012/07/30)
164    o pkg/autodiff:
165      note about monitor and snap-shot of ad-variables:
166      a) need to apply ADEXCH before monitor or output of ad-vars to include
167       overlap contributions (was done for adjDump but missing for monitor).
168      b) since ADEXCH implies adding overlap values to interior array, machine
169       truncation error is expected when adding an ADEXCH call in the middle of
170       the time-stepping (although mathematically identical).
171      modifs:
172      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
173        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
174      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
175        apply ADEXCH before monitor or snap-shot of ad-variables:
176           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
177      - implement new method (copy+adexch) for snap-shot and monitor of main model
178        ad-vars (initially not used by default -> output unchanged).
179      - change default (set to 2) to use new method and update few output_adm.txt
180        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
181        and both tutorial_tracer_adjsens tests).
182      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
183        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
184    o pkg/ctrl:
185      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
186      generic control variables via
187      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
188      Only required customization should be S/R ctrl_map_ini_genarr.F
189      (routine in repository contains example)
190    o pkg/exf:
191      - fix and refine checking of surface-relaxation setting when using EXF
192    o verification (adjoint exp):
193      - reduce length of simulation by half for experiment global_ocean.cs32x15
194        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
195    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
196      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
197        of KE that can occur with aggressive optimization
198      + put quadratic bottom drag calculation in separated loops (only done if
199        using bottomDragQuadratic)
200    o model/src: CG2D_NSA
201      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
202         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
203      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
204         change cg2d residual target to be expressed in Wunits (=> do not normalise
205         RHS ; this fix global_max Pb with TAF); update output.
206    o verification/tutorial_tracer_adjsens:
207       improve parameter consistency (and get rid of warnings):
208       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
209       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
210       - use staggerTimeStep (for stability) in som81; use default rotation period.
211    o pkg/exch2:
212      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
213        reset to 0 = 1 long line in X)
214    o pkg/mdsio:
215      - fix reading of dimensions from meta file for large-size domain
216    o model/src:
217      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
218      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
219        Cubed-Sphere Exch with CS-corners inside the domain;
220        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
221        globalArea and to set hasWetCSCorners.
222      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
223        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
224      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
225        useCDscheme and useCubedSphereExchange).
226    o pkg/seaice/seaice_growth.F :
227      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
228        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
229        when the previous code was not correct.
230      - in all cases diagnoze the boundary condition mismatch to SIaaflux
231      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
232        that term to QNET (essentially to set the melt/freeze water to 0degC).
233        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
234    o verification/global_ocean.cs32x15/input.seaice :
235      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
236      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
237      - update results (output.seaice.txt) accordingly.
238    o verification/lab_sea/input/data.seaice :
239      - remove SEAICEheatConsFix, which is now be tested
240        in global_ocean.cs32x15. The presently coded fix
241        is only consistent with real fresh water + nlfs.
242      - update results (output.txt) accordingly.
243    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
244    o AD_CONFIG.h file:
245      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
246      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
247        add it explicitly in each fortran src file where it is needed.
248        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
249        thus introducing potentially wrong dependency; therefore, better to include
250        it only where it's really needed, and after any other included OPTIONS file
251        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
252        or ALLOW_TANGENTLINEAR_RUN).
253    
254    checkpoint63p (2012/07/06)
255    o pkg/autodiff:
256      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
257      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
258        which are now read from new parameter file "data.autodiff" (inAdExact
259        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
260      - add file "data.autodiff" in all verification/*/input_ad/ directories.
261      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
262        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
263    o verification/tutorial_tracer_adjsens/
264      - add extra sub-verification which uses "SOM" advection scheme
265        (2nd Order-Moment Advection Scheme, Prather Limiter) with
266          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
267        and in data:
268          multiDimAdvection=.TRUE.,
269          tempAdvScheme=81,
270          saltAdvScheme=81,
271    o model/src:
272      - introduce ALLOW_BALANCE_RELAX which allow the removal
273       of the global mean of relaxation terms by setting
274       balanceThetaClimRelax and balanceSaltClimRelax
275      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
276       This case is now treated appropriately in seaice_growth.F
277    o pkg/seaice:
278      - do balanceEmPmR and balanceQnet based on the net fluxes
279        (SItflux) that enter the ocean+ice system rather than QNET
280        and EMPMR. Works best in real fresh water.
281      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
282        out of the diagnotics bloc, and stored in global arrays.
283    
284    checkpoint63o (2012/06/29)
285    o vertical mixing schemes:
286      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
287      - replace computation of density (in Function STATE1, opps_calc.F) by a call
288        to S/R FIND_RHO_SCALAR
289      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
290        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
291        affects output (vermix.ggl90) at truncation level.
292    o testreport:
293      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
294        (nSx,nSy) for the number of threads (from eedata.mth)
295    o model/src:
296      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
297        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
298    o verification/tutorial_tracer_adjsens/
299      - compile with ALLOW_CG2D_NSA
300      - run with nonlinFreeSurf=3
301      - update reference output_adm.txt
302    o tools/genmake2:
303      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
304        refine usePROFILES switching off (only when NetCDF is not available).
305    o verification (atmospheric set-up):
306      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
307    o pkg/profiles : refine profiles and files handling.
308    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
309    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
310      - changes to use model/src/the_main_loop.F rather than the ecco version
311        in ecco type adjoint runs.
312    o model/src:
313      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
314      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
315      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
316    o model/src:
317      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
318      update output of test experiment bottom_ctrl_5x5.      update output of test experiment bottom_ctrl_5x5.
319  o pkg/generic_advdiff:  o pkg/generic_advdiff:
320    - implement vertical bi-harmonic diffusion (for now, only for T & S and    - implement vertical bi-harmonic diffusion (for now, only for T & S and

Legend:
Removed from v.1.1670  
changed lines
  Added in v.1.1723

  ViewVC Help
Powered by ViewVC 1.1.22