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Geometry diagnostic

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Once the vertical discretization or geometry is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a geometry diagnostic tool was developed.

Source-safe whereabouts

The latest source code is in the Mohid_V4 repository, inside the small tools\GeometryDiagnostic folder.


The inputs required are a bathymetry grid data file, a geometry file, an hdf5 output filename and a grid data output filename.


IN_MODEL    : GeometryDiagnostics.dat


BATIM    : Biscay_Level2__.new2
GEOMETRY : D:\Aplica\BiscayAplica\GeneralData\Ocean\Geometry\Level2\Geometry.dat
OUT_FILE       : geomdiag_new2.hdf5
OUT_GRIDDATA3D : geomdiag_new2.dat


The outputs are an hdf5 file and a three-dimensional grid data file.


For all horizontal cells i, j, there is one bottom layer kbottom that defines the bottom layer thickness DWZ(i, j, kbottom); where DWZ is the 3D matrix that defines the layers thickness for every water column.

LowerLayerThickness(i,j) = DWZ(i,j, kbottom)


Is the ratio of neighboring cells bottom layer thickness along the X axis.

aux = DWZ(i,j, kbottom)/DWZ(i,j-1, kbottom)
LowerLayerThicknessGradU(i,j) = min( aux, 1/aux)


Is the ratio of neighboring cells bottom layer thickness along the Y axis.

aux = DWZ(i,j, kbottom)/DWZ(i-1,j, kbottom)
LowerLayerThicknessGradV(i,j) = min( aux, 1/aux)

See also