Faster Force-Directed Graphs with d3-force-reuse

.block

license: gpl-3.0
height: 600

README.md

A simple example showing how to use d3-force-reuse. This library provides d3.forceManyBodyReuse(), which is a faster replacement for d3.forceManyBody() included in d3-force. d3-force-reuse achieves this performance improvement by reusing Barnes-Hut approximations instead of calculating a new one at each tick of the algorithm. See d3-force-reuse and the research paper for more details:

Robert Gove. "It Pays to Be Lazy: Reusing Force Approximations to Compute Better Graph Layouts Faster." Proceedings of Forum Media Technology, 2018. Preprint PDF.

Forked from Mike Bostock's force-directed layout example.

d3-force-reuse.js

// Copyright 2018 Two Six Labs, LLC. v1.0.0 d3-force-reuse https://github.com/twosixlabs/d3-force-reuse/
(function (global, factory) {
	typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports, require('d3-quadtree')) :
	typeof define === 'function' && define.amd ? define(['exports', 'd3-quadtree'], factory) :
	(factory((global.d3 = global.d3 || {}),global.d3));
}(this, (function (exports,d3Quadtree) { 'use strict';

var constant = function(x) {
  return function() {
    return x;
  };
};

var manyBodyReuse = function() {
  var nodes,
      node,
      alpha,
      iter = 0,
      tree,
      updateClosure,
      updateBH,
      strength = constant(-30),
      strengths,
      distanceMin2 = 1,
      distanceMax2 = Infinity,
      theta2 = 0.81;

  function jiggle() {
    return (Math.random() - 0.5) * 1e-6;
  }

  function x(d) {
    return d.x;
  }

  function y(d) {
    return d.y;
  }

  updateClosure = function () {
    return function (i) {
      if (i % 13 === 0) {
        return true;
      } else {
        return false;
      }
    };
  };

  function force(_) {
    var i, n = nodes.length;
    if (!tree || updateBH(iter, nodes)) {
      tree = d3Quadtree.quadtree(nodes, x, y).visitAfter(accumulate);
      nodes.update.push(iter);
    }
    for (alpha = _, i = 0; i < n; ++i) node = nodes[i], tree.visit(apply);
    ++iter;
  }

  function initialize() {
    if (!nodes) return;
    iter = 0;
    nodes.update = [];
    updateBH = updateClosure();
    tree = null;
    var i, n = nodes.length, node;
    strengths = new Array(n);
    for (i = 0; i < n; ++i) node = nodes[i], strengths[node.index] = +strength(node, i, nodes);
  }

  function accumulate(quad) {
    var strength = 0, q, c, weight = 0, x, y, i;

    // For internal nodes, accumulate forces from child quadrants.
    if (quad.length) {
      for (x = y = i = 0; i < 4; ++i) {
        if ((q = quad[i]) && (c = Math.abs(q.value))) {
          strength += q.value, weight += c, x += c * q.x, y += c * q.y;
        }
      }
      quad.x = x / weight;
      quad.y = y / weight;
    }

    // For leaf nodes, accumulate forces from coincident quadrants.
    else {
      q = quad;
      q.x = q.data.x;
      q.y = q.data.y;
      do strength += strengths[q.data.index];
      while (q = q.next);
    }

    quad.value = strength;
  }

  function apply(quad, x1, _, x2) {
    if (!quad.value) return true;

    var x = quad.x - node.x,
        y = quad.y - node.y,
        w = x2 - x1,
        l = x * x + y * y;

    // Apply the Barnes-Hut approximation if possible.
    // Limit forces for very close nodes; randomize direction if coincident.
    if (w * w / theta2 < l) {
      if (l < distanceMax2) {
        if (x === 0) x = jiggle(), l += x * x;
        if (y === 0) y = jiggle(), l += y * y;
        if (l < distanceMin2) l = Math.sqrt(distanceMin2 * l);
        node.vx += x * quad.value * alpha / l;
        node.vy += y * quad.value * alpha / l;
      }
      return true;
    }

