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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/autodiff: |
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re-write active I/O high-level (control) S/R: |
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- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
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- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
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- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
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MDS_READ/WRITE_FIELD); change loops to multi-threads. |
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- update and merge active_file_control_slice.flow into active_file_control.flow |
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- update the calls in lower level S/R (active_file.F, active_file_g.F and |
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active_file_ad.F) keeping the argument list and function unchanged. |
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- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
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=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
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o autodiff and RS=real*4: |
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- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
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ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
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- change argument type of 3-D mask argument to _RS to match type in the call |
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(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
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o pkg/thsice: |
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- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
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- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
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fresh-water flux: uniform correction or proportional to local precip. |
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o pkg/ctrl: |
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- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
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- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
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ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
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- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
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checkpoint63q (2012/07/30) |
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o pkg/autodiff: |
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note about monitor and snap-shot of ad-variables: |
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a) need to apply ADEXCH before monitor or output of ad-vars to include |
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overlap contributions (was done for adjDump but missing for monitor). |
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b) since ADEXCH implies adding overlap values to interior array, machine |
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truncation error is expected when adding an ADEXCH call in the middle of |
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the time-stepping (although mathematically identical). |
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modifs: |
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- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
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declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
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- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
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apply ADEXCH before monitor or snap-shot of ad-variables: |
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=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
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- implement new method (copy+adexch) for snap-shot and monitor of main model |
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ad-vars (initially not used by default -> output unchanged). |
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- change default (set to 2) to use new method and update few output_adm.txt |
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with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
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and both tutorial_tracer_adjsens tests). |
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- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
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and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
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o pkg/ctrl: |
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enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
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generic control variables via |
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#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
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Only required customization should be S/R ctrl_map_ini_genarr.F |
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(routine in repository contains example) |
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o pkg/exf: |
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- fix and refine checking of surface-relaxation setting when using EXF |
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o verification (adjoint exp): |
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- reduce length of simulation by half for experiment global_ocean.cs32x15 |
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(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
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o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
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- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
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of KE that can occur with aggressive optimization |
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+ put quadratic bottom drag calculation in separated loops (only done if |
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using bottomDragQuadratic) |
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o model/src: CG2D_NSA |
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- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
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and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
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- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
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change cg2d residual target to be expressed in Wunits (=> do not normalise |
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RHS ; this fix global_max Pb with TAF); update output. |
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o verification/tutorial_tracer_adjsens: |
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improve parameter consistency (and get rid of warnings): |
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- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
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- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
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- use staggerTimeStep (for stability) in som81; use default rotation period. |
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o pkg/exch2: |
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- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
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reset to 0 = 1 long line in X) |
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o pkg/mdsio: |
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- fix reading of dimensions from meta file for large-size domain |
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o model/src: |
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- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
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- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
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Cubed-Sphere Exch with CS-corners inside the domain; |
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make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
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globalArea and to set hasWetCSCorners. |
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- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
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metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
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- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
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useCDscheme and useCubedSphereExchange). |
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o pkg/seaice/seaice_growth.F : |
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- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
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for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
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when the previous code was not correct. |
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- in all cases diagnoze the boundary condition mismatch to SIaaflux |
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- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
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that term to QNET (essentially to set the melt/freeze water to 0degC). |
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when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
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o verification/global_ocean.cs32x15/input.seaice : |
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- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
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- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
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- update results (output.seaice.txt) accordingly. |
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o verification/lab_sea/input/data.seaice : |
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- remove SEAICEheatConsFix, which is now be tested |
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in global_ocean.cs32x15. The presently coded fix |
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is only consistent with real fresh water + nlfs. |
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- update results (output.txt) accordingly. |
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o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
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o AD_CONFIG.h file: |
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- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
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- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
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add it explicitly in each fortran src file where it is needed. |
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motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
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thus introducing potentially wrong dependency; therefore, better to include |
