There is an attribute avoidOverlap=[0,1] in some physics like BarnesHut http://visjs.org/docs/network/physics.html?#
You can try it here at the bottom under physics http://visjs.org/examples/network/other/configuration.html
like adding this attribute into your physics option
var options = {
... "physics": {
"barnesHut": {
"avoidOverlap": 1
},
}
}