    // Otherwise, process points directly.
    else if (quad.length || l >= distanceMax2) return;

    // Limit forces for very close nodes; randomize direction if coincident.
    if (quad.data !== node || quad.next) {
      if (x === 0) x = jiggle(), l += x * x;
      if (y === 0) y = jiggle(), l += y * y;
      if (l < distanceMin2) l = Math.sqrt(distanceMin2 * l);
    }

    do if (quad.data !== node) {
      // Use the coordinates of the node and not the quad region.
      x = quad.data.x - node.x;
      y = quad.data.y - node.y;
      l = x * x + y * y;

      w = strengths[quad.data.index] * alpha / l;

      node.vx += x * w;
      node.vy += y * w;
    } while (quad = quad.next);
  }

  force.initialize = function(_) {
    nodes = _;
    initialize();
  };

  force.strength = function(_) {
    return arguments.length ? (strength = typeof _ === "function" ? _ : constant(+_), initialize(), force) : strength;
  };

  force.distanceMin = function(_) {
    return arguments.length ? (distanceMin2 = _ * _, force) : Math.sqrt(distanceMin2);
  };

  force.distanceMax = function(_) {
    return arguments.length ? (distanceMax2 = _ * _, force) : Math.sqrt(distanceMax2);
  };

  force.theta = function(_) {
    return arguments.length ? (theta2 = _ * _, force) : Math.sqrt(theta2);
  };

  force.update = function(_) {
    return arguments.length ? (updateClosure = _, updateBH = updateClosure(), force) : updateClosure;
  };

  return force;
};

exports.forceManyBodyReuse = manyBodyReuse;

Object.defineProperty(exports, '__esModule', { value: true });

})));

index.html

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

.links line {
  stroke: #999;
  stroke-opacity: 0.6;
}

.nodes circle {
  stroke: #fff;
  stroke-width: 1.5px;
}

</style>
<svg width="960" height="600"></svg>
<script src="https://d3js.org/d3.v4.min.js"></script>
<script src="d3-force-reuse.js"></script>
<script>

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

var color = d3.scaleOrdinal(d3.schemeCategory20);

var simulation = d3.forceSimulation()
    .force("link", d3.forceLink().id(function(d) { return d.id; }))
    .force("charge", d3.forceManyBodyReuse())
    .force("center", d3.forceCenter(width / 2, height / 2));

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

  var link = svg.append("g")
      .attr("class", "links")
    .selectAll("line")
    .data(graph.links)
    .enter().append("line")
      .attr("stroke-width", function(d) { return Math.sqrt(d.value); });

  var node = svg.append("g")
      .attr("class", "nodes")
    .selectAll("circle")
    .data(graph.nodes)
    .enter().append("circle")
      .attr("r", 5)
      .attr("fill", function(d) { return color(d.group); })
      .call(d3.drag()
          .on("start", dragstarted)
          .on("drag", dragged)
          .on("end", dragended));

  node.append("title")
      .text(function(d) { return d.id; });

  simulation
      .nodes(graph.nodes)
      .on("tick", ticked);

  simulation.force("link")
      .links(graph.links);

  function ticked() {
    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; });

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

function dragstarted(d) {
  if (!d3.event.active) simulation.alphaTarget(0.3).restart();
  d.fx = d.x;
  d.fy = d.y;
}

function dragged(d) {
  d.fx = d3.event.x;
  d.fy = d3.event.y;
}

function dragended(d) {
  if (!d3.event.active) simulation.alphaTarget(0);
  d.fx = null;
  d.fy = null;
}

