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revision 1.1645 by jmc, Wed Apr 4 16:18:50 2012 UTC revision 1.1711 by jmc, Thu Aug 9 20:36:11 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/exf:
8      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
9        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
10    o verification/*/code_ad:
11      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
12      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
13      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
14        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
15    o pkg/seaice :
16      - added possibility to change ice strength/PRESS0 relationship to
17        HEFF, according to the following run time parameters
18        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
19        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
20        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
21    o pkg/ggl90 :
22      - added run time flag mxlSurfFlag to include the code that ensure
23        mixing between first and second level (previously included as a comment)
24    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
25      - add test of newly added dumpAdByRec=T option where
26        we write all records to one file per variable.
27    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
28      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
29        to check that this code is ok with taf and compiles in adjoint.
30    o pkg/autodiff :
31      - added run time param dumpAdByRec : ad dump format switch.
32        If true then write all records to one file per variable.
33        Else write one file per record (remains the default).
34      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
35    o pkg/seaice:
36     - Added SEAICEuseTILT run time switch : if set to
37       false then omit the tilt term in seaice dynamics.
38     - Fix free drift calculation.
39    o pkg/shelfice:
40      When initializing SHELFICEDragQuadratic, set default to be
41      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
42      but retain option to set it independently
43      (inconsistenty spotted by Veronique Dansereau)
44    o eesupp/inc:
45      - in EEPARAMS.h, add real-type constant for some frequently used simple number
46         (0,1,2,1/2), with name explicitly referring to RS/RL type.
47    o model/src:
48      - move balancing of relaxation terms to new S/R balance_relax.F.
49    o pkg/autodiff:
50      re-write active I/O high-level (control) S/R:
51      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
52      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
53      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
54        MDS_READ/WRITE_FIELD); change loops to multi-threads.
55      - update and merge active_file_control_slice.flow into active_file_control.flow
56      - update the calls in lower level S/R (active_file.F, active_file_g.F and
57        active_file_ad.F) keeping the argument list and function unchanged.
58      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
59        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
60      - new low-level active I/O routines, one for each type (RL/RS), for active var
61        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
62        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
63        right type.
64    o autodiff and RS=real*4:
65      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
66        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
67      - change argument type of 3-D mask argument to _RS to match type in the call
68        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
69    o pkg/thsice:
70      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
71      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
72        fresh-water flux: uniform correction or proportional to local precip.
73    o pkg/ctrl:
74      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
75      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
76                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
77      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
78    
79    checkpoint63q (2012/07/30)
80    o pkg/autodiff:
81      note about monitor and snap-shot of ad-variables:
82      a) need to apply ADEXCH before monitor or output of ad-vars to include
83       overlap contributions (was done for adjDump but missing for monitor).
84      b) since ADEXCH implies adding overlap values to interior array, machine
85       truncation error is expected when adding an ADEXCH call in the middle of
86       the time-stepping (although mathematically identical).
87      modifs:
88      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
89        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
90      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
91        apply ADEXCH before monitor or snap-shot of ad-variables:
92           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
93      - implement new method (copy+adexch) for snap-shot and monitor of main model
94        ad-vars (initially not used by default -> output unchanged).
95      - change default (set to 2) to use new method and update few output_adm.txt
96        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
97        and both tutorial_tracer_adjsens tests).
98      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
99        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
100    o pkg/ctrl:
101      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
102      generic control variables via
103      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
104      Only required customization should be S/R ctrl_map_ini_genarr.F
105      (routine in repository contains example)
106    o pkg/exf:
107      - fix and refine checking of surface-relaxation setting when using EXF
108    o verification (adjoint exp):
109      - reduce length of simulation by half for experiment global_ocean.cs32x15
110        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
111    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
112      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
113        of KE that can occur with aggressive optimization
114      + put quadratic bottom drag calculation in separated loops (only done if
115        using bottomDragQuadratic)
116    o model/src: CG2D_NSA
117      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
118         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
119      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
120         change cg2d residual target to be expressed in Wunits (=> do not normalise
121         RHS ; this fix global_max Pb with TAF); update output.
122    o verification/tutorial_tracer_adjsens:
123       improve parameter consistency (and get rid of warnings):
124       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
125       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
126       - use staggerTimeStep (for stability) in som81; use default rotation period.
