Set here the atomic structure to include, and the coordination
neighbour atoms, for each coordination polytope.
Structure
It is often useful to recreate in a group the atomic
structure existing in the parent object. For each coordination
polyhedron, this includes all the atoms defining the polyhedron
vertices, plus the central atom.
When
Structure is set to
Copy, atoms
are copied to the groups just created.
When
Structure is set to
Link, atoms
are linked to the groups just created.
When
Structure is set to
None, atoms
are ignored.
Filter
After collecting a list of atoms close enough to the group,
a filtering condition may be applied. This can be very useful
to avoid atom superposition, resulting for example from atoms
copied before to different groups.
When
Filter is set to
Class,
atoms belonging to another groups are ignored.
When
Filter is set to
Child, atoms not
belonging directly to the group parent are ignored.
When
Filter is set to
Identical, atoms
closer than a given distance (currently
1.0E-2,
as defined in
GAMGI_MATH_TOLERANCE_STRUCTURE) to
a previous atom are ignored.
When
Filter is set to
None, no filtering
condition is applied.
Visible
When the mix product of four vertices (defining a face and a new vertex),
is larger than
Visible the face is visible from the vertex and
must be replaced. Increasing
Visible may reduce face reconstruction,
but may result in numerical inaccuracies. The whole calculation is very
sensitive to this parameter, so it should be handled carefully. Currently
the maximum allowed value is
1.0E-5.
For complex systems, where different faces have almost the same orientation,
forming curved surfaces, setting
Visible to
0 might eliminate
numerical errors.
Coplanar
The initial triangle faces are merged when the mix product
of four vertices (belonging to both faces) is smaller than
Coplanar. Increasing
Coplanar promotes face merging,
but may result in numerical inaccuracies. Currently the maximum
allowed value is
1.0E-1.
Setting
Coplanar to
0 disables face merging,
so all faces will be triangles.
Neighbours
Set here the neighbour atoms that should be considered around each central atom.
The sampling universe is always the object currently selected. When the
central atom does not belong to the current object, an error is shown.
Element defines the atomic element of the neighbours that should
be considered. When
Element is empty (the default), all atomic
elements will be considered.
Users can set the number of closest neighbours that should be considered
using
Number, or the radius of the sphere around the central
atom that should be sampled, using
Radius. When these are empty
(the default), all atoms in the sampling universe will be considered.