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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 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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|
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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 |
| 21 |
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which are now read from new parameter file "data.autodiff" (inAdExact |
| 22 |
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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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|
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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); |
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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: |
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- 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. |
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o ad test experiments: |
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- update and rename to "ad_optfile.local" local AD-optfile specific to a |
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particular adjoint verification experiment (in verification/*/code_ad/) |
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o pkg/seaice & pkg/exf: |
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- Part two of ECCO-CLIVAR code merges. |
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Completes merge of seaice area relax. code. |
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Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
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to be set in EXF_OPTIONS.h since this pkg controls its I/O |
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(and avoids second CPP option in SEAICE_OPTIONS.h) |
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- change default value of costIceStart & costIceEnd to a valid date. |
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- add snowPrecip to HSNOW in seaice_growth |
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o pkg/ptracers: |
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- move ptracers summary and setup check into separated S/R ; add a check for |
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valid PTRACERS_Iter0 value (error+stop or just warning). |
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o pkg/cal (+ pkg/ecco): |
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- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
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as input; and for AD, unless both are not differentiable (e.g., k index)). |
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o model/src: |
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- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
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is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
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temporary set to usingZCoords value (to be changed to F when using shelfice). |
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- hydrostatic pressure: implement partial cell near the surface also for |
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Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
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usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
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o pkg/ctrl/ctrl_init.F: |
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- add a formal parameter to s/r ctrl_init_rec to print |
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xx_$(ctrl_valiable)_file for easier debugging |
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- move call of cal_* routines into the if-block where they are really |
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needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
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to specify a startdate |
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o pkg/seaice: |
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- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
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global_ocean.cs32x15/code versions). |
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- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
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verification experiment global_ocean.cs32x15.seaice and update results. |
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o pkg/exf: |
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- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
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(according to useExfYearlyFields). |
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o pkg/cal: |
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- move calendar setting & summary (previously in cal_readparams.F) into new |
| 173 |
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S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
| 174 |
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length of the simulation is set (after SET_PARMS call); This is an attempt |
| 175 |
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to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
| 176 |
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- For safety: keep a record of pkg/cal parameter settings status |
| 177 |
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to allow to STOP if one pkg/cal S/R is called too early. |
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- add a stop in all basic pkg/cal subroutines if called before setting is done. |
| 179 |
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- modify cal_getdate.F: stop when nothing was returned; |
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if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
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this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
| 182 |
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|
| 183 |
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checkpoint63l (2012/04/04) |
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o pkg/bbl: |
| 185 |
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- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
| 186 |
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update global_with_exf output.yearly.txt file. |
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o pkg/cal: |
| 188 |
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- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
| 189 |
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- remove 2 unsused and very short (1 line only) functions ; |
| 190 |
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- remove unsused subroutines from AD-Diff list. |
| 191 |
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o model/src: |
| 192 |
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- start to implement clean wait to stop in initialization S/R (config_check.F, |
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packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
| 194 |
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o folowing PRINT_MESSAGE changes: |
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- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
| 196 |
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o pkg/bbl: |
| 197 |
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- modification so it can work with z* |
| 198 |
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- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
| 199 |
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- global_with_exf/input.yearly verification; changes output.yearly.txt |
| 200 |
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o eesupp/src: |
| 201 |
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- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
| 202 |
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writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
| 203 |
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- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
| 204 |
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# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
| 205 |
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- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
| 206 |
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- when using MPI, always set usingMPI=T ; set default accordingly and stop |
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if not consistent. |
| 208 |
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- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
| 209 |
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argument is zero (in case called within single-thread section). |
| 210 |
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o pkg/fizhi: |
| 211 |
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clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
| 212 |
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in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
| 213 |
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o pkg/exch2: |
| 214 |
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- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
| 215 |
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activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
| 216 |
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- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
| 217 |
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but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
| 218 |
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with bad ones coming from a not-yet-updated halo. |
| 219 |
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This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
| 220 |
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o pkg/frazil: |
| 221 |
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move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
| 222 |
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http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
| 223 |
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o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
| 224 |
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o verification/lab_sea |
| 225 |
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* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
| 226 |
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* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
| 227 |
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* nTimeSteps 3 -> 4 |
| 228 |
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* changed reference output accordingly |
| 229 |
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o pkg/ctrl: |
| 230 |
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* fix ctrl_get_gen for xx_sst, xx_sss |
| 231 |
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o pkg/fizhi: |
| 232 |
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- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
| 233 |
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update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
| 234 |
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- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
| 235 |
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fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
| 236 |
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clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
| 237 |
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o pkg/gmredi: |
| 238 |
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- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
| 239 |
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o pkg/fizhi: |
| 240 |
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- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
| 241 |
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(old)aces open64 tuv test. |
| 242 |
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o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
| 243 |
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o pkg/mom_vecinv: |
| 244 |
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- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
| 245 |
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set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
| 246 |
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with non-lin free-surf). |
| 247 |
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o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
| 248 |
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in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
| 249 |
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some compilers (gfortran 4.6.0 on MacOS) |
| 250 |
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o momentum: |
| 251 |
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- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
| 252 |
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& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
| 253 |
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fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
| 254 |
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|
| 255 |
|
checkpoint63k (2012/03/17) |
| 256 |
o model/src: |
o model/src: |
| 257 |
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
| 258 |
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
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