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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: |
| 8 |
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note about monitor and snap-shot of ad-variables: |
| 9 |
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a) need to apply ADEXCH before monitor or output of ad-vars to include |
| 10 |
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overlap contributions (was done for adjDump but missing for monitor). |
| 11 |
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b) since ADEXCH implies adding overlap values to interior array, machine |
| 12 |
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truncation error is expected when adding an ADEXCH call in the middle of |
| 13 |
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the time-stepping (although mathematically identical). |
| 14 |
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modifs: |
| 15 |
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- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
| 16 |
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apply ADEXCH before monitor or snap-shot of ad-variables: |
| 17 |
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=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
| 18 |
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- implement new method (copy+adexch) for snap-shot and monitor of main model |
| 19 |
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ad-vars (but not yet used by default). |
| 20 |
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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). |
| 22 |
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o pkg/ctrl: |
| 23 |
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enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
| 24 |
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generic control variables via |
| 25 |
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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: |
| 29 |
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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); |
| 56 |
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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 |
| 78 |
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in global_ocean.cs32x15. The presently coded fix |
| 79 |
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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" |
| 87 |
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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). |
| 91 |
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|
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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 ; |
| 95 |
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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 |
| 97 |
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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 |
| 105 |
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and in data: |
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multiDimAdvection=.TRUE., |
| 107 |
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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 |
| 111 |
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of the global mean of relaxation terms by setting |
| 112 |
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balanceThetaClimRelax and balanceSaltClimRelax |
| 113 |
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- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
| 114 |
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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. |
| 121 |
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|
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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 |
| 126 |
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to S/R FIND_RHO_SCALAR |
| 127 |
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- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
| 128 |
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and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
| 129 |
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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) |
| 133 |
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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) |
| 135 |
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related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
| 136 |
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o verification/tutorial_tracer_adjsens/ |
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- compile with ALLOW_CG2D_NSA |
| 138 |
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- run with nonlinFreeSurf=3 |
| 139 |
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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 ; |
| 142 |
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refine usePROFILES switching off (only when NetCDF is not available). |
| 143 |
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o verification (atmospheric set-up): |
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- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
| 145 |
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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. |
| 147 |
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o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
| 148 |
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- changes to use model/src/the_main_loop.F rather than the ecco version |
| 149 |
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in ecco type adjoint runs. |
| 150 |
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o model/src: |
| 151 |
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- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
| 152 |
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- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
| 153 |
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- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
| 154 |
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o model/src: |
| 155 |
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- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
| 156 |
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update output of test experiment bottom_ctrl_5x5. |
| 157 |
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o pkg/generic_advdiff: |
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- implement vertical bi-harmonic diffusion (for now, only for T & S and |
| 159 |
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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, |
| 162 |
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not sure when; but new reference results look ok in terms of grdchk) |
| 163 |
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o verification/1D_ocean_ice_column/ |
| 164 |
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For verification purposes, the exact adjoint rather than an approx. |
| 165 |
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should be used (e.g., to comare against F.D. or TLM). |
| 166 |
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removed autodiff_inadmode*_ad.F routines in code_ad/ |
| 167 |
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Update results/ accordingly. |
| 168 |
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o pkg/cal: |
| 169 |
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- change cal_getdate.F so that output date is function of input time only |
| 170 |
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(less ambiguous, not mixed up with input iteration number). |
| 171 |
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- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
| 172 |
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o pkg/diagnostics: |
| 173 |
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- implement calendarDumps also for stats-diags |
| 174 |
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- implement calendarDumps also for snap-shot output (negative freq) |
| 175 |
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- for now, ignores calendarDumps if non-zero phase-lag. |
| 176 |
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|
| 177 |
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checkpoint63n (2012/06/04) |
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o model/src: |
| 179 |
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- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
| 180 |
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between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
| 181 |
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- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
