| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/diagnostics (velocity potential solver): |
| 8 |
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- fix initialisation of main diagonal matrix (for overlap values) |
| 9 |
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o tools/build_options: |
| 10 |
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- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
| 11 |
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into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
| 12 |
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- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
| 13 |
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* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
| 14 |
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* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
| 15 |
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and use "-devel" testreport option for standard testing on baudelaire. |
| 16 |
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o pkg/grdchk: |
| 17 |
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- Assume that all gradient-check position are within the same tile |
| 18 |
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corresponding to global indices (iGloTile,jGloTile) and that |
| 19 |
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positions (i,j indices or nbeg) are local to this tile; |
| 20 |
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- set tile local-indices and proc. number according to tile global-indices; |
| 21 |
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- remove grdchkwhichproc from namelist (retired param); |
| 22 |
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- send adjoint gradient to all procs so that all procs print it to STDOUT; |
| 23 |
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- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
| 24 |
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o adding package bbl (Bottom Boundary Layer) |
| 25 |
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description in MITgcm/pkg/bbl/bbl_description.tex |
| 26 |
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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 |
| 34 |
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changed reference output for those that crossed tile boundaries |
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(changed choices of gradient check positions) |
| 36 |
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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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|
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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 |
| 47 |
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at each level (new S/R OBCS_DIAG_BALANCE). |
| 48 |
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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 |
| 50 |
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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 |
| 55 |
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- add a check about nvarlength |
| 56 |
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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); |
| 59 |
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- add specific parameter (default = main code CG2D params) for solver; |
| 60 |
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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 |
| 62 |
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adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
| 63 |
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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 |
| 66 |
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(so that it's really the potential anomaly at the cell center); |
| 67 |
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affect solution only if z* with full pressure in EOS. |
| 68 |
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- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
| 69 |
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update output (because of z* in totPhiHyd and viscA4 changes); |
| 70 |
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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 |
| 76 |
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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 |
| 79 |
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- fix computation of endrec in s/r ctrl_init_rec |
| 80 |
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- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
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o pkg/seaice/seaice_growth.F |
| 82 |
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- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
| 83 |
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remove then obsolete STORE directives |
| 84 |
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- fix STORE directives for tice and tices, so that only the |
| 85 |
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appropriate part of the fields are stored (and not the entire |
| 86 |
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field); update global_ocean.cs32x15.seaice AD output. |
| 87 |
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- cosmetic changes: adjust CPP flags and indentation for better |
| 88 |
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legibilty |
| 89 |
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o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
| 90 |
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Chris Wilson) |
| 91 |
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o pkg/gmredi: |
| 92 |
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Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
| 93 |
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and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
| 94 |
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|
| 95 |
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checkpoint63 (2011/07/11) |
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o pkg/exch2: |
| 97 |
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- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
| 98 |
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- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
| 99 |
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(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
| 100 |
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increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
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o pkg/diagnostics: |
| 102 |
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- deal with pairs of post-processed diags which are computed together; in |
| 103 |
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particular, re-order list of diags within 1 file to save 2nd computation. |
| 104 |
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- add S/R to compute velocity stream-function (called after velocity-potential |
| 105 |
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calculation) from divergence free transport -> new diagnostics "PsiVEL". |
| 106 |
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- add parameter to select grid-point location where PsiVEL == 0. |
