Cavities Model Mode
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Parameters for this Model mode are set in the Cavity Parameters dialog, Input1 menu.

This Model mode shows the surface enclosing the centerpoint locations of a given-sized particle (sphere) within the structure. By setting the particle size to zero, you can show the actual reciprocal of the crystal structure.

There are two steps to the location of this surface. First (grid calculation), the unit cell is sampled at the given Grid spacing and Offset, to get the distance to the surface of the nearest atom. This calculation need not be repeated unless the unit cell, atom coordinates or atom radii, or the Grid spacing or Offset are changed. Second (surface evaluation), at plot time the surface which outlines the given Particle radius (i.e. a three dimensional contour surface) is drawn. Multiple unit cells are drawn by duplicating the surface segments in the central unit cell, which increases drawing or rendering time, but not grid calculation or surface location time.

The grid calculation uses the current atom radii (Atoms dialog, Input1 menu). Presumably these are full ionic, covalent or van der Waals radii. The radii can all be changed by a factor with the Atoms-Global dialog (Input2 menu).

Since a single unit cell is sampled from 0 to 1, and offsets and multiple cells extend in the positive axis directions, automatic centering should normally be selected in the Centering/Displacement dialog (Input2 menu).

The calculations involved in this mode are essentially independent of those involved in the other Model modes. If you want to switch between Cavities mode and other modes, to compare the the actual structure with cavities, it may be helpful to set the Boundary Option and other conditions to match.

When showing a single unit cell with no offsets, the Boundary should be set to Unit Cell, 0-1 inclusive. It is usually helpful show the unit cell edges with the Axes/Unit Cell option (Input2 menu). The unit-cell Displacements (button in the Axes/Unit Cell dialog) should all be set to zero.

When displaying in Cavities mode with multiple unit cells and/or offset unit cells, showing the actual structure with the same boundaries requires using the Enter Forms boundary option. Symmetry for the faces should be None, and the bounding faces should be those of the unit cell, at central distances which are suitable fractions (to take account of Offsets) and/or multiples of the d-spacing. The d-spacing is printed out for each form after it is entered. If the boundary is initially set up for Unit Cell (previous paragraph), and then switched to Enter Forms, the appropriate faces will be entered and the central distances/d-spacings given. Note that Offsets will require negative central distances. For example, if the Cavities volume is offset by 0.25 on the a-axis, the bounding faces cutting the a-axis should be (100) at central distance 1.25d and (-100) at -0.25d (where d is d-spacing).

Note that atoms with small radii have little influence on the configuration of cavities, and such atoms can usually be omitted. For example when doing silicates using ionic radii, silicon atoms may be omitted. Even using covalent or van der Waals radii the silicon atoms do not greatly influence the configuration of cavities. Of course if the Particle radius is set to zero, the locations of omitted small atoms may show up as isolated cavities, but this may be minimized by setting the Grid spacing to a value larger than the small atoms. Thus omitting small atoms improves the speed of the calculations in two ways; directly by reducing the number of atoms considered in the grid calculation step; and indirectly by allowing larger grid spacing.

Cavities-mode drawings may be saved as VRML Files. Rotation of a small Cavities-mode drawing may be faster in a VRML viewer than in ATOMS, primarily because the viewer saves all the individual polygons comprising the surface in memory, and does not have to calculate them for each view. However, for large drawings storage of all this information may cause the viewer to use virtual memory, which can bring the entire process essentially to a halt.

There are two zeolite structures set up for Cavities mode in the /SAMPLES sub-folder, LINDE_L.STR and ZSM5.STR. Open these files and switch to the Cavities Model mode.

Using stereopairs is usually very helpful in Cavities mode.

The ray-tracing program POV-Ray can be used to make a very smooth-appearing cavities drawing. To do this, select POV-Ray in the File menu and be sure the Spheres box is checked.