Clustered Force Layout 4.0

<!doctype html>
<meta charset="utf-8">
<body>
<script src="//d3js.org/d3.v4.min.js"></script>
<script>

let margin = {top: 100, right: 100, bottom: 100, left: 100};

let width = 960,
    height = 500,
    padding = 1.5, // separation between same-color circles
    clusterPadding = 6, // separation between different-color circles
    maxRadius = 12;
    
let n = 200, // total number of nodes
    m = 10, // number of distinct clusters
    z = d3.scaleOrdinal(d3.schemeCategory20),
    clusters = new Array(m);

let svg = d3.select('body')
    .append('svg')
    .attr('height', height)
    .attr('width', width)
    .append('g').attr('transform', 'translate(' + width / 2 + ',' + height / 2 + ')');

let nodes = d3.range(200).map(() => {
    let i = Math.floor(Math.random() * m),
        radius = Math.sqrt((i + 1) / m * -Math.log(Math.random())) * maxRadius,
        d = {cluster: i, r: radius};
    if (!clusters[i] || (radius > clusters[i].r)) clusters[i] = d;
    return d;
});

let circles = svg.append('g')
      .datum(nodes)
    .selectAll('.circle')
      .data(d => d)
    .enter().append('circle')
      .attr('r', (d) => d.r)
      .attr('fill', (d) => z(d.cluster))
      .attr('stroke', 'black')
      .attr('stroke-width', 1);

let simulation = d3.forceSimulation(nodes)
    .velocityDecay(0.2)
    .force("x", d3.forceX().strength(.0005))
    .force("y", d3.forceY().strength(.0005))
    .force("collide", collide)
    .force("cluster", clustering)
    .on("tick", ticked);

function ticked() {
    circles
        .attr('cx', (d) => d.x)
        .attr('cy', (d) => d.y);
}

// These are implementations of the custom forces.
function clustering(alpha) {
    nodes.forEach(function(d) {
      var cluster = clusters[d.cluster];
      if (cluster === d) return;
      var x = d.x - cluster.x,
          y = d.y - cluster.y,
          l = Math.sqrt(x * x + y * y),
          r = d.r + cluster.r;
      if (l !== r) {
        l = (l - r) / l * alpha;
        d.x -= x *= l;
        d.y -= y *= l;
        cluster.x += x;
        cluster.y += y;
      }  
    });
}

function collide(alpha) {
  var quadtree = d3.quadtree()
      .x((d) => d.x)
      .y((d) => d.y)
      .addAll(nodes);

nodes.forEach(function(d) {
    var r = d.r + maxRadius + Math.max(padding, clusterPadding),
        nx1 = d.x - r,
        nx2 = d.x + r,
        ny1 = d.y - r,
        ny2 = d.y + r;
    quadtree.visit(function(quad, x1, y1, x2, y2) {

if (quad.data && (quad.data !== d)) {
        var x = d.x - quad.data.x,
            y = d.y - quad.data.y,
            l = Math.sqrt(x * x + y * y),
            r = d.r + quad.data.r + (d.cluster === quad.data.cluster ? padding : clusterPadding);
        if (l < r) {
          l = (l - r) / l * alpha;
          d.x -= x *= l;
          d.y -= y *= l;
          quad.data.x += x;
          quad.data.y += y;
        }
      }
      return x1 > nx2 || x2 < nx1 || y1 > ny2 || y2 < ny1;
    });
  });
}
</script>

https://d3js.org/d3.v4.min.js