Select here the parameters to measure the point symmetry.
Periodicity
When the
No option is chosen (the default), all elements
of symmetry are taken into account, and the chemical
point group is determined. When the
Yes option
is chosen, all elements of symmetry related with rotations
of order different from 6, 4, 3, 2 are ignored. The reported
crystallographic point group is thus the maximum point symmetry
that could be achieved in the center of this aggregate, if it
was in a periodic crystal.
For example, a C5v chemical group becomes a Cs crystallographic
point group because after discarding the C5 axis, only one
of the five mirror planes can be considered as a true element
of symmetry in a periodic system. A chemical Ih becomes a Th
crystallographic group, because after discarding the C5 axes,
the remaining planes and axes form five different sets of cubic
Th symmetry, although only one can be considered at a time.
Everytime the chemical group is found, the crystallographic
group can also be determined. Usually this crystallographic group
is not unique. For example, a D12h chemical group can be either
a D4h or a D6h crystallographic group. GAMGI shows the
various crystallographic groups that cover all the possible
operations of symmetry, in sequence, with their symmetry
operations and symmetry elements. In particular, chemical C0v
becomes C4v or C6v, chemical D0h becomes D4h or D6h and chemical
Kh becomes D4h or D6h or Oh crystallographic groups respectively.
Tolerance
The elements of symmetry of a molecule depend entirely of the
tolerance applied to the operations of symmetry. GAMGI uses
the same tolerance for all operations: the maximum distance
that is tolerated between initial and transformed coordinates.
GAMGI tries to find all the symmetry elements independently,
and in general each of these elements requires a different
tolerance. Thus, for a given tolerance, some elements
may be recognized and others may go missing, resulting in
an inconsistent set of symmetry elements. When this happens,
the group is reported
Undefined. The solution is to
increase the tolerance (so valid elements might be found)
or to decrease it (so fake elements might be discarded).
When the transformed coordinates for a given symmetry element
are closer than the
Initial tolerance, GAMGI attempts
to optimize the symmetry element, to get transformed coordinates
closer than the
Final tolerance. When the transformed
coordinates do not pass the
Initial tolerance or when
the optimization fails, the attempted element is discarded.
When the transformed coordinates pass the
Final tolerance,
the element is accepted.
During optimization, GAMGI will never attempt to change the atoms,
only the symmetry elements. To disable optimization, just set
Initial equal to
Final tolerance.