Molecule setup

For unary mixtures, the syntax is
[number of sites in rigid body]

class [interaction class] site [x] [y] [z] orient [px] [py] [pz]
class [interaction class] site [x] [y] [z] orient [px] [py] [pz]
where [x] is the $ x$-coordinates of the site in the molecule frame and [px] is the $ x$-component of the angle-axis rotation $ \vec{p}$ in the molecule frame. For sites with only isotropic interactions, the input for $ \vec{p}$ is ignored. For best performance, place the molecule's sites such that the origin corresponds with the molecule's center of mass.

For $ n$-ary mixtures, the syntax is

n-ary
[arity]

[number fraction of this species] [optional atom symbol]
[number of sites in this rigid body]
[normal site lines]

[number fraction of this species]
[number of sites in this rigid body]
[normal site lines]
The optional atom symbol will cause atoms of different species to have different atom symbols in the output xyz file. Default is `O'.



David Wales 2017-09-21