GAMGI Interfaces: Group Create

# Group Create

- Type
- Scope
- View

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.
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