public void randomwalk(int v) {
// weighted random walk
RandomWalk rw = new RandomWalk(p_w);
int status = rw.stay_move();
ArrayList<Integer> walkpath = new ArrayList<Integer>();
Integer u = v;
walkpath.add(v);
while (status == 1) // keep moving until status = 0
{
u = rw.move(G, u);
if (u == null) // no neighbors
break;
if (!walkpath.contains(u)) walkpath.add(u);
status = rw.stay_move();
}
// System.out.println("walking length: "+ Integer.toString(walkpath.size()));
for (int i = 0; i < walkpath.size(); i++)
for (int j = i + 1; j < walkpath.size(); j++) {
int m = walkpath.get(i);
int n = walkpath.get(j);
if (!G.containsEdge(m, n)) {
double distance = Math.abs(socialposition.get(m) - socialposition.get(n));
double prob = linkprob(distance, (j - i));
if (random.nextDouble() < prob) {
G.setEdgeWeight((DefaultWeightedEdge) G.addEdge(m, n), 1);
}
} else {
DefaultWeightedEdge edge = G.getEdge(m, n);
G.setEdgeWeight(edge, G.getEdgeWeight(edge) + 1);
}
}
return;
}
// global attachment -- with prob 1
public void globalattach(int v) throws IOException {
Integer u = random.nextInt(N);
while (u == v) u = random.nextInt(N);
if (!G.containsEdge(v, u)) {
G.setEdgeWeight((DefaultWeightedEdge) G.addEdge(v, u), 1);
} else {
DefaultWeightedEdge edge = G.getEdge(v, u);
G.setEdgeWeight(edge, G.getEdgeWeight(edge) + 1);
}
}
/**
* Add edges connecting this cell and its 8 (or less) neighbors
*
* @param row
* @param col
*/
private void addEdges(int row, int col) {
System.out.println("Adding (" + row + ", " + col + ")");
// Add weighted edge
// North
if (row > 0 && g.containsVertex(cellContainer[row][col])) {
g.addEdge(cellContainer[row][col], cellContainer[row - 1][col]);
g.setEdgeWeight(g.getEdge(cellContainer[row][col], cellContainer[row - 1][col]), 1);
// NE
if (col < colCount - 1 && g.containsVertex(cellContainer[row - 1][col + 1])) {
g.addEdge(cellContainer[row][col], cellContainer[row - 1][col + 1]);
g.setEdgeWeight(
g.getEdge(cellContainer[row][col], cellContainer[row - 1][col + 1]), Math.sqrt(2.0));
}
}
// East
if (col < colCount - 1 && g.containsVertex(cellContainer[row][col + 1])) {
g.addEdge(cellContainer[row][col], cellContainer[row][col + 1]);
g.setEdgeWeight(g.getEdge(cellContainer[row][col], cellContainer[row][col + 1]), 1);
// SE
if (row < rowCount - 1 && g.containsVertex(cellContainer[row + 1][col + 1])) {
g.addEdge(cellContainer[row][col], cellContainer[row + 1][col + 1]);
g.setEdgeWeight(
g.getEdge(cellContainer[row][col], cellContainer[row + 1][col + 1]), Math.sqrt(2.0));
}
}
// South
if (row < rowCount - 1 && g.containsVertex(cellContainer[row + 1][col])) {
g.addEdge(cellContainer[row][col], cellContainer[row + 1][col]);
g.setEdgeWeight(g.getEdge(cellContainer[row][col], cellContainer[row + 1][col]), 1);
// SW
if (col > 0 && g.containsVertex(cellContainer[row + 1][col - 1])) {
g.addEdge(cellContainer[row][col], cellContainer[row + 1][col - 1]);
g.setEdgeWeight(
g.getEdge(cellContainer[row][col], cellContainer[row + 1][col - 1]), Math.sqrt(2.0));
}
}
// West
if (col > 0 && g.containsVertex(cellContainer[row][col - 1])) {
g.addEdge(cellContainer[row][col], cellContainer[row][col - 1]);
g.setEdgeWeight(g.getEdge(cellContainer[row][col], cellContainer[row][col - 1]), 1);
// NW
if (row > 0 && g.containsVertex(cellContainer[row - 1][col - 1])) {
g.addEdge(cellContainer[row][col], cellContainer[row - 1][col - 1]);
g.setEdgeWeight(
g.getEdge(cellContainer[row][col], cellContainer[row - 1][col - 1]), Math.sqrt(2.0));
}
}
}
/**
* Compute the log-probability that each observation arises for each ant. This is represented by a
* simple weighted graph, where the absence of an edge represents zero probability that the given
* observation was caused by the given ant. Currently the log-prob is set to be a truncated iid
* Gaussian around an ant location.
*
* @param probabilityGraph The probability graph being constructed.
* @param edgeMap A sorted map of the edges in probabilityGraph.
* @param thisObservedPosMap Observed points along with index.
