Author Topic: Make more bonds  (Read 2051 times)

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Offline Anders Blom

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Make more bonds
« on: June 23, 2015, 22:29 »
VNL will by default only display bonds between atoms which are within a particular distance from each other, quite specifically their joint covalent radius +10% or closer. This means that if you stretch a structure a bit, the bonds may disappear. Now, since ATK 2015 and earlier (things will change in version 2016, when we add bonded force fields) doesn't use the bonds for anything in the calculations (only the actual distance between atoms are used), this has no influence on any computed results - only your pictures.

But, sometimes it's nice to see bonds anyway. So, I made a plugin that lets you adjust the "fuzz factor", i.e. the 10% mentioned above. So now you can set it to 20% if you want also atoms that are farther apart to appear bonded, or a lower value if you have too many bonds (it can happen also). The plugin works both in the Viewer and Builder and requires ATK 2014 or newer.

To install it, open the AddOn Manager, click Local install to install the zip file, then restart VNL. The new tool will appear as "Bond control" in the right-hand side plugin panel (under "Select" in the Builder). The value you can specify is 1+the fuzz factor (default 0.10).

See screenshots! The molecule obviously doesn't need a fuzz factor of 1, but illustrates the concept. The Tausonite crystal (SrTiO3 cubic, taken from the built-in database) looks a lot better with fuzz factor 0.04 (try the default value 1.1 in the plugin and you will see).

Offline ams_nanolab

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Re: Make more bonds
« Reply #1 on: June 25, 2015, 10:33 »
Thanks ... very useful utility  :)
« Last Edit: June 25, 2015, 10:42 by ams_nanolab »