QuantumATK Forum

NanoLab => Plugin Development => Topic started by: Anders Blom on June 23, 2015, 22:29

Title: Make more bonds
Post by: Anders Blom 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).
Title: Re: Make more bonds
Post by: ams_nanolab on June 25, 2015, 10:33
Thanks ... very useful utility  :)
Title: Re: Make more bonds
Post by: orhan on February 22, 2021, 03:45
Hello Anders,

I tried to install your plugin- fuzz factor, but it gives some error. Do you have an updated version of this plugin?
Title: Re: Make more bonds
Post by: mlee on February 22, 2021, 11:22
Recent version doesn't need to install additional plug-in. You can see the Fuzz factor in Graphics properties of builder.
Title: Re: Make more bonds
Post by: orhan on February 27, 2021, 03:34
Awesome. Thanks a lot. :)