Force Directed Graph with minimal animation-in

HTML

<script src="http://d3js.org/d3.v3.min.js"></script>
<div id="theVizness"></div>

CSS

body { height: 800px; }

#theVizness{
    position: relative;
    width: 50%;
    height: 50%;
    border: 1px solid black;
}
.file {
    stroke: #fff;
    stroke-width: 2px;
}

.link {
    stroke: #999;
    stroke-opacity: .6;
}
.loading {
    font-size: 18px;
    font-family: Arial;
}

JavaScript

var width = $("#theVizness").width(),
    height = $("#theVizness").height();

var color = d3.scale.ordinal().range(["#ff0000", "#fff000", "#ff4900"]);

var force = d3.layout.force()
    .charge(-120)
    .linkDistance(30)
    .size([width, height]);

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

var loading = svg.append("text")
    .attr("class", "loading")
    .attr("x", width / 2)
    .attr("y", height / 2)
    .attr("dy", ".35em")
    .style("text-anchor", "middle")
    .text("Loading...");

d3.json("https://dl.dropboxusercontent.com/u/5772230/ForceDirectData.json", function (error, json) {
    var nodes = json.nodes;
    
    nodes[0].fixed = true;
    nodes[0].x = width / 2;
    nodes[0].y = height / 2;
    
    force.nodes(nodes)
        .links(json.links)
        .charge(function(d){
            var charge = -500;
            if (d.index === 0) charge = 10 * charge;
            return charge;
        });
    
    var link = svg.selectAll(".link")
        .data(json.links)
        .enter().append("line")
        .attr("class", "link")              
        .style("stroke-width", 1);
    
        var files = svg.selectAll(".file")
        .data(json.nodes)
        .enter().append("circle")
        .attr("class", "file")
        .attr("r", 10)
        .attr("fill", function (d) {
            return color(d.colorGroup);
        });
    var totalNodes = files[0].length;
    
    files.append("title")
        .text(function (d) { return d.name; });
    
    force.start();
    for (var i = totalNodes * totalNodes; i > 0; --i) force.tick();
    
    link.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; });
    
    files.attr("cx", function (d) { return d.x; })
        .attr("cy", function (d) { return d.y; })
        .attr("class",...