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...");

/*
ForceDirectData.json
{
    "nodes":[
      {"name":"File1.exe","colorGroup":0},
      {"name":"File2.exe","colorGroup":0},
      {"name":"File3.exe","colorGroup":0},
      {"name":"File4.exe","colorGroup":0},
      {"name":"File5.exe","colorGroup":0},
      {"name":"File6.exe","colorGroup":0},
      {"name":"File7.exe","colorGroup":0},
      {"name":"File8.exe","colorGroup":0},
      {"name":"File8.exe","colorGroup":0},
      {"name":"File9.exe","colorGroup":0}
    ],
    "links":[
      {"source":1,"target":0,"value":10},
      {"source":2,"target":0,"value":35},
      {"source":3,"target":0,"value":50},
      {"source":4,"target":0,"value":50},
      {"source":5,"target":0,"value":65},
      {"source":6,"target":0,"value":65},
      {"source":7,"target":0,"value":81},
      {"source":8,"target":0,"value":98},
      {"source":9,"target":0,"value":100}
    ]
}
*/

d3.json("https://dl.dropboxusercontent.com/u/5772230/ForceDirectData.json", function (error, json) {
    var nodes = json.nodes;
    force.nodes(nodes)
        .links(json.links)
        .linkDistance(function (d) {
            return d.value * 1.5;
        })
        .charge(function(d){
            var charge = -500;
            
            if (d.index === 0) charge = 0;
            
            return charge;
        })
        .friction(0.4);
    
    var link = svg.selectAll(".link")
        .data(json.links)
        .enter().append("line")
    ...