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it only where it's really needed, and after any other included OPTIONS file |
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(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
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or ALLOW_TANGENTLINEAR_RUN). |
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checkpoint63p (2012/07/06) |
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o pkg/autodiff: |
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- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
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- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
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which are now read from new parameter file "data.autodiff" (inAdExact |
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previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
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- add file "data.autodiff" in all verification/*/input_ad/ directories. |
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- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
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mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
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o verification/tutorial_tracer_adjsens/ |
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- add extra sub-verification which uses "SOM" advection scheme |
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(2nd Order-Moment Advection Scheme, Prather Limiter) with |
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#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
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and in data: |
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multiDimAdvection=.TRUE., |
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tempAdvScheme=81, |
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saltAdvScheme=81, |
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o model/src: |
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- introduce ALLOW_BALANCE_RELAX which allow the removal |
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of the global mean of relaxation terms by setting |
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balanceThetaClimRelax and balanceSaltClimRelax |
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- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
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This case is now treated appropriately in seaice_growth.F |
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o pkg/seaice: |
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- do balanceEmPmR and balanceQnet based on the net fluxes |
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(SItflux) that enter the ocean+ice system rather than QNET |
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and EMPMR. Works best in real fresh water. |
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- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
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out of the diagnotics bloc, and stored in global arrays. |
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checkpoint63o (2012/06/29) |
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o vertical mixing schemes: |
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- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
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- replace computation of density (in Function STATE1, opps_calc.F) by a call |
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to S/R FIND_RHO_SCALAR |
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- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
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and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
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affects output (vermix.ggl90) at truncation level. |
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o testreport: |
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- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
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(nSx,nSy) for the number of threads (from eedata.mth) |
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o model/src: |
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- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
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related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
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o verification/tutorial_tracer_adjsens/ |
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- compile with ALLOW_CG2D_NSA |
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- run with nonlinFreeSurf=3 |
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- update reference output_adm.txt |
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o tools/genmake2: |
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- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
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refine usePROFILES switching off (only when NetCDF is not available). |
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o verification (atmospheric set-up): |
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- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
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o pkg/profiles : refine profiles and files handling. |
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o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
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o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
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- changes to use model/src/the_main_loop.F rather than the ecco version |
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in ecco type adjoint runs. |
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o model/src: |
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- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
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- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
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- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
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o model/src: |
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- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
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update output of test experiment bottom_ctrl_5x5. |
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o pkg/generic_advdiff: |
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- implement vertical bi-harmonic diffusion (for now, only for T & S and |
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only explicitly). |
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o verification/bottom_ctrl_5x5/ |
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update reference output (results changed quite some time ago, |
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not sure when; but new reference results look ok in terms of grdchk) |
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o verification/1D_ocean_ice_column/ |
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For verification purposes, the exact adjoint rather than an approx. |
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should be used (e.g., to comare against F.D. or TLM). |
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removed autodiff_inadmode*_ad.F routines in code_ad/ |
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Update results/ accordingly. |
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o pkg/cal: |
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- change cal_getdate.F so that output date is function of input time only |
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(less ambiguous, not mixed up with input iteration number). |
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- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
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o pkg/diagnostics: |
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- implement calendarDumps also for stats-diags |
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- implement calendarDumps also for snap-shot output (negative freq) |
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- for now, ignores calendarDumps if non-zero phase-lag. |
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checkpoint63n (2012/06/04) |
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o model/src: |
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- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
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between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
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- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
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similar to calc_r_star.F); update results of experiment internal_wave and |
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tutorial_global_oce_in_p (affected @ truncation level). |
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o pkg/shelfice: |
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- add parameterisation of advective-diffusive flux into the ice shelf |
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according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
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- simply eps3/3a computation |
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o eesupp: |
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- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
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between tiles, just fill-in edges assuming locally periodic subdomain) and |
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add corresponding exchange subroutines (EXCH0); |
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- new CG-solver version (_EX0) for disconnected-tiles special case. |
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o model/src (CG-solvers): |
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- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
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(similar final residual output and max-Iter number as with standard version); |
| 228 |
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- allows to store and use lowest-residual solution (standard & _SR versions); |
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- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
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- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
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o eesup/src: |
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- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
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ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
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o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
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|
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checkpoint63m (2012/04/27) |
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o pkg/shelfice: |
o pkg/shelfice: |
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- account for partical cells in surface level below ice-shelf for hydrostatic |
- account for partical cells in surface level below ice-shelf for hydrostatic |
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pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
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