Lines in a ModRedundant input section use the following syntax:
[Type] N1 [N2 [N3 [N4]]] [A | F] [Type] N1 [N2 [N3 [N4]]] B [Type] N1 [N2 [N3 [N4]]] K | R [Type] N1 [N2 [N3 [N4]]] D [Type] N1 [N2 [N3 [N4]]] H diag-elem [Type] N1 [N2 [N3 [N4]]] S nsteps stepsize
N1, N2, N3, and N4 are atom numbers or wildcards (discussed below). Atom numbering begins at 1, and any dummy atoms are not counted.
The atom numbers are followed by a one-character code letter indicating the coordinate modification to be performed; the action code is sometimes followed by additional required parameters as indicated above. If no action code is included, the default action is to add the specified coordinate. These are the available action codes:
A | Activate the coordinate for optimization if it has been frozen. |
F | Freeze the coordinate in the optimization. |
B | Add the coordinate and build all related coordinates. |
K | Remove the coordinate and kill all related coordinates containing this coordinate. |
R | Remove the coordinate from the definition list (but not the related coordinates). |
D | Calculate numerical second derivatives for the row and column of the initial Hessian for this coordinate. |
H | Change the diagonal element for this coordinate in the initial Hessian to diag-elem. |
S | Perform a relaxed potential energy surface scan. Increment the coordinate by stepsize a total of nsteps times, performing an optimization from each resulting starting geometry. |
An asterisk (*) in the place of an atom number indicates a wildcard. Here are some examples of wildcard use:
* | All atoms specified by Cartesian coordinates. |
* * | All defined bonds. |
3 * | All defined bonds with atom 3. |
* * * | All defined valence angles. |
* 4 * | All defined valence angles around atom 4. |
* * * * | All defined dihedral angles. |
* 3 4 * | All defined dihedral angles around the bond connecting atoms 3 and 4. |
By default, the coordinate type is determined from the number of atoms specified: Cartesian coordinates for 1 atom, bond stretch for 2 atoms, valence angle for 3 atoms, and dihedral angle for 4 atoms. Optionally, type can be used to designate these and additional coordinate types:
X | Cartesian coordinates. |
B | Bond length. |
A | Valence angle. |
D | Dihedral angle. |
L | Linear bend specified by three atoms (if N4 is -1) or by four atoms, where the fourth atom is used to determine the 2 orthogonal directions of the linear bend. |