Psi (Bond-Plane) Angle Force List
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Dialog Box: Psi (Bond-Plane) Angle Force List [Forces menu]

This is for "automatic" psi bond-plane angle location - VIBRATZ searches the structure for psi angles using the specified atom types (usually atomic numbers) and distance and angle limits. For "manual" psi angle location, using sequence numbers of specific generated atoms, or by point-and-click, see Manual Psi.

The upper list gives the current 4-atom psi (bond-plane) angle forces. The data for each one is in a single line in the scrolling list or spreadsheet. To add a new entry, press the down arrow key while the focus is on the last row, or click the Add button. The lower list gives the specifications for each force constant in terms of atom types - an unlimited number of specifications is allowed (there must be at least one).

No. This is the number in the angle list.

Fcon This is the number in the overall force constant list.

Force. Note that angle forces may be specified in either in md-A or in md/A. This choice is made in the Control window or the Basic Parameters dialog (Settings menu).

Nspc. Number of atom type specifications for this angle (lower list).

Lst Sq. If this box is checked, this force constant will be included in least-squares refinement.

Dmax12/Dmax23/Dmax34. These are the maximum bond distances for each of the three legs.

PsiMin/Psimax. Minimum and maximum values for the psi angle. The psi angle itself is the complement of the angle between bond vector 1-2 and the perpendicular to the plane 2-3-4. The angle is zero if all four atoms lie in a plane. Psi angles assume the following sign convention. Viewing the plane defined by atoms 2, 3 and 4 down the 3-4 vector (atom 3 nearest), the psi angle is positive if the projection of the 2-1 vector is traced in a clockwise direction from the extension of the 2-3-4 plane. However, if atoms 3 and 4 are the same type or chemical species, it would be a matter of chance which one is taken first, and therefore whether the psi angle is positive or negative. Thus if the psi angle is other than zero it is taken to be positive and the number 3 and 4 atoms are switched if necessary to be consistent with this choice. The displacement or s-vectors have direction such as to increase the value of the psi angle. If the psi angle is zero, the s-vector of the central or number 2 atom is given direction (sign) so that its z-component is positive; or if z is near zero, so that the x-component is positive; or if the s-vector is nearly parallel to y, so that the y-component is positive.

For these reasons, negative values for the angle limits have no meaning. Angle limit values of zero will skip angle tests..
One only. If this box is checked, one one psi coordinate will be located for each central atom (atom 2). This should be used for a configuration such as CO3, for example. In this case, assuming all the O atoms are equivalent and are the same type, three psi coordinates will be located if this box is not checked. Indeed, occasions when more than one psi coordinate is needed for a given central atom must be rare, if they exist at all.

Once specifications have been entered, the force-constant values and least-squares flags may be changed in the overall Forces List, accessible from the Control Window.