Molecule

This is a quick hack to draw two parallel links between nodes. Yes, you can scale it to more than two nodes, but it gets increasingly awkward. The alternative is to compute the paths manually, say by computing the perpendicular vector of the vector between the node centers, and offsetting the links accordingly.

<!DOCTYPE html>
<meta charset="utf-8">
<style>

.link line {
  stroke: #696969;
}

.link line.separator {
  stroke: #fff;
  stroke-width: 2px;
}

.node circle {
  stroke: #000;
  stroke-width: 1.5px;
}

.node text {
  font: 10px sans-serif;
  pointer-events: none;
}

</style>
<body>
<script src="//d3js.org/d3.v3.min.js"></script>
<script>

var width = 960,
    height = 500;

var color = d3.scale.category20();

var radius = d3.scale.sqrt()
    .range([0, 6]);

var svg = d3.select("body").append("svg")
    .attr("width", width)
    .attr("height", height);

var force = d3.layout.force()
    .size([width, height])
    .charge(-400)
    .linkDistance(function(d) { return radius(d.source.size) + radius(d.target.size) + 20; });

d3.json("graph.json", function(error, graph) {
  if (error) throw error;

force
      .nodes(graph.nodes)
      .links(graph.links)
      .on("tick", tick)
      .start();

var link = svg.selectAll(".link")
      .data(graph.links)
    .enter().append("g")
      .attr("class", "link");

link.append("line")
      .style("stroke-width", function(d) { return (d.bond * 2 - 1) * 2 + "px"; });

link.filter(function(d) { return d.bond > 1; }).append("line")
      .attr("class", "separator");

var node = svg.selectAll(".node")
      .data(graph.nodes)
    .enter().append("g")
      .attr("class", "node")
      .call(force.drag);

node.append("circle")
      .attr("r", function(d) { return radius(d.size); })
      .style("fill", function(d) { return color(d.atom); });

node.append("text")
      .attr("dy", ".35em")
      .attr("text-anchor", "middle")
      .text(function(d) { return d.atom; });

node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
  }
});
</script>

https://d3js.org/d3.v3.min.js