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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 verification/matrix_example: |
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- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
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MPI and mutlti-threaded testing. |
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o pkg/matrix: |
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- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
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- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
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- fix for multi-threaded (remove DATA statement); |
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- use standard DIFFERENT_MULTIPLE function; |
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- add MATRIX_OPTIONS.h |
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o verification/matrix_example: |
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To allow to split the domain in several tiles, change the domain size |
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from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
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Western side) of land points. |
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o (*_)write_pickup: |
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- fix few bugs in mypackage_read/write_pickup.F |
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- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
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array of length 1 (was caught by compiler syntax-check). |
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o pkg/diagnostics (velocity potential solver): |
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- fix initialisation of main diagonal matrix (for overlap values) |
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o tools/build_options: |
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- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
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into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
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- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
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* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
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* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
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and use "-devel" testreport option for standard testing on baudelaire. |
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o pkg/grdchk: |
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- Assume that all gradient-check position are within the same tile |
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corresponding to global indices (iGloTile,jGloTile) and that |
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positions (i,j indices or nbeg) are local to this tile; |
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- set tile local-indices and proc. number according to tile global-indices; |
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- remove grdchkwhichproc from namelist (retired param); |
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- send adjoint gradient to all procs so that all procs print it to STDOUT; |
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- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
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o adding package bbl (Bottom Boundary Layer) |
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description in MITgcm/pkg/bbl/bbl_description.tex |
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example/test experiment in MITgcm_contrib/bbl |
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o adjoint verifications |
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- changed 5 experiments to multi-tiles |
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* global_ocean.90x40x15 |
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* obcs_ctrl |
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* offline_exf_seaice |
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* tutorial_dic_adjoffline |
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* tutorial_tracer_adjsens |
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changed reference output for those that crossed tile boundaries |
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(changed choices of gradient check positions) |
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- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
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- temporary bug fix in grdchk_loc.F for obcs |
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o genmake2 & testreport |
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- add target "obj" (just for OBJFILES files) to Makefile; |
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- add option to specify FEXTRAFLAGS on command line. |
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o pkg/mypackage: |
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- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
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checkpoint63a (2011/08/02) |
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o pkg/diagnostics (velocity potential): |
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- fix velocity-potential calculation when using OBCS: balance net inflow |
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at each level (new S/R OBCS_DIAG_BALANCE). |
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- fix some of the problems with OBCS in stream-function calculation. |
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o pkg/exf/exf_readparms.F |
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- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
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EXF_NML_OBCS) more consistent, so that you need not have these lists |
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in data.exf when they are not used. |
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o optim/optim_readdata.F: |
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- add some output about obcs variables that might help debugging |
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- add a check about nvarlength |
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o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
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o pkg/diagnostics (velocity potential): |
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- fix mask for OBCS (still problems in stream-function with OBCS); |
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- add specific parameter (default = main code CG2D params) for solver; |
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- in case of poor convergence, use solution corresponding to lowest residual. |
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o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
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adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
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and should be avoided where possible. |
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o model/src (rStar): |
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- include r* effect on reference-state (PhiRef) in totPhiHyd |
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(so that it's really the potential anomaly at the cell center); |
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affect solution only if z* with full pressure in EOS. |
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- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
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update output (because of z* in totPhiHyd and viscA4 changes); |
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- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
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@ constant r) until interpolation at constant r is implemented. |
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o pkg/diagnostics |
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- fix RCENTER diagnostics in case cell center is not at interface middle |
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o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
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this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
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that THETA and SALT are "conservative temperature" and "absolute |
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salinity" |
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o pkg/ctrl |
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- fix computation of endrec in s/r ctrl_init_rec |
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- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
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o pkg/seaice/seaice_growth.F |
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- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
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remove then obsolete STORE directives |
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- fix STORE directives for tice and tices, so that only the |
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appropriate part of the fields are stored (and not the entire |
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field); update global_ocean.cs32x15.seaice AD output. |
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- cosmetic changes: adjust CPP flags and indentation for better |
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legibilty |
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o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
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Chris Wilson) |
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o pkg/gmredi: |
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Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
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and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
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checkpoint63 (2011/07/11) |
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o pkg/exch2: |
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- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
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- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
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(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
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increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