| 182 |
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similar to calc_r_star.F); update results of experiment internal_wave and |
| 183 |
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tutorial_global_oce_in_p (affected @ truncation level). |
| 184 |
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o pkg/shelfice: |
| 185 |
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- add parameterisation of advective-diffusive flux into the ice shelf |
| 186 |
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according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
| 187 |
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- simply eps3/3a computation |
| 188 |
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o eesupp: |
| 189 |
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- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
| 190 |
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between tiles, just fill-in edges assuming locally periodic subdomain) and |
| 191 |
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add corresponding exchange subroutines (EXCH0); |
| 192 |
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- new CG-solver version (_EX0) for disconnected-tiles special case. |
| 193 |
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o model/src (CG-solvers): |
| 194 |
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- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
| 195 |
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(similar final residual output and max-Iter number as with standard version); |
| 196 |
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- allows to store and use lowest-residual solution (standard & _SR versions); |
| 197 |
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- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
| 198 |
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- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
| 199 |
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o eesup/src: |
| 200 |
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- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
| 201 |
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ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
| 202 |
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o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
| 203 |
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|
| 204 |
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checkpoint63m (2012/04/27) |
| 205 |
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o pkg/shelfice: |
| 206 |
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- account for partical cells in surface level below ice-shelf for hydrostatic |
| 207 |
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pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
| 208 |
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o ad test experiments: |
| 209 |
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- update and rename to "ad_optfile.local" local AD-optfile specific to a |
| 210 |
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particular adjoint verification experiment (in verification/*/code_ad/) |
| 211 |
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o pkg/seaice & pkg/exf: |
| 212 |
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- Part two of ECCO-CLIVAR code merges. |
| 213 |
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Completes merge of seaice area relax. code. |
| 214 |
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Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
| 215 |
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to be set in EXF_OPTIONS.h since this pkg controls its I/O |
| 216 |
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(and avoids second CPP option in SEAICE_OPTIONS.h) |
| 217 |
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- change default value of costIceStart & costIceEnd to a valid date. |
| 218 |
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- add snowPrecip to HSNOW in seaice_growth |
| 219 |
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o pkg/ptracers: |
| 220 |
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- move ptracers summary and setup check into separated S/R ; add a check for |
| 221 |
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valid PTRACERS_Iter0 value (error+stop or just warning). |
| 222 |
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o pkg/cal (+ pkg/ecco): |
| 223 |
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- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
| 224 |
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as input; and for AD, unless both are not differentiable (e.g., k index)). |
| 225 |
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o model/src: |
| 226 |
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- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
| 227 |
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is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
| 228 |
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temporary set to usingZCoords value (to be changed to F when using shelfice). |
| 229 |
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- hydrostatic pressure: implement partial cell near the surface also for |
| 230 |
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Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
| 231 |
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usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
| 232 |
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o pkg/ctrl/ctrl_init.F: |
| 233 |
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- add a formal parameter to s/r ctrl_init_rec to print |
| 234 |
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xx_$(ctrl_valiable)_file for easier debugging |
| 235 |
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- move call of cal_* routines into the if-block where they are really |
| 236 |
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needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
| 237 |
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to specify a startdate |
| 238 |
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o pkg/seaice: |
| 239 |
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- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
| 240 |
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global_ocean.cs32x15/code versions). |
| 241 |
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- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
| 242 |
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verification experiment global_ocean.cs32x15.seaice and update results. |
| 243 |
|
o pkg/exf: |
| 244 |
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- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
| 245 |
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(according to useExfYearlyFields). |
| 246 |
|
o pkg/cal: |
| 247 |
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- move calendar setting & summary (previously in cal_readparams.F) into new |
| 248 |
|
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
| 249 |
|
length of the simulation is set (after SET_PARMS call); This is an attempt |
| 250 |
|
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
| 251 |
|
- For safety: keep a record of pkg/cal parameter settings status |
| 252 |
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to allow to STOP if one pkg/cal S/R is called too early. |
| 253 |
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- add a stop in all basic pkg/cal subroutines if called before setting is done. |
| 254 |
|
- modify cal_getdate.F: stop when nothing was returned; |
| 255 |
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if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
| 256 |
|
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
| 257 |
|
|
| 258 |
|
checkpoint63l (2012/04/04) |
| 259 |
|
o pkg/bbl: |
| 260 |
|
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
| 261 |
|
update global_with_exf output.yearly.txt file. |
| 262 |
|
o pkg/cal: |
| 263 |
|
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
| 264 |
|
- remove 2 unsused and very short (1 line only) functions ; |
| 265 |
|
- remove unsused subroutines from AD-Diff list. |
| 266 |
|
o model/src: |
| 267 |
|
- start to implement clean wait to stop in initialization S/R (config_check.F, |
| 268 |
|
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
| 269 |
|
o folowing PRINT_MESSAGE changes: |
| 270 |
|
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
| 271 |
o pkg/bbl: |
o pkg/bbl: |
| 272 |
- modification so it can work with z* |
- modification so it can work with z* |
| 273 |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
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