Point Group Symmetry

Example application for calculating the symmetry in a molecule file. All specific structures should have corresponding elements in the same position generic structure does. Planes are characterized by the surface normal direction (taken in the direction from the coordinate origin) and distance from the coordinate origin to the plane in the direction of the surface normal. Inversion is characterized by location of the inversion center. Rotation is characterized by a vector (distance+direction) from the origin to the rotation axis, axis direction and rotation order. Rotations are in the clockwise direction looking opposite to the direction of the axis. Note that this definition of the rotation axis is not unique, since an arbitrary multiple of the axis direction can be added to the position vector without changing actual operation. Mirror rotation is defined by the same parameters as normal rotation, but the origin is now unambiguous since it defines the position of the plane associated with the axis.

Options

sh symmetry.sh [maxaxisorder value] [maxoptcycles value] [same value] [primary value] [final value] [minoptstep value] [maxoptstep value] [gradstep value] [minchange value] [minchgcycles value] inputFile

[maxaxisorder value]

Maximum order of rotation axis to look for. Default value: 20

[maxoptcycles value]

Maximum allowed number of cycles in symmetry element optimization. Default value: 200

[same value]

Atoms are colliding if distance falls below this value. Default value: 0.0010

[primary value]

Initial loose criterion for atom equivalence. Default value: 0.05

[final value]

Final criterion for atom equivalence. Default value: 0.05

[minoptstep value]

Termination criterion in symmetry element optimization. Default value: 1.0E-7

[maxoptstep value]

Largest step allowed in symmetry element optimization. Default value: 0.5

[gradstep value]

Finite step used in numeric gradient evaluation. Default value: 1.0E-7

[minchange value]

Minimum allowed change in target methodName. Default value: 1.0E-10

[minchgcycles value]

Number of minchange cycles before optimization stops. Default value: 5

inputFile

Molecul input file.