Select (Node)

Select a list of pre-defined sites on molecules

Overview

The Select node assembles a list of sites from a species, and which can then be iterated over and reference by other nodes (e.g. the Calculate* nodes).

Description

The Select node assembles a list of coordinates (and axes, if present) for one or more defined sites. The mechanism of selection can be controlled to provide exclusions with other sites (e.g. based on the parent molecule containing the site) or select only sites within a given distance of another reference point. Iteration over the sites is performed via the ForEach branch.

When nesting Select nodes in analysis routines, the selection of sites can be carefully controlled in order to avoid unwanted groups of selected nodes. For instance, the SameMoleculeAsSite keyword allows another Select node to be reference, and which will force the current Select node to only select a site if it is present in the same molecule as the other site.

Branching

The hidden ForEach keyword / branch is executed for each site selected by the node, and may contain any other analysis-style nodes, including other Select nodes.

Available Parameters

The following parameters are exported by the node:

Parameter	Description
`nSelected`	The number of sites currently selected by the node
`index`	The index of the current site in the ForEach loop. Note that this index is just the “local” index for the loop, and does not have any relation to the indices of the sites per se.
`stackIndex`	The “stack” index of the current site in the ForEach loop. This reflects the ordering of the sites as they are calculated from the configuration and so are tied to the atom indexing.
`siteIndex`	The “global stack” index of the current site over all possible sites targeted by the selection.

Thus, if there are N sites of a given type, the index for a given site will change based on how many of the N are selected according to other criteria (i.e. within a certain distance, not on the same molecule etc.) while a given site’s stackIndex will remain the same regardless of how many are selected, provided N does not change (i.e. the population of molecules in the Configuration is static).

Similarly, the siteIndex remains constant for a given site regardless of how many species sites are requested for selection. So, if three sites are provided having N, M, and O sites respectively, then the siteIndex number goes from 1...(N+M+O), with sites from N always being numbered 1...N, sites from M being numbered N+1...N+M, and sites from O being numbered N+M+1...N+M+O.

Options

Sites

Keyword	Arguments	Default	Description
`Site`	`name` `[name...]`	–	A list of named sites to select.

Control

Keyword	Arguments	Default	Description
`SameMoleculeAsSite`	`name`	–	Request that selected sites come from the molecule containing the current site in the named `Select` node.
`ExcludeSameMolecule`	`name` `[name...]`	–	Exclude sites from the selection if they are present in the same molecule as the current site in any of the named `SelectNode`s.
`ExcludeSameSite`	`name` `[name...]`	–	Exclude sites from the selection if they are the current site in any of the named `SelectNode`s.
`ReferenceSite`	Select	–	Site from the named `Select` node to be used as a reference point when determining inclusions / exclusions.
`InclusiveRange`	`min` `max`	–	Distance range from `ReferenceSite` within which sites are selected.

Last modified November 27, 2024: docs: Updated for 1.6 release (#2000) (8cbaf4e5f)