</script>

miserables.json

{
  "nodes": [
    {"id": "Myriel", "group": 1},
    {"id": "Napoleon", "group": 1},
    {"id": "Mlle.Baptistine", "group": 1},
    {"id": "Mme.Magloire", "group": 1},
    {"id": "CountessdeLo", "group": 1},
    {"id": "Geborand", "group": 1},
    {"id": "Champtercier", "group": 1},
    {"id": "Cravatte", "group": 1},
    {"id": "Count", "group": 1},
    {"id": "OldMan", "group": 1},
    {"id": "Labarre", "group": 2},
    {"id": "Valjean", "group": 2},
    {"id": "Marguerite", "group": 3},
    {"id": "Mme.deR", "group": 2},
    {"id": "Isabeau", "group": 2},
    {"id": "Gervais", "group": 2},
    {"id": "Tholomyes", "group": 3},
    {"id": "Listolier", "group": 3},
    {"id": "Fameuil", "group": 3},
    {"id": "Blacheville", "group": 3},
    {"id": "Favourite", "group": 3},
    {"id": "Dahlia", "group": 3},
    {"id": "Zephine", "group": 3},
    {"id": "Fantine", "group": 3},
    {"id": "Mme.Thenardier", "group": 4},
    {"id": "Thenardier", "group": 4},
    {"id": "Cosette", "group": 5},
    {"id": "Javert", "group": 4},
    {"id": "Fauchelevent", "group": 0},
    {"id": "Bamatabois", "group": 2},
    {"id": "Perpetue", "group": 3},
    {"id": "Simplice", "group": 2},
    {"id": "Scaufflaire", "group": 2},
    {"id": "Woman1", "group": 2},
    {"id": "Judge", "group": 2},
    {"id": "Champmathieu", "group": 2},
    {"id": "Brevet", "group": 2},
    {"id": "Chenildieu", "group": 2},
    {"id": "Cochepaille", "group": 2},
    {"id": "Pontmercy", "group": 4},
    {"id": "Boulatruelle", "group": 6},
    {"id": "Eponine", "group": 4},
    {"id": "Anzelma", "group": 4},
    {"id": "Woman2", "group": 5},
    {"id": "MotherInnocent", "group": 0},
    {"id": "Gribier", "group": 0},
    {"id": "Jondrette", "group": 7},
    {"id": "Mme.Burgon", "group": 7},
    {"id": "Gavroche", "group": 8},
    {"id": "Gillenormand", "group": 5},
    {"id": "Magnon", "group": 5},
    {"id": "Mlle.Gillenormand", "group": 5},
    {"id": "Mme.Pontmercy", "group": 5},
    {"id": "Mlle.Vaubois", "group": 5},
    {"id": "Lt.Gillenormand", "group": 5},
    {"id": "Marius", "group": 8},
    {"id": "BaronessT", "group": 5},
    {"id": "Mabeuf", "group": 8},
    {"id": "Enjolras", "group": 8},
    {"id": "Combeferre", "group": 8},
    {"id": "Prouvaire", "group": 8},
    {"id": "Feuilly", "group": 8},
    {"id": "Courfeyrac", "group": 8},
    {"id": "Bahorel", "group": 8},
    {"id": "Bossuet", "group": 8},
    {"id": "Joly", "group": 8},
    {"id": "Grantaire", "group": 8},
    {"id": "MotherPlutarch", "group": 9},
    {"id": "Gueulemer", "group": 4},
    {"id": "Babet", "group": 4},
    {"id": "Claquesous", "group": 4},
    {"id": "Montparnasse", "group": 4},
    {"id": "Toussaint", "group": 5},
    {"id": "Child1", "group": 10},
    {"id": "Child2", "group": 10},
    {"id": "Brujon", "group": 4},
    {"id": "Mme.Hucheloup", "group": 8}
  ],
  "links": [
    {"source": "Napoleon", "target": "Myriel", "value": 1},
    {"source": "Mlle.Baptistine", "target": "Myriel", "value": 8},
    {"source": "Mme.Magloire", "target": "Myriel", "value": 10},
    {"source": "Mme.Magloire", "target": "Mlle.Baptistine", "value": 6},
    {"source": "CountessdeLo", "target": "Myriel", "value": 1},
    {"source": "Geborand", "target": "Myriel", "value": 1},
    {"source": "Champtercier", "target": "Myriel", "value": 1},
