Dialog Box - called from: Input1 Menu
This dialog controls the Cavities Model mode which uses the 3D system capabilities - if your system does not support 3D display the Cavities Model mode is not available. It is applicable to crystals only (not molecules or polymers). The Model Mode is selected in the Display Menu or the Dialog Bar - Left.
Grid spacing. This is the approximate spacing in Angstroms between sample points - the actual spacing may be slightly reduced from this value to give an integral number of points across the unit cell. This should be considerably smaller than the radius of the smallest atom. Values of 0.1 to 0.4 are reasonable. Time of the calculation is proportional to the cube of this number.
Particle radius. This is the radius of the sphere which is presumed to exist in the cavities. The volume shown is that enclosing possible centerpoint locations of this sphere. If this radius is zero, the volume shown will simply be that not occupied by the atoms of the structure.
Show cell faces. If this box is checked, the surface where the cavity volume crosses the unit-cell faces is shown in a different color (next paragraph). If not checked, it may be possible to see completely through a channel, although this requires that the channel be fairly straight. The inner surface is then given a different color (next paragraph).
List Coords [Coordinates]. This will list the fractional coordinates of all grid points which can accomodate the sphere of the specified Particle radius. The listing is made to a text file, CAVVAL.ATD, and this file is then displayed in a Text window (see Types of Windows).
Colors - Outer surface and Cell faces/Inner. The first color is for the outer or exterior surface of the cavities, inside the unit cell. If the Show cell faces box (above) is checked, the second color is for the surfaces where the cavities cross the unit-cell faces. The cell-face surfaces may be especially important in judging the continuity of the cavities. If the Show cell faces box (above) is not checked, the second color is for the inside or inner surface of the cavities themselves. The material parameters used (3D Parameters/Materials, Input2 menu) are those for polyhedra. As for polyhedra, the specular component is usually best kept small.
In VRML files the viewer controls the color of inner surfaces - it is impossible to specify the color without redrawing the surface (i.e. there is only one color per surface in a VRML file). Some viewers may make the inner surfaces the same color as outer surfaces (there may be a switch specifying that surfaces are "double sided"), some may make them black and some may make them transparent. For VRML files it is safest to check the Show cell faces box above.
Offset (fraction of unit cell). This allows the boundaries of the crystal volume shown to be offset by a fraction of the unit cell (axis length). The offset is always in a positive direction, and the lower and upper boundaries are offset by the same amount. The Offsets shift the boundaries of the volume shown, not the unit cell itself or the unit-cell Displacements in the Axes/Unit Cell option.
Number of unit cells. You may display multiple integral unit cells in any of the axis directions. The extra unit cells extend in the positive directions of the axes. You cannot display fractions of unit cells.
Porosity. This is the fraction of the volume of the unit cell which can accomodate the given size particle. The value shown is for the the last plot (which could be printed or file output, rather than screen display). To get true porosity, set the Particle radius to zero.
Changing the Grid spacing or Offset requires a recalculation of the grid, and thus you must select Calculate in the Dialog Bar - Left or File menu. Changing other parameters only requires Replot.