By default redundant internal coordinates are generated for use in geometry optimizations. Connectivity is inferred by comparing inter-atomic distances with the sum of the van der Waals radii of the two atoms involved in a possible bond, times a scaling factor. The scaling factor is an input parameter of ZCOORD which maybe changed from its default value of 1.3. Under some circumstances (unusual bonding, bond dissociation, ...) it will be necessary to augment the automatically generated list of internal coordinates to force some specific internal coordinates to be included in among the internal coordinates. This is accomplished by including the optional directive ZCOORD within the geometry directive. The general form of the ZCOORD directive is as follows:
ZCOORD
CVR_SCALING <real value>
BOND <integer i> <integer j> \
[<real value>] [<string name>] [constant]
ANGLE <integer i> <integer j> <integer k> \
[<real value>] [<string name>] [constant]`
TORSION <integer i> <integer j> <integer k> <integer l> \
[<real value>] [<string name>] [constant]
END
The centers i, j, k and l must be specified using the numbers of the
centers, as supplied in the input for the Cartesian coordinates. The
ZCOORD input parameters are defined as follows:
cvr_scaling-- scaling factor applied to van der Waals radii.bond-- a bond between the two centers.angle-- an angle among the three atoms i, j and k.torsion-- a torsion (or dihedral) angle. The angle between the planes i-j-k and j-k-l.
A value may be specified for a user-defined internal coordinate, in which case it is forced upon the input Cartesian coordinates while attempting to make only small changes in the other internal coordinates. If no value is provided the value implicit in the input coordinates is kept. If the keyword constant is specified, then that internal variable is not modified during a geometry optimization with DRIVER. Each internal coordinate may also be named either for easy identification in the output, or for the application of constraints (Applying constraints in geometry optimizations).
If the keyword adjust is specified on the main GEOMETRY directive, only ZCOORD data may be specified and it can be used to change the user-defined internal coordinates, including adding/removing constraints and changing their values.
Internal coordinates specified as constant in a ZCOORD directive or in the constants section of a ZMATRIX directive, will be frozen at their initial values if a geometry optimization is performed with DRIVER (Section 20).
If internal coordinates have the same name (give or take an optional sign for torsions) then they are forced to have the same value. This may be used to force bonds or angles to be equal even if they are not related by symmetry.
When atoms have been specified by their Cartesian coordinates, and internal coordinates are not being used, it is possible to freeze the cartesian position of selected atoms. This is useful for such purposes as optimizing a molecule absorbed on the surface of a cluster with fixed geometry. Only the gradients associated with the active atoms are computed. This can result in a big computational saving, since gradients associated with frozen atoms are forced to zero (Note, however, that this destroys the translational and rotational invariance of the gradient. This is not yet fully accommodated by the STEPPER geometry optimization software, and can sometimes result in slower convergence of the optimization. The DRIVER optimization package does not suffer from this problem).
The SET directive is used to freeze atoms, by specifying a directive of the form:
set geometry:actlist <integer list_of_center_numbers>
This defines only the centers in the list as active. All other centers will have zero force assigned to them, and will remain frozen at their starting coordinates during a geometry optimization.
For example, the following directive specifies that atoms numbered 1, 5, 6, 7, 8, and 15 are active and all other atoms are frozen:
set geometry:actlist 1 5:8 15
or equivalently,
set geometry:actlist 1 5 6 7 8 15
If this option is not specified by entering a SET directive, the default behavior in the code is to treat all atoms as active. To revert to this default behavior after the option to define frozen atoms has been invoked, the UNSET directive must be used. The form of the UNSET directive is as follows:
unset geometry:actlist
The following example will impose a constraint on the K-O bond with a length of three angstroms.
geometry
K 0. 0.0000 0.0000
O 0. 0.0000 3.2000
H 0. -0.7644 3.8162
H 0. 0.7644 3.8162
end
geometry adjust
zcoord
bond 1 2 3. ko constant
end
end