AddOnSphere (Node)
Add molecules to a box, positioning them on the surface of a sphere
| Context | Generation |
| Name Required? | No |
| Branches | – |
Overview
The AddOnSphere node creates molecule copies of a target species in a box, placing them on the surface of a sphere of specified size. It is therefore useful in the creation of assembled structures such as micelles.
Periodic species cannot be used by this node, nor can
CoordinateSets
.
Description
Aside from the geometric constraints placed on the positioning of the molecules the behaviour of the node is similar to the {{> node “Add” >}}. Options specific to this node are detailed below. Otherwise the behaviour is identical to the
Add
node (see its documentation for explanations of other parameters).
Options
Target
| Keyword | Arguments | Default | Description |
|---|---|---|---|
SpeciesSite |
name |
– | Required Target species to add along with the reference site for positional purposes. Note that the site must be unique in the parent species (i.e. it cannot represent a number of dynamic sites) and if orientation is required it must also have axes defined. |
Radius |
expr |
5.0 |
Radius of the sphere upon which to place molecules. |
Distributions |
PointDistributionStyle |
Fibonacci |
Method of point distribution on the sphere. |
Variance |
expr |
0.0 |
Random variance to apply to generated positions. |
Orient |
bool |
false |
Whether to orient placed molecules along the surface tangent, using a site axis as a reference. |
Axis |
Axis |
X |
Axis to use if orienting site. |