Site Block
Specifies a reference site on a species for use by calculation / analysis routines
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
| Keyword | Arguments | Default | Description |
|---|---|---|---|
EndSite |
int |
– | Indicates the end of the current Site block. |
Origin |
int[int...] |
– | Define the origin of the site to be the geometric mean of the coordinates of the atom(s) with the indices provided. |
OriginMassWeighted |
int[int...] |
– | Define the origin of the site to be the mass-weighted average of the coordinates of the atom(s) with the indices provided. |
XAxis |
int[int...] |
– | Define the reference point indicating the x-axis of the site to be the geometric mean of the coordinates of the atom(s) with the indices provided. |
YAxis |
int[int...] |
– | Define the reference point indicating the y-axis of the site to be the geometric mean of the coordinates of the atom(s) with the indices provided. |
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