Boundary - Slice
Previous  Top  Next

Dialog Box - called from: Boundary Dialog

This dialog may apply either to individual atoms, or to molecules (in which case the dialog title will be Slice - Molecules ). In the latter case, bonded groups in the unit cell will be identified and the center of each taken as the non-weighted average of atomic positions. Then the boundaries will be determined with respect to the molecular centers.

This gives a section of a crystal structure parallel to a given face, with the thickness of the X-ray d-spacing, or a multiple thereof. Such a "slice" is intended primarily to represent a growth layer, but is often useful for illustrating special structural features.

In addition to the indices of the face, you need to specify several other things. An Alignment vector is also necessary - when the calculation is complete, the slice will be lying in the plane of the screen or paper and this vector will be vertical (parallel to z). The vector must lie in the slice: a vector [uvw] lying in a face (hkl) satisfies the condition hu+ kv + lw = 0. If the default alignment vector is chosen, the alignment vector will be taken as the intersection of the face (hkl) with the face (100), whose indices are given by the vector cross product (hkl)x(100). If the slice face (hkl) is (100), the alignment vector will be taken as its intersection with (010), which is the vector [001].

You must also specify the Height and Width of the slice, parallel and perpendicular to the alignment vector.

The location of the slice within the crystal structure must also be specified in terms of the Offset from the origin. One can specify different offsets, or boundary locations, for each atom (set of symmetry equivalent atoms) in case the slice is not considered to be strictly planar (see below). The Thickness of the slice is a fraction of the d-spacing: in most cases it should be 1.0.

Atoms lying exactly on the "upper" boundary - (the face to which the slice is defined to be parallel) are excluded from the slice, whereas atoms lying exactly on the "lower" boundary (the face with indices negative to the "upper" face) are included.

The Use individual atom offsets checkbox allows the boundary surface to be non-planar with respect to the centers of the atoms. If you use this option, you should revise the offsets for the forms during atom input - the overall offset entered in this section sets the default values. It is also used as the default for display of edges of the slice (the display forms can be changed in the Crystal Forms for Display dialog), and to determine preliminary unit-cell search limits for atoms during the calculation; thus this overall offset and the offsets for individual atoms should not differ too much.
Systematic absences can be used to take account of d-spacings which are a submultiple of those obtained solely from the cell parameters because of non-primitive lattices, screw axes or glide planes. The subdivision of the central distance for each form is done when the d-spacing is calculated, after OK is clicked; to see the d-spacing values you must re-select the dialog. You cannot manually edit or add absences as in pre-V4.0 ATOMS. The Custom symmetry option does not contain information on systematic absences - if you want to use systematic absences, you should switch to the Space Group symmetry option.

slice