    {"source": "Cravatte", "target": "Myriel", "value": 1},
    {"source": "Count", "target": "Myriel", "value": 2},
    {"source": "OldMan", "target": "Myriel", "value": 1},
    {"source": "Valjean", "target": "Labarre", "value": 1},
    {"source": "Valjean", "target": "Mme.Magloire", "value": 3},
    {"source": "Valjean", "target": "Mlle.Baptistine", "value": 3},
    {"source": "Valjean", "target": "Myriel", "value": 5},
    {"source": "Marguerite", "target": "Valjean", "value": 1},
    {"source": "Mme.deR", "target": "Valjean", "value": 1},
    {"source": "Isabeau", "target": "Valjean", "value": 1},
    {"source": "Gervais", "target": "Valjean", "value": 1},
    {"source": "Listolier", "target": "Tholomyes", "value": 4},
    {"source": "Fameuil", "target": "Tholomyes", "value": 4},
    {"source": "Fameuil", "target": "Listolier", "value": 4},
    {"source": "Blacheville", "target": "Tholomyes", "value": 4},
    {"source": "Blacheville", "target": "Listolier", "value": 4},
    {"source": "Blacheville", "target": "Fameuil", "value": 4},
    {"source": "Favourite", "target": "Tholomyes", "value": 3},
    {"source": "Favourite", "target": "Listolier", "value": 3},
    {"source": "Favourite", "target": "Fameuil", "value": 3},
    {"source": "Favourite", "target": "Blacheville", "value": 4},
    {"source": "Dahlia", "target": "Tholomyes", "value": 3},
    {"source": "Dahlia", "target": "Listolier", "value": 3},
    {"source": "Dahlia", "target": "Fameuil", "value": 3},
    {"source": "Dahlia", "target": "Blacheville", "value": 3},
    {"source": "Dahlia", "target": "Favourite", "value": 5},
    {"source": "Zephine", "target": "Tholomyes", "value": 3},
    {"source": "Zephine", "target": "Listolier", "value": 3},
    {"source": "Zephine", "target": "Fameuil", "value": 3},
    {"source": "Zephine", "target": "Blacheville", "value": 3},
    {"source": "Zephine", "target": "Favourite", "value": 4},
    {"source": "Zephine", "target": "Dahlia", "value": 4},
    {"source": "Fantine", "target": "Tholomyes", "value": 3},
    {"source": "Fantine", "target": "Listolier", "value": 3},
    {"source": "Fantine", "target": "Fameuil", "value": 3},
    {"source": "Fantine", "target": "Blacheville", "value": 3},
    {"source": "Fantine", "target": "Favourite", "value": 4},
    {"source": "Fantine", "target": "Dahlia", "value": 4},
    {"source": "Fantine", "target": "Zephine", "value": 4},
    {"source": "Fantine", "target": "Marguerite", "value": 2},
    {"source": "Fantine", "target": "Valjean", "value": 9},
    {"source": "Mme.Thenardier", "target": "Fantine", "value": 2},
    {"source": "Mme.Thenardier", "target": "Valjean", "value": 7},
    {"source": "Thenardier", "target": "Mme.Thenardier", "value": 13},
    {"source": "Thenardier", "target": "Fantine", "value": 1},
    {"source": "Thenardier", "target": "Valjean", "value": 12},
    {"source": "Cosette", "target": "Mme.Thenardier", "value": 4},
    {"source": "Cosette", "target": "Valjean", "value": 31},
    {"source": "Cosette", "target": "Tholomyes", "value": 1},
    {"source": "Cosette", "target": "Thenardier", "value": 1},
    {"source": "Javert", "target": "Valjean", "value": 17},
    {"source": "Javert", "target": "Fantine", "value": 5},
    {"source": "Javert", "target": "Thenardier", "value": 5},
