Raw data: building blocks for custom functions

cartesian: vector of atomic Cartesian coordinates.

The cartesian {...} block defines a component returning a flat vector containing the Cartesian coordinates of all participating atoms, in the order $(x_1, y_1, z_1, \cdots, x_n, y_n, z_n)$ .

List of keywords (see also for additional options):

• atoms $\langle\,$ Group of atoms$\,\rangle$
  Context: cartesian
  Acceptable values: Block atoms {...}
  Description: Defines the atoms whose coordinates make up the value of the component. If rotateReference or centerReference are defined, coordinates are evaluated within the moving frame of reference.

distancePairs: set of pairwise distances between two groups.

The distancePairs {...} block defines a $N_{\mathrm{1}}\times{}N_{\mathrm{2}}$ -dimensional variable that includes all mutual distances between the atoms of two groups. This can be useful, for example, to develop a new variable defined over two groups, by using the scriptedFunction feature.

List of keywords (see also for additional options):

• group1: see definition of group1 (distance component)
• group2: analogous to group1
• forceNoPBC: see definition of forceNoPBC (distance component)

This component returns a $N_{\mathrm{1}}\times{}N_{\mathrm{2}}$ -dimensional vector of numbers, each ranging from 0 to the largest possible distance within the chosen boundary conditions.