* @param thisParticlePosMap Current particle locations.
* @param obsSums
* @param antSums
* @return Sum of edge weights
*/
private double computeLogProbabilityGraph(
SimpleWeightedGraph<Vertex, DefaultWeightedComparableEdge> probabilityGraph,
ValueSortedMap<DefaultWeightedComparableEdge, Double> edgeMap,
HashMap<Vertex, Point> thisObservedPosMap,
HashMap<Vertex, AntPath> thisParticlePathMap) {
/** Initialize vertices. */
edgeMap.clear();
probabilityGraph.addVertex(falseNegative);
probabilityGraph.addVertex(falsePositive);
for (Vertex v : thisObservedPosMap.keySet()) {
probabilityGraph.addVertex(v);
DefaultWeightedComparableEdge edge = probabilityGraph.addEdge(v, falsePositive);
probabilityGraph.setEdgeWeight(edge, falsePositiveLogProb);
edgeMap.put(edge, falsePositiveLogProb);
}
for (Vertex v : thisParticlePathMap.keySet()) {
probabilityGraph.addVertex(v);
DefaultWeightedComparableEdge edge = probabilityGraph.addEdge(v, falseNegative);
probabilityGraph.setEdgeWeight(edge, falseNegativeLogProb);
edgeMap.put(edge, falseNegativeLogProb);
}
/** Compute probability of each observation given each ant path */
for (Entry<Vertex, Point> obsEntry : thisObservedPosMap.entrySet()) {
for (Entry<Vertex, AntPath> parEntry : thisParticlePathMap.entrySet()) {
double logprob = observationLogProbGivenAntPath(obsEntry.getValue(), parEntry.getValue());
if (logprob > logProbThreshold) {
DefaultWeightedComparableEdge edge =
probabilityGraph.addEdge(obsEntry.getKey(), parEntry.getKey());
probabilityGraph.setEdgeWeight(edge, logprob);
edgeMap.put(edge, logprob);
}
}
}
/** Adjust probabilities according to log-probability of an AntPath existing. */
for (Entry<Vertex, AntPath> antEntry : thisParticlePathMap.entrySet()) {
Set<DefaultWeightedComparableEdge> edge = probabilityGraph.edgesOf(antEntry.getKey());
double antProb = antEntry.getValue().getCurrentLogProb();
for (DefaultWeightedComparableEdge e : edge) {
double ew = probabilityGraph.getEdgeWeight(e);
probabilityGraph.setEdgeWeight(e, ew + antProb);
// edgeMap.remove(edge);
edgeMap.put(e, ew + antProb);
}
}
/**
* ANG -- to do Interaction effects: -- probability of false negative higher when multiple ants
* in same area. however, there is a high probability that there will be SOME observation in the
* area. -- probability of a false positive higher when there is one ant in a region. this is
* because sometimes one ant is split into two.
*/
/** compute vertex sums */
// Utils.computeVertexSums(probabilityGraph);
double totalLogProb = Utils.maxstar(edgeMap);
return totalLogProb;
}
// Calculate the contribution of current vertex's shortest-path graph to final edge betweenness
// (Newman algorithm)
// M. E. J. Newman and M. Girvan, Finding and evaluating community structure in networks, Physical
// Review E69, 026113 (2004)
private SimpleWeightedGraph<String, DefaultWeightedEdge> NewmanAlgorithm(
Multigraph<String, DefaultEdge> shortestPathGraph, String thisVertex) {
if (shortestPathGraph.edgeSet().size() == 0) // No outer degree
return null;
// 1. Initialize the edge betweenness digraph
SimpleWeightedGraph<String, DefaultWeightedEdge> edgeBetweennessDigraph =
new SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
// Add vertices
for (String curVertex : shortestPathGraph.vertexSet())
edgeBetweennessDigraph.addVertex(curVertex);
// 2. Deal with corresponding edges
// 2.1. Calculate vertex distance and weight
// 2.1.1. Initialize related variables
HashMap<String, Integer> mapVertexDistance = new HashMap<String, Integer>(); // Vertex distance
for (String curVertex : shortestPathGraph.vertexSet()) mapVertexDistance.put(curVertex, 0);
HashMap<String, Double> mapVertexWeight = new HashMap<String, Double>(); // Vertex weight
for (String curVertex : shortestPathGraph.vertexSet()) mapVertexWeight.put(curVertex, 1.0);
Queue<String> verticesQueue = new LinkedList<String>(); // Store the queue of operated vertices
// 2.1.2. Traverse the shortest-path digraph, get corresponding vertex distance and weight
verticesQueue.add(thisVertex);
String currentVertex = thisVertex;
while (!verticesQueue.isEmpty()) {
// 2.1.2.1. Read the bottom vertex in the queue, deal with all adjacent edges
for (DefaultEdge curEdge : shortestPathGraph.edgesOf(currentVertex)) {
String targetVertex = shortestPathGraph.getEdgeTarget(curEdge);
if (mapVertexDistance.get(targetVertex)
== 0) { // Target vertex value hasn't been evaluated yet