| 107 |
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o eesupp/src: |
| 108 |
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new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
| 109 |
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(specific S/R needed with exch2 topology - for now, just print an error msg) |
| 110 |
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o pkg/shelfice |
| 111 |
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- Implement friction velocity-dependent transfer coefficients following |
| 112 |
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Holland and Jenkins, JPO, 1999 |
| 113 |
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Original code by M. Losch with small modifs. |
| 114 |
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Enable with CPP option SHI_ALLOW_GAMMAFRICT |
| 115 |
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and runtime flag SHELFICEuseGammaFrict |
| 116 |
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o verification lab_sea & global_ocean.cs32x15: |
| 117 |
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- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
| 118 |
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does not miss some dependencies (but is slower) and also works with many files |
| 119 |
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(default makedepend limitation for AD built). |
| 120 |
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- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
| 121 |
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o pkg/diagnostics: |
| 122 |
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- add run-time parameter "useMissingValue" (def=False) to fill land-point |
| 123 |
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(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
| 124 |
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This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
| 125 |
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- Extend the use of "missing_value" setting from data.diagnostics for the case |
| 126 |
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of counter-diagnostics (where fraction-weight is zero). This applies both to |
| 127 |
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MNC and MDS output files. |
| 128 |
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o pkg/seaice/seaice_growth.F: |
| 129 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
| 130 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
| 131 |
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non-legacy seaice_solve4temp. |
| 132 |
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- add diagnostic of the residual sublimation freshwater flux (the freshwater |
| 133 |
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flux taken from the ocean if the total actual latent heat fluxes exceed |
| 134 |
|
the maximum) |
| 135 |
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- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
| 136 |
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fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
| 137 |
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- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
| 138 |
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SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
| 139 |
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- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
| 140 |
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- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
| 141 |
|
o verification 1D_ocean_ice_column: |
| 142 |
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made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
| 143 |
|
update results |
| 144 |
|
o pkg/diagnostics: |
| 145 |
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- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
| 146 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
| 147 |
|
diag points to the primary (filled-up) diag to used for post processing. |
| 148 |
|
- Update Velocity-potential computation using post-processed diag framework. |
| 149 |
|
==> Change the ordering of fields and time-periods in MDS output file |
| 150 |
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when using periodic averaging: now writes one time record with the full set |
| 151 |
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of fields for this time period, then the next time reccord (it used to be |
| 152 |
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one field with the full set of time records then the next field). |
| 153 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
| 154 |
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|
| 155 |
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checkpoint62z (2011/06/21) |
| 156 |
|
o adjoint monitor: |
| 157 |
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- Add adjoint monitor output for packages exf, seaice |
| 158 |
|
and update relevant testreport output |
| 159 |
|
o pkg/seaice: |
| 160 |
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- re-order diags inits so that they appear in order in available_diagnostics.log |
| 161 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
| 162 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
| 163 |
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- modified diag: SIdA; output actual effect, as the description states. |
| 164 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
| 165 |
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- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
| 166 |
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(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
| 167 |
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and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
| 168 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
| 169 |
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- added diagnostics for seaice generic tracers (SItr*). |
| 170 |
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- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
| 171 |
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- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
| 172 |
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I. Fenty: 18-Jun-2011: |
| 173 |
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Minor changes to seaice package: |
| 174 |
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1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
| 175 |
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added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
| 176 |
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- Differentiated "regularization variables" from "floor variables" |
| 177 |
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* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
| 178 |
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* hiceMin became SEAICE_hice_reg (old hiceMin) |
| 179 |
|
(with _reg meaning regularization variable) |
| 180 |
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- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
| 181 |
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so as to ensure energy conservation when going between phases |
| 182 |
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- A22 was not used anywhere |
