PoreCapsule.
roughness
(self)¶Calculate surface roughness. In the case of a capsule pore one can visualize pulling the cylindric section pore apart, thus flattening the interior surface. The roughness is then determined by calculating the standard deviation of the binding site silicon atoms peaks and valleys.
It is therefore enough to calculate the distances towards a specific axis, which in this case will be the central axis. The mean value \(\bar r\) of the silicon distances \(r_i\) of silicon \(i\) towards the pore center, is calculated by
with the number of silicon atoms \(n\). Hereby only the silicon atoms within the cyldirc part are considered. This mean value is used in the square root roughness calculation
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