Dialog Box - called from: Transform Menu
This option will expand a crystal structure on certain planes, increasing the length of the selected axis, creating space near the expansion planes, but leaving the actual structure within layers unchanged.. It operates on input atoms, leaving the symmetry unchanged.
Any atoms which are exactly on the expansion planes (for example K atoms in a mica structure) will remain on the expansion planes, and thus bonds from these atoms to other parts of the structure will be lengthened. Bonds connecting structural layers (that is, any bonds crossing the expansion planes) will also be lengthened.
The Expansion factor is the amount by which the selected axis is increased. For example, if the c-axis is 10.0 Angstroms before conversion, an expansion factor of 1.5 will change it to 15.0 Angstroms.
Expand on axis. This selects the axis to be lengthened. Fractional coordinates of most atoms on this axis will be changed. The other two axes, and fractional coordinates on these axes, will be unchanged. Thus the structure will be expanded on the principal plane or unit-cell face which cuts the chosen axis - this plane is not always perpendicular to the axis. For example if the chosen axis is c, the expansion is on the (001) plane.
Number of planes. There are often several symmetrically identical planes cutting the selected axis. For example, there may be identical mirror planes at 0.0 and 0.5. You must determine this number from examination of the space-group symmetry.
Expand at zero. There may be a choice of location of the expansion planes. Normally this will be a choice between the set of planes at fractional coordinate zero (on the expanded axis) and another set at some rational fractions. For example, if the Number of planes is 2, there may be a set at 0.0 and 0.5 and another at 0.25 and 0.75. If the Expand at zero box is checked, the expansion will be at the first set.
At the moment an arbitrary location of the expansion plane is not supported, and for low-symmetry crystals, or those which have a choice of more than two locations, it may be necessary to adjust all coordinates so that the expansion plane is at zero. If this situation is common, support for arbitrary location will be added. Support for expansion planes other than unit-cell faces could also be added if necessary.
Tolerance. This is used to decide if an atom is exactly on the expansion plane, in which case its coordinate on the expansion axis will not be changed - that is, it will remain exactly on this plane. Tolerance is in fractional coordinate units (not Angstroms). If you want atoms which are exactly on the expansion plane to remain in continuity with the remainder of the structure, their fractional coordinates on the expansion axis should be changed by greater than the tolerance. Usually this will result in duplication of the atoms.