127    o pkg/exch2:
128      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
129        reset to 0 = 1 long line in X)
130    o pkg/mdsio:
131      - fix reading of dimensions from meta file for large-size domain
132    o model/src:
133      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
134      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
135        Cubed-Sphere Exch with CS-corners inside the domain;
136        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
137        globalArea and to set hasWetCSCorners.
138      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
139        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
140      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
141        useCDscheme and useCubedSphereExchange).
142    o pkg/seaice/seaice_growth.F :
143      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
144        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
145        when the previous code was not correct.
146      - in all cases diagnoze the boundary condition mismatch to SIaaflux
147      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
148        that term to QNET (essentially to set the melt/freeze water to 0degC).
149        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
150    o verification/global_ocean.cs32x15/input.seaice :
151      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
152      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
153      - update results (output.seaice.txt) accordingly.
154    o verification/lab_sea/input/data.seaice :
155      - remove SEAICEheatConsFix, which is now be tested
156        in global_ocean.cs32x15. The presently coded fix
157        is only consistent with real fresh water + nlfs.
158      - update results (output.txt) accordingly.
159    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
160    o AD_CONFIG.h file:
161      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
162      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
163        add it explicitly in each fortran src file where it is needed.
164        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
165        thus introducing potentially wrong dependency; therefore, better to include
166        it only where it's really needed, and after any other included OPTIONS file
167        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
168        or ALLOW_TANGENTLINEAR_RUN).
169    
170    checkpoint63p (2012/07/06)
171    o pkg/autodiff:
172      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
173      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
174        which are now read from new parameter file "data.autodiff" (inAdExact
175        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
176      - add file "data.autodiff" in all verification/*/input_ad/ directories.
177      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
178        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
179    o verification/tutorial_tracer_adjsens/
180      - add extra sub-verification which uses "SOM" advection scheme
181        (2nd Order-Moment Advection Scheme, Prather Limiter) with
182          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
183        and in data:
184          multiDimAdvection=.TRUE.,
185          tempAdvScheme=81,
186          saltAdvScheme=81,
187    o model/src:
188      - introduce ALLOW_BALANCE_RELAX which allow the removal
189       of the global mean of relaxation terms by setting
190       balanceThetaClimRelax and balanceSaltClimRelax
191      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
192       This case is now treated appropriately in seaice_growth.F
193    o pkg/seaice:
194      - do balanceEmPmR and balanceQnet based on the net fluxes
195        (SItflux) that enter the ocean+ice system rather than QNET
196        and EMPMR. Works best in real fresh water.
197      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
198        out of the diagnotics bloc, and stored in global arrays.
199    
200    checkpoint63o (2012/06/29)
201    o vertical mixing schemes:
202      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
203      - replace computation of density (in Function STATE1, opps_calc.F) by a call
204        to S/R FIND_RHO_SCALAR
205      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
206        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
207        affects output (vermix.ggl90) at truncation level.
208    o testreport:
209      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
210        (nSx,nSy) for the number of threads (from eedata.mth)
211    o model/src:
212      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
213        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
214    o verification/tutorial_tracer_adjsens/
215      - compile with ALLOW_CG2D_NSA
216      - run with nonlinFreeSurf=3
217      - update reference output_adm.txt
218    o tools/genmake2:
219      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
220        refine usePROFILES switching off (only when NetCDF is not available).
221    o verification (atmospheric set-up):
222      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
223    o pkg/profiles : refine profiles and files handling.
224    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
225    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
226      - changes to use model/src/the_main_loop.F rather than the ecco version
227        in ecco type adjoint runs.
228    o model/src:
229      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
230      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
231      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
232    o model/src:
233      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
234        update output of test experiment bottom_ctrl_5x5.
235    o pkg/generic_advdiff:
236      - implement vertical bi-harmonic diffusion (for now, only for T & S and
237        only explicitly).