    {"source": "Javert", "target": "Mme.Thenardier", "value": 1},
    {"source": "Javert", "target": "Cosette", "value": 1},
    {"source": "Fauchelevent", "target": "Valjean", "value": 8},
    {"source": "Fauchelevent", "target": "Javert", "value": 1},
    {"source": "Bamatabois", "target": "Fantine", "value": 1},
    {"source": "Bamatabois", "target": "Javert", "value": 1},
    {"source": "Bamatabois", "target": "Valjean", "value": 2},
    {"source": "Perpetue", "target": "Fantine", "value": 1},
    {"source": "Simplice", "target": "Perpetue", "value": 2},
    {"source": "Simplice", "target": "Valjean", "value": 3},
    {"source": "Simplice", "target": "Fantine", "value": 2},
    {"source": "Simplice", "target": "Javert", "value": 1},
    {"source": "Scaufflaire", "target": "Valjean", "value": 1},
    {"source": "Woman1", "target": "Valjean", "value": 2},
    {"source": "Woman1", "target": "Javert", "value": 1},
    {"source": "Judge", "target": "Valjean", "value": 3},
    {"source": "Judge", "target": "Bamatabois", "value": 2},
    {"source": "Champmathieu", "target": "Valjean", "value": 3},
    {"source": "Champmathieu", "target": "Judge", "value": 3},
    {"source": "Champmathieu", "target": "Bamatabois", "value": 2},
    {"source": "Brevet", "target": "Judge", "value": 2},
    {"source": "Brevet", "target": "Champmathieu", "value": 2},
    {"source": "Brevet", "target": "Valjean", "value": 2},
    {"source": "Brevet", "target": "Bamatabois", "value": 1},
    {"source": "Chenildieu", "target": "Judge", "value": 2},
    {"source": "Chenildieu", "target": "Champmathieu", "value": 2},
    {"source": "Chenildieu", "target": "Brevet", "value": 2},
    {"source": "Chenildieu", "target": "Valjean", "value": 2},
    {"source": "Chenildieu", "target": "Bamatabois", "value": 1},
    {"source": "Cochepaille", "target": "Judge", "value": 2},
    {"source": "Cochepaille", "target": "Champmathieu", "value": 2},
    {"source": "Cochepaille", "target": "Brevet", "value": 2},
    {"source": "Cochepaille", "target": "Chenildieu", "value": 2},
    {"source": "Cochepaille", "target": "Valjean", "value": 2},
    {"source": "Cochepaille", "target": "Bamatabois", "value": 1},
    {"source": "Pontmercy", "target": "Thenardier", "value": 1},
    {"source": "Boulatruelle", "target": "Thenardier", "value": 1},
    {"source": "Eponine", "target": "Mme.Thenardier", "value": 2},
    {"source": "Eponine", "target": "Thenardier", "value": 3},
    {"source": "Anzelma", "target": "Eponine", "value": 2},
    {"source": "Anzelma", "target": "Thenardier", "value": 2},
    {"source": "Anzelma", "target": "Mme.Thenardier", "value": 1},
    {"source": "Woman2", "target": "Valjean", "value": 3},
    {"source": "Woman2", "target": "Cosette", "value": 1},
    {"source": "Woman2", "target": "Javert", "value": 1},
    {"source": "MotherInnocent", "target": "Fauchelevent", "value": 3},
    {"source": "MotherInnocent", "target": "Valjean", "value": 1},
    {"source": "Gribier", "target": "Fauchelevent", "value": 2},
    {"source": "Mme.Burgon", "target": "Jondrette", "value": 1},
    {"source": "Gavroche", "target": "Mme.Burgon", "value": 2},
    {"source": "Gavroche", "target": "Thenardier", "value": 1},
    {"source": "Gavroche", "target": "Javert", "value": 1},
    {"source": "Gavroche", "target": "Valjean", "value": 1},
