Modifying a force layout

<!DOCTYPE html>
	<meta charset="utf-8">
	<title>Modifying a force layout v4</title>

<style>

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

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

.node.a { fill: #1f77b4; }
		.node.b { fill: #ff7f0e; }
		.node.c { fill: #2ca02c; }

</style>
	<body>
		<script src="//d3js.org/d3.v4.js"></script>
		<script>

var width = 960,
			height = 500;

var color = d3.scaleOrdinal(d3.schemeCategory10);

var nodes = [],
			links = [];

var simulation = d3.forceSimulation()
			.force("link", d3.forceLink().distance(200).strength(.6))
			.force("charge", d3.forceManyBody())
			// use forceX and forceY instead to change the relative positioning
			// .force("centering", d3.forceCenter(width/2, height/2))
			.force("x", d3.forceX(width/2))
			.force("y", d3.forceY(height/2))
			.on("tick", tick);

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

var a = createNode("a");
			var b = createNode("b");
			var c = createNode("c");

nodes= [a];
			start();

// 1. add the links
			setTimeout(function() {
				nodes= [a,b,c];
				links.push({source: a, target: b}, {source: a, target: c}, {source: b, target: c});
				start();
			}, 1000);

// 2. Remove node B and associated links.
			setTimeout(function() {
				// remove b
				nodes = [a,c];
				// remove a-b
				links = [links[1]];
				start();
			}, 2000);

// Add node B back.
		setTimeout(function() {
			b = createNode("b")
			nodes.push(b);
			links.push({source: a, target: b}, {source: b, target: c});
			start();
		}, 3000);

function createNode(id) {
			return {id: id, x: width/2, y:height/2}
		}

function start() {
			
			var nodeElements = svg.selectAll(".node").data(nodes, function(d){return d.id});
			var linkElements = svg.selectAll(".link").data(links);

nodeElements.enter().append("circle").attr("class", function(d) {return "node " + d.id; }).attr("r", 8);
			linkElements.enter().insert("line", ".node").attr("class", "link");

nodeElements.exit().remove();
			linkElements.exit().remove();

simulation.nodes(nodes)
			simulation.force("link").links(links)
			simulation.restart();
		}

function tick() {
			var nodeElements = svg.selectAll(".node");
			var linkElements = svg.selectAll(".link");

nodeElements.attr("cx", function(d,i) {return d.x; })
			.attr("cy", function(d) { return d.y; })

linkElements.attr("x1", function(d) { return d.source.x; })
			.attr("y1", function(d) { return d.source.y; })
			.attr("x2", function(d) { return d.target.x; })
			.attr("y2", function(d) { return d.target.y; });

}

</script>

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