238    o verification/bottom_ctrl_5x5/
239      update reference output (results changed quite some time ago,
240      not sure when; but new reference results look ok in terms of grdchk)
241    o verification/1D_ocean_ice_column/
242      For verification purposes, the exact adjoint rather than an approx.
243      should be used (e.g., to comare against F.D. or TLM).
244      removed autodiff_inadmode*_ad.F routines in code_ad/
245      Update results/ accordingly.
246    o pkg/cal:
247      - change cal_getdate.F so that output date is function of input time only
248        (less ambiguous, not mixed up with input iteration number).
249      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
250    o pkg/diagnostics:
251      - implement calendarDumps also for stats-diags
252      - implement calendarDumps also for snap-shot output (negative freq)
253      - for now, ignores calendarDumps if non-zero phase-lag.
254    
255    checkpoint63n (2012/06/04)
256    o model/src:
257      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
258        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
259      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
260        similar to calc_r_star.F); update results of experiment internal_wave and
261        tutorial_global_oce_in_p (affected @ truncation level).
262    o pkg/shelfice:
263      - add parameterisation of advective-diffusive flux into the ice shelf
264        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
265      - simply eps3/3a computation
266    o eesupp:
267     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
268       between tiles, just fill-in edges assuming locally periodic subdomain) and
269       add corresponding exchange subroutines (EXCH0);
270     - new CG-solver version (_EX0) for disconnected-tiles special case.
271    o model/src (CG-solvers):
272     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
273       (similar final residual output and max-Iter number as with standard version);
274     - allows to store and use lowest-residual solution (standard & _SR versions);
275     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
276     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
277    o eesup/src:
278     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
279       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
280    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
281    
282    checkpoint63m (2012/04/27)
283    o pkg/shelfice:
284     - account for partical cells in surface level below ice-shelf for hydrostatic
285       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
286    o ad test experiments:
287     - update and rename to "ad_optfile.local" local AD-optfile specific to a
288       particular adjoint verification experiment (in verification/*/code_ad/)
289    o pkg/seaice & pkg/exf:
290     - Part two of ECCO-CLIVAR code merges.
291       Completes merge of seaice area relax. code.
292       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
293       to be set in EXF_OPTIONS.h since this pkg controls its I/O
294       (and avoids second CPP option in SEAICE_OPTIONS.h)
295     - change default value of costIceStart & costIceEnd to a valid date.
296     - add snowPrecip to HSNOW in seaice_growth
297    o pkg/ptracers:
298     - move ptracers summary and setup check into separated S/R ; add a check for
299       valid PTRACERS_Iter0 value (error+stop or just warning).
300    o pkg/cal (+ pkg/ecco):
301     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
302       as input; and for AD, unless both are not differentiable (e.g., k index)).
303    o model/src:
304     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
305       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
306       temporary set to usingZCoords value (to be changed to F when using shelfice).
307     - hydrostatic pressure: implement partial cell near the surface also for
308       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
309       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
310    o pkg/ctrl/ctrl_init.F:
311     - add a formal parameter to s/r ctrl_init_rec to print
312       xx_$(ctrl_valiable)_file for easier debugging
313     - move call of cal_* routines into the if-block where they are really
314       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
315       to specify a startdate
316    o pkg/seaice:
317     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
318       global_ocean.cs32x15/code versions).
319     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
320       verification experiment global_ocean.cs32x15.seaice and update results.
321    o pkg/exf:
322     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
323       (according to useExfYearlyFields).
324    o pkg/cal:
325     - move calendar setting & summary (previously in cal_readparams.F) into new
326       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
327       length of the simulation is set (after SET_PARMS call); This is an attempt
328       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
329     - For safety: keep a record of pkg/cal parameter settings status
330               to allow to STOP if one pkg/cal S/R is called too early.
331     - add a stop in all basic pkg/cal subroutines if called before setting is done.
332     - modify cal_getdate.F: stop when nothing was returned;
333       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
334       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
335    
336  checkpoint63l (2012/04/04)  checkpoint63l (2012/04/04)
337  o pkg/bbl:  o pkg/bbl:
338    - 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);

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