Using OVITO to determine H2O in a SiO2

OVITO
1

Hello,

I am trying to find a way to count the number of H2O molecules in an SiO2 substrate using OVITOs cluster analysis.

How would I separate H2O molecules from other similar bonds that are being created in the substrate e.g. SiO2, HO2 etc. At the moment cluster analysis only gives the size of the clusters created but I haven’t figured out how to specify the required molecule.

Thanks,
Aanstasis

2

If there are no bonds or molecule identifiers present in your input data, I would suggest using OVITO’s Create Bonds modifier with (an appropriate) pair-wise cutoff set for H-O only, and then use the Cluster Analysis modifier in Neighbor mode: Bonds.

3

Thank you!