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o pkg/diagnostics: |
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- deal with pairs of post-processed diags which are computed together; in |
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particular, re-order list of diags within 1 file to save 2nd computation. |
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- add S/R to compute velocity stream-function (called after velocity-potential |
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calculation) from divergence free transport -> new diagnostics "PsiVEL". |
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- add parameter to select grid-point location where PsiVEL == 0. |
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o eesupp/src: |
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new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
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(specific S/R needed with exch2 topology - for now, just print an error msg) |
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o pkg/shelfice |
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- Implement friction velocity-dependent transfer coefficients following |
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Holland and Jenkins, JPO, 1999 |
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Original code by M. Losch with small modifs. |
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Enable with CPP option SHI_ALLOW_GAMMAFRICT |
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and runtime flag SHELFICEuseGammaFrict |
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o verification lab_sea & global_ocean.cs32x15: |
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- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
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does not miss some dependencies (but is slower) and also works with many files |
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(default makedepend limitation for AD built). |
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- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
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o pkg/diagnostics: |
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- add run-time parameter "useMissingValue" (def=False) to fill land-point |
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(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
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This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
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- Extend the use of "missing_value" setting from data.diagnostics for the case |
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of counter-diagnostics (where fraction-weight is zero). This applies both to |
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MNC and MDS output files. |
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o pkg/seaice/seaice_growth.F: |
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- add 'a priori' cap of latent heat flux based on actual mass considerations |
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when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
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non-legacy seaice_solve4temp. |
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- add diagnostic of the residual sublimation freshwater flux (the freshwater |
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flux taken from the ocean if the total actual latent heat fluxes exceed |
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the maximum) |
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- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
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fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
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- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
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SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
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- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
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- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
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o verification 1D_ocean_ice_column: |
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made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
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update results |
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o pkg/diagnostics: |
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- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
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which are not filled-up but computed from other diags ; In this case, the mate |
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diag points to the primary (filled-up) diag to used for post processing. |
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- Update Velocity-potential computation using post-processed diag framework. |
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==> Change the ordering of fields and time-periods in MDS output file |
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when using periodic averaging: now writes one time record with the full set |
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of fields for this time period, then the next time reccord (it used to be |
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one field with the full set of time records then the next field). |
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Note: this is now similar to NetCDF (MNC) output file. <== |
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|
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checkpoint62z (2011/06/21) |
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o adjoint monitor: |
o adjoint monitor: |
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- Add adjoint monitor output for packages exf, seaice |
- Add adjoint monitor output for packages exf, seaice |
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and update relevant testreport output |
and update relevant testreport output |
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- modified diag: SIdA; output actual effect, as the description states. |
- modified diag: SIdA; output actual effect, as the description states. |
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- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
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- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
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(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
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and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
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- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
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- added diagnostics for seaice genereic tracers (SItr*). |
- added diagnostics for seaice generic tracers (SItr*). |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
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I. Fenty: 18-Jun-2011: |
I. Fenty: 18-Jun-2011: |
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Minor changes to seaice package: |
Minor changes to seaice package: |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
| 192 |
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
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- Differentiated "regularization variables" from "floor variables" |
- Differentiated "regularization variables" from "floor variables" |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
* hiceMin became SEAICE_hice_reg (old hiceMin) |
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(with _reg meaning regularization variable) |
(with _reg meaning regularization variable) |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
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so as to ensure energy conservation when going between phases |
so as to ensure energy conservation when going between phases |
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- A22 was not used anywhere |
- A22 was not used anywhere |
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2) Changed regularization procedure for heffActual and hsnowActual to ensure |
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
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well-boundedness and smooth adjoint in seaice_growth.F |
well-boundedness and smooth adjoint in seaice_growth.F |
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3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
| 203 |
because the old regularization always set heffActual >= 0.05 cm |
because the old regularization always set heffActual >= 0.05 cm |
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4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
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on AREA when HEFF > 0. |
on AREA when HEFF > 0. |
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- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
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requiring that DISABLE_AREA_FLOOR *not* be defined |
requiring that DISABLE_AREA_FLOOR *not* be defined |
| 208 |
Affected verifications: |
Affected verifications: |
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- 1D_ocean_ice_column (output.txt output_adm.txt) |
- 1D_ocean_ice_column (output.txt output_adm.txt) |
| 210 |
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
| 215 |
- add pieces of code to compute velocity potential at each level (new diagnostics |
- add pieces of code to compute velocity potential at each level (new diagnostics |
| 216 |
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
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for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
| 218 |
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- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
| 219 |
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diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
| 220 |
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and in diagnostics_fract_fill.F (do not need a valid pointer for the |
| 221 |
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diagnostics counter-mate); check that definition of counter-diagnostic |
| 222 |
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includes a valid counter-mate (in diagnostics_set_levels.F). |
| 223 |
o model/src (rStar): |
o model/src (rStar): |
| 224 |
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
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affect solution only if z* with full pressure in EOS; |
affect solution only if z* with full pressure in EOS; |
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