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revision 1.1641 by dimitri, Mon Apr 2 04:34:07 2012 UTC revision 1.1698 by jmc, Sun Jul 29 22:44:01 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:
8      note about monitor and snap-shot of ad-variables:
9      a) need to apply ADEXCH before monitor or output of ad-vars to include
10       overlap contributions (was done for adjDump but missing for monitor).
11      b) since ADEXCH implies adding overlap values to interior array, machine
12       truncation error is expected when adding an ADEXCH call in the middle of
13       the time-stepping (although mathematically identical).
14      modifs:
15      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
16        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
17      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
18        apply ADEXCH before monitor or snap-shot of ad-variables:
19           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
20      - implement new method (copy+adexch) for snap-shot and monitor of main model
21        ad-vars (initially not used by default -> output unchanged).
22      - change default (set to 2) to use new method and update few output_adm.txt
23        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
24        and both tutorial_tracer_adjsens tests).
25      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
26        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
27    o pkg/ctrl:
28      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
29      generic control variables via
30      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
31      Only required customization should be S/R ctrl_map_ini_genarr.F
32      (routine in repository contains example)
33    o pkg/exf:
34      - fix and refine checking of surface-relaxation setting when using EXF
35    o verification (adjoint exp):
36      - reduce length of simulation by half for experiment global_ocean.cs32x15
37        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
38    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
39      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
40        of KE that can occur with aggressive optimization
41      + put quadratic bottom drag calculation in separated loops (only done if
42        using bottomDragQuadratic)
43    o model/src: CG2D_NSA
44      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
45         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
46      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
47         change cg2d residual target to be expressed in Wunits (=> do not normalise
48         RHS ; this fix global_max Pb with TAF); update output.
49    o verification/tutorial_tracer_adjsens:
50       improve parameter consistency (and get rid of warnings):
51       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
52       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
53       - use staggerTimeStep (for stability) in som81; use default rotation period.
54    o pkg/exch2:
55      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
56        reset to 0 = 1 long line in X)
57    o pkg/mdsio:
58      - fix reading of dimensions from meta file for large-size domain
59    o model/src:
60      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
61      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
62        Cubed-Sphere Exch with CS-corners inside the domain;
63        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
64        globalArea and to set hasWetCSCorners.
65      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
66        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
67      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
68        useCDscheme and useCubedSphereExchange).
69    o pkg/seaice/seaice_growth.F :
70      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
71        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
72        when the previous code was not correct.
73      - in all cases diagnoze the boundary condition mismatch to SIaaflux
74      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
75        that term to QNET (essentially to set the melt/freeze water to 0degC).
76        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
77    o verification/global_ocean.cs32x15/input.seaice :
78      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
79      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
80      - update results (output.seaice.txt) accordingly.
81    o verification/lab_sea/input/data.seaice :
82      - remove SEAICEheatConsFix, which is now be tested
83        in global_ocean.cs32x15. The presently coded fix
84        is only consistent with real fresh water + nlfs.
85      - update results (output.txt) accordingly.
86    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
87    o AD_CONFIG.h file:
88      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
89      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
90        add it explicitly in each fortran src file where it is needed.
91        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
92        thus introducing potentially wrong dependency; therefore, better to include
93        it only where it's really needed, and after any other included OPTIONS file
94        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
95        or ALLOW_TANGENTLINEAR_RUN).
96    
97    checkpoint63p (2012/07/06)
98    o pkg/autodiff:
99      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
100      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
101        which are now read from new parameter file "data.autodiff" (inAdExact
102        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
103      - add file "data.autodiff" in all verification/*/input_ad/ directories.
104      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
105        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
106    o verification/tutorial_tracer_adjsens/
107      - add extra sub-verification which uses "SOM" advection scheme
108        (2nd Order-Moment Advection Scheme, Prather Limiter) with
109          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
110        and in data:
111          multiDimAdvection=.TRUE.,
112          tempAdvScheme=81,
113          saltAdvScheme=81,
114    o model/src:
115      - introduce ALLOW_BALANCE_RELAX which allow the removal
116       of the global mean of relaxation terms by setting
117       balanceThetaClimRelax and balanceSaltClimRelax
118      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
119       This case is now treated appropriately in seaice_growth.F
120    o pkg/seaice:
121      - do balanceEmPmR and balanceQnet based on the net fluxes
122        (SItflux) that enter the ocean+ice system rather than QNET
123        and EMPMR. Works best in real fresh water.
124      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
125        out of the diagnotics bloc, and stored in global arrays.
126    
127    checkpoint63o (2012/06/29)
128    o vertical mixing schemes:
129      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
130      - replace computation of density (in Function STATE1, opps_calc.F) by a call
131        to S/R FIND_RHO_SCALAR
132      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
133        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
134        affects output (vermix.ggl90) at truncation level.
135    o testreport:
136      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
137        (nSx,nSy) for the number of threads (from eedata.mth)
138    o model/src:
139      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
140        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
141    o verification/tutorial_tracer_adjsens/
142      - compile with ALLOW_CG2D_NSA
143      - run with nonlinFreeSurf=3
144      - update reference output_adm.txt
145    o tools/genmake2:
146      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
147        refine usePROFILES switching off (only when NetCDF is not available).
