Site Block

Overview

The Site block defines a named analysis site on a Species that can later be referenced in one of the analysis modules.

Site blocks must always be defined within the Species to which they relate. Multiple Site blocks can be defined within a single Species.

Keywords

Example

Methanol

Given the species atoms as:

Species 'Methanol'
  # Atoms
  Atom    1    C  3.413690e-01  1.199640e-01  -4.430163e-02  'CT'  1.450000e-01
  Atom    2    O  -9.265791e-01  -3.425229e-01  -4.577432e-01  'OH'  -6.830000e-01
  Atom    3    H  -1.468049e+00  -4.997640e-01  3.024601e-01  'HO'  4.180000e-01
  Atom    4    H  2.750356e-01  1.114836e+00  3.749080e-01  'HC'  4.000000e-02
  Atom    5    H  1.027597e+00  1.519417e-01  -8.758279e-01  'HC'  4.000000e-02
  Atom    6    H  7.506264e-01  -5.444546e-01  7.005046e-01  'HC'  4.000000e-02

  ...
EndSpecies

We could define the following sites:

Hydroxyl Proton

Centered on the alcohol proton, with no defined axes.

Site  'C(OH)'
  Origin  3
EndSite

Centre of Methyl Group

Origin located at the geometric centre of the three methyl hydrogens.

Site  'C(OH)'
  Origin  4 5 6
EndSite

Hydroxyl Oxygen (with axes)

Centred on the oxygen, and using the carbon to define the absolute direction of the x-axis, and the alcohol proton to define the implied direction of the y-axis.

Site  'C(OH)'
  Origin  2
  XAxis  1
  YAxis  3
EndSite