    {"source": "Gillenormand", "target": "Cosette", "value": 3},
    {"source": "Gillenormand", "target": "Valjean", "value": 2},
    {"source": "Magnon", "target": "Gillenormand", "value": 1},
    {"source": "Magnon", "target": "Mme.Thenardier", "value": 1},
    {"source": "Mlle.Gillenormand", "target": "Gillenormand", "value": 9},
    {"source": "Mlle.Gillenormand", "target": "Cosette", "value": 2},
    {"source": "Mlle.Gillenormand", "target": "Valjean", "value": 2},
    {"source": "Mme.Pontmercy", "target": "Mlle.Gillenormand", "value": 1},
    {"source": "Mme.Pontmercy", "target": "Pontmercy", "value": 1},
    {"source": "Mlle.Vaubois", "target": "Mlle.Gillenormand", "value": 1},
    {"source": "Lt.Gillenormand", "target": "Mlle.Gillenormand", "value": 2},
    {"source": "Lt.Gillenormand", "target": "Gillenormand", "value": 1},
    {"source": "Lt.Gillenormand", "target": "Cosette", "value": 1},
    {"source": "Marius", "target": "Mlle.Gillenormand", "value": 6},
    {"source": "Marius", "target": "Gillenormand", "value": 12},
    {"source": "Marius", "target": "Pontmercy", "value": 1},
    {"source": "Marius", "target": "Lt.Gillenormand", "value": 1},
    {"source": "Marius", "target": "Cosette", "value": 21},
    {"source": "Marius", "target": "Valjean", "value": 19},
    {"source": "Marius", "target": "Tholomyes", "value": 1},
    {"source": "Marius", "target": "Thenardier", "value": 2},
    {"source": "Marius", "target": "Eponine", "value": 5},
    {"source": "Marius", "target": "Gavroche", "value": 4},
    {"source": "BaronessT", "target": "Gillenormand", "value": 1},
    {"source": "BaronessT", "target": "Marius", "value": 1},
    {"source": "Mabeuf", "target": "Marius", "value": 1},
    {"source": "Mabeuf", "target": "Eponine", "value": 1},
    {"source": "Mabeuf", "target": "Gavroche", "value": 1},
    {"source": "Enjolras", "target": "Marius", "value": 7},
    {"source": "Enjolras", "target": "Gavroche", "value": 7},
    {"source": "Enjolras", "target": "Javert", "value": 6},
    {"source": "Enjolras", "target": "Mabeuf", "value": 1},
    {"source": "Enjolras", "target": "Valjean", "value": 4},
    {"source": "Combeferre", "target": "Enjolras", "value": 15},
    {"source": "Combeferre", "target": "Marius", "value": 5},
    {"source": "Combeferre", "target": "Gavroche", "value": 6},
    {"source": "Combeferre", "target": "Mabeuf", "value": 2},
    {"source": "Prouvaire", "target": "Gavroche", "value": 1},
    {"source": "Prouvaire", "target": "Enjolras", "value": 4},
    {"source": "Prouvaire", "target": "Combeferre", "value": 2},
    {"source": "Feuilly", "target": "Gavroche", "value": 2},
    {"source": "Feuilly", "target": "Enjolras", "value": 6},
    {"source": "Feuilly", "target": "Prouvaire", "value": 2},
    {"source": "Feuilly", "target": "Combeferre", "value": 5},
    {"source": "Feuilly", "target": "Mabeuf", "value": 1},
    {"source": "Feuilly", "target": "Marius", "value": 1},
    {"source": "Courfeyrac", "target": "Marius", "value": 9},
    {"source": "Courfeyrac", "target": "Enjolras", "value": 17},
    {"source": "Courfeyrac", "target": "Combeferre", "value": 13},
    {"source": "Courfeyrac", "target": "Gavroche", "value": 7},
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  ]
}

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