148    o verification (atmospheric set-up):
149      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
150    o pkg/profiles : refine profiles and files handling.
151    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
152    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
153      - changes to use model/src/the_main_loop.F rather than the ecco version
154        in ecco type adjoint runs.
155    o model/src:
156      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
157      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
158      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
159    o model/src:
160      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
161        update output of test experiment bottom_ctrl_5x5.
162    o pkg/generic_advdiff:
163      - implement vertical bi-harmonic diffusion (for now, only for T & S and
164        only explicitly).
165    o verification/bottom_ctrl_5x5/
166      update reference output (results changed quite some time ago,
167      not sure when; but new reference results look ok in terms of grdchk)
168    o verification/1D_ocean_ice_column/
169      For verification purposes, the exact adjoint rather than an approx.
170      should be used (e.g., to comare against F.D. or TLM).
171      removed autodiff_inadmode*_ad.F routines in code_ad/
172      Update results/ accordingly.
173    o pkg/cal:
174      - change cal_getdate.F so that output date is function of input time only
175        (less ambiguous, not mixed up with input iteration number).
176      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
177    o pkg/diagnostics:
178      - implement calendarDumps also for stats-diags
179      - implement calendarDumps also for snap-shot output (negative freq)
180      - for now, ignores calendarDumps if non-zero phase-lag.
181    
182    checkpoint63n (2012/06/04)
183    o model/src:
184      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
185        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
186      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
187        similar to calc_r_star.F); update results of experiment internal_wave and
188        tutorial_global_oce_in_p (affected @ truncation level).
189    o pkg/shelfice:
190      - add parameterisation of advective-diffusive flux into the ice shelf
191        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
192      - simply eps3/3a computation
193    o eesupp:
194     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
195       between tiles, just fill-in edges assuming locally periodic subdomain) and
196       add corresponding exchange subroutines (EXCH0);
197     - new CG-solver version (_EX0) for disconnected-tiles special case.
198    o model/src (CG-solvers):
199     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
200       (similar final residual output and max-Iter number as with standard version);
201     - allows to store and use lowest-residual solution (standard & _SR versions);
202     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
203     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
204    o eesup/src:
205     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
206       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
207    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
208    
209    checkpoint63m (2012/04/27)
210    o pkg/shelfice:
211     - account for partical cells in surface level below ice-shelf for hydrostatic
212       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
213    o ad test experiments:
214     - update and rename to "ad_optfile.local" local AD-optfile specific to a
215       particular adjoint verification experiment (in verification/*/code_ad/)
216    o pkg/seaice & pkg/exf:
217     - Part two of ECCO-CLIVAR code merges.
218       Completes merge of seaice area relax. code.
219       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
220       to be set in EXF_OPTIONS.h since this pkg controls its I/O
221       (and avoids second CPP option in SEAICE_OPTIONS.h)
222     - change default value of costIceStart & costIceEnd to a valid date.
223     - add snowPrecip to HSNOW in seaice_growth
224    o pkg/ptracers:
225     - move ptracers summary and setup check into separated S/R ; add a check for
226       valid PTRACERS_Iter0 value (error+stop or just warning).
227    o pkg/cal (+ pkg/ecco):
228     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
229       as input; and for AD, unless both are not differentiable (e.g., k index)).
230    o model/src:
231     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
232       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
233       temporary set to usingZCoords value (to be changed to F when using shelfice).
234     - hydrostatic pressure: implement partial cell near the surface also for
235       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
236       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
237    o pkg/ctrl/ctrl_init.F:
238     - add a formal parameter to s/r ctrl_init_rec to print
239       xx_$(ctrl_valiable)_file for easier debugging
240     - move call of cal_* routines into the if-block where they are really
241       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
242       to specify a startdate
243    o pkg/seaice:
244     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
245       global_ocean.cs32x15/code versions).
246     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
247       verification experiment global_ocean.cs32x15.seaice and update results.
248    o pkg/exf:
249     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
250       (according to useExfYearlyFields).
251    o pkg/cal:
252     - move calendar setting & summary (previously in cal_readparams.F) into new
253       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
254       length of the simulation is set (after SET_PARMS call); This is an attempt
255       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
256     - For safety: keep a record of pkg/cal parameter settings status
257               to allow to STOP if one pkg/cal S/R is called too early.
258     - add a stop in all basic pkg/cal subroutines if called before setting is done.
259     - modify cal_getdate.F: stop when nothing was returned;
260       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
261       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
262    
263    checkpoint63l (2012/04/04)
264    o pkg/bbl:
265      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
266        update global_with_exf output.yearly.txt file.
267    o pkg/cal:
268      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
269      - remove 2 unsused and very short (1 line only) functions ;
270      - remove unsused subroutines from AD-Diff list.
271    o model/src:
272      - start to implement clean wait to stop in initialization S/R (config_check.F,
273         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
274    o folowing PRINT_MESSAGE changes:
275      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
276  o pkg/bbl:  o pkg/bbl:
277    - modification so it can work with z*    - modification so it can work with z*
278    - replace deltaT with dTtracerLev(k) for asynchronous time stepping    - replace deltaT with dTtracerLev(k) for asynchronous time stepping

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