| 183 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
| 184 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
| 185 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
| 186 |
|
because the old regularization always set heffActual >= 0.05 cm |
| 187 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
| 188 |
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on AREA when HEFF > 0. |
| 189 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
| 190 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
| 191 |
|
Affected verifications: |
| 192 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
| 193 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
| 194 |
|
o pkg/diagnostics: |
| 195 |
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- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
| 196 |
|
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
| 197 |
|
(was _RL, now integer) with option = 0 to retrieve all levels. |
| 198 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
| 199 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
| 200 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
| 201 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
| 202 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
| 203 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
| 204 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
| 205 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
| 206 |
|
o model/src (rStar): |
| 207 |
|
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
| 208 |
|
affect solution only if z* with full pressure in EOS; |
| 209 |
|
update output of test-exp global_ocean.90x40x15. |
| 210 |
|
o pkg/seaice: |
| 211 |
|
- introduce siEps=1e-5 parameter |
| 212 |
|
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
| 213 |
|
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
| 214 |
|
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
| 215 |
|
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
| 216 |
|
as well as ice cover age and ridging index (attached to AREA). |
| 217 |
|
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
| 218 |
|
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
| 219 |
|
Up to SItrMaxNum=3 tracers can be used simultaneously. |
| 220 |
|
o pkg/salt_plume: |
| 221 |
|
-introduce SPsalFRAC run time parameter that sets the fraction of the |
| 222 |
|
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
| 223 |
|
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
| 224 |
|
o model debug options: |
| 225 |
|
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
| 226 |
|
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
| 227 |
|
- Refine debug-msg printing selection (3 new levels): |
| 228 |
|
debugMode : controls printing of debug messages (sequence of S/R calls). |
| 229 |
|
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
| 230 |
|
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
| 231 |
|
debLevA = 1 ; /* level of minimum aux. msg printing */ |
| 232 |
|
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
| 233 |
|
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
| 234 |
|
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
| 235 |
|
debLevE = 5 ; /* level of extensive debug printing */ |
| 236 |
|
New debugLevel default: with default debugMode value (=F), |
| 237 |
|
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
| 238 |
|
and if debugMode=T, default debugLevel = 4 (debLevD). |
| 239 |
|
Relation with previous settings: |
| 240 |
|
debLevB (=2) corresponds to former debLevA (=1) |
| 241 |
|
debLevD (=4) corresponds to former debLevB (=2) |
| 242 |
|
Note: |
| 243 |
|
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
| 244 |
|
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
| 245 |
|
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
| 246 |
|
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
| 247 |
|
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
| 248 |
|
o pkg/obcs: |
| 249 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
| 250 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
| 251 |
|
o pkg/thsice: |
| 252 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
| 253 |
|
2nd layer seaice sublimation (unlikely to happen) |
| 254 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
| 255 |
|
done in gad_advection & seaice_advection). |
| 256 |
|
o adjoint: |
| 257 |
|
bug fix spotted by Gael Forget: |
| 258 |
|
seaice_advection and thsice_advection still had |
| 259 |
|
legacy CPP options to avoid CS corner updates for adjoint |
| 260 |
|
o pkg/seaice: |
| 261 |
|
=> Change some of the defaults (2011/05/29): |
| 262 |
|
- change SEAICEuseFluxForm default (from False to True) |
| 263 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
| 264 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
| 265 |
|
avection scheme is used without any diffusion. |
| 266 |
|
also: |
| 267 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
| 268 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
| 269 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
| 270 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
| 271 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
| 272 |
|
update results of test exp.: |
| 273 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
| 274 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
| 275 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
| 276 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
| 277 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
| 278 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
| 279 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
| 280 |
o pkg/seaice/seaice_growth.F: |
o pkg/seaice/seaice_growth.F: |
| 281 |
- use Ian Fenty's capping formulas for actual ice |
- use Ian Fenty's capping formulas for actual ice |
| 282 |
thickness thoughout EVOLUTION branch. |
thickness thoughout EVOLUTION branch. |
| 283 |
- put treatment pathological case #2) in CPP brackets |
- put treatment pathological case #2) in CPP brackets |
| 284 |
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
| 285 |
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
| 286 |
o pkg/seaice: |
o pkg/seaice: |
| 287 |
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
| 288 |
pass the Laplacian diffusivity (in m/s2) diffKh as a parameter; |
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
| 289 |
also pass fac as a param, which can be 1. (to update the tendency |
also pass fac as a param, which can be 1. (to update the tendency |
| 290 |
field) or the time step (to update the field itself). |
field) or the time step (to update the field itself). |
| 291 |
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
| 292 |
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
| 293 |
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
| 294 |
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
| 295 |
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
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- note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
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is specified to be >0, then DIFF1 is set to 0. |
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| 296 |
o pkg/seaice: |
o pkg/seaice: |
| 297 |
diffusion with centered advection scheme (diffus.F & advect.F): |
diffusion with centered advection scheme (diffus.F & advect.F): |
| 298 |
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
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