mapVertexDistance.put(targetVertex, mapVertexDistance.get(currentVertex) + 1);
mapVertexWeight.put(targetVertex, mapVertexWeight.get(currentVertex));
verticesQueue.add(targetVertex);
}
// Target vertex value has already been set to source vertex distance plus 1
else if (mapVertexDistance.get(targetVertex) == (mapVertexDistance.get(currentVertex) + 1))
mapVertexWeight.put(
targetVertex, mapVertexWeight.get(targetVertex) + mapVertexWeight.get(currentVertex));
}
// 2.1.2.2. All adjacent edges have been treated, remove the bottom element
verticesQueue.remove();
currentVertex = verticesQueue.peek();
}
// 2.2. Calculate the contribution of every edges to the edge betweenness
// 2.2.1. Sort the vertices descendingly by the distance to the first vertex
List<Map.Entry<String, Integer>> listVertexDistance =
new ArrayList<Map.Entry<String, Integer>>(mapVertexDistance.entrySet());
Collections.sort(
listVertexDistance,
new Comparator<Map.Entry<String, Integer>>() { // Sorting the list descendingly
@Override
public int compare(Entry<String, Integer> o1, Entry<String, Integer> o2) {
return (o2.getValue().compareTo(o1.getValue()));
}
});
// 2.2.2. Traverse the shortest-path digraph with the sorted vertices list
for (Map.Entry<String, Integer> thisVertexDistance : listVertexDistance) {
currentVertex = thisVertexDistance.getKey();
for (DefaultEdge curEdge : shortestPathGraph.edgesOf(currentVertex)) {
// 2.2.2.1. Get the source vertex
String sourceVertex = shortestPathGraph.getEdgeSource(curEdge);
String targetVertex = shortestPathGraph.getEdgeTarget(curEdge);
String anotherVertex = "";
if (currentVertex.equals(sourceVertex)) anotherVertex = targetVertex;
else if (currentVertex.equals(targetVertex)) anotherVertex = sourceVertex;
// 2.2.2.2. Calculate the value of the sum of all adjacent edges plus 1
double totalSubWeights = 1.0;
for (DefaultWeightedEdge curSubEdge : edgeBetweennessDigraph.edgesOf(currentVertex))
totalSubWeights += edgeBetweennessDigraph.getEdgeWeight(curSubEdge);
// 2.2.2.3. The new edge weight is calculated as totalSubWeights * (the quotient of the
// weights of the two terminals)
double wi = mapVertexWeight.get(anotherVertex);
double wj = mapVertexWeight.get(currentVertex);
totalSubWeights /= wi / wj;
// 2.2.2.4. Add new edge with correct weight into the edge betweenness digraph
DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
edgeBetweennessDigraph.addEdge(anotherVertex, currentVertex, newEdge);
edgeBetweennessDigraph.setEdgeWeight(newEdge, totalSubWeights);
}
}
return edgeBetweennessDigraph;
}
// Create shortest-path graph for every vertex by depth-first traversal algorithm
private Multigraph<String, DefaultEdge> DijkstraAlgorithm(
WeightedMultigraph<String, DefaultWeightedEdge> originalGraph, String thisVertex) {
// 1. Simplify the multi-graph of the active power flow into a simple graph
SimpleWeightedGraph<String, DefaultWeightedEdge> originalSimpleGraph =
new SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
for (String curVertex : originalGraph.vertexSet()) originalSimpleGraph.addVertex(curVertex);
for (DefaultWeightedEdge curEdge : originalGraph.edgeSet()) {
String sourceVertex = originalGraph.getEdgeSource(curEdge);
String targetVertex = originalGraph.getEdgeTarget(curEdge);
if (originalSimpleGraph.containsEdge(sourceVertex, targetVertex)) {
DefaultWeightedEdge modifiedEdge = originalSimpleGraph.getEdge(sourceVertex, targetVertex);
double newEdgeWeight =
originalSimpleGraph.getEdgeWeight(modifiedEdge) + originalGraph.getEdgeWeight(curEdge);
originalSimpleGraph.setEdgeWeight(modifiedEdge, newEdgeWeight);
} else {
DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
originalSimpleGraph.addEdge(sourceVertex, targetVertex, newEdge);
originalSimpleGraph.setEdgeWeight(newEdge, originalGraph.getEdgeWeight(curEdge));
}
}
// Issue (2010/10/25): Maybe larger amount of active power transfer still means weaker
// relationship between the two terminal buses of a certain branch,
// thus originalSimpleGraph other than inverseGraph should be used here.
// Use the inverse of active power to build a new weighted directed graph (the larger the active
// power is, the close the two buses will be)
// SimpleDirectedWeightedGraph<String, DefaultWeightedEdge> inverseGraph =
// new SimpleDirectedWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
// for (String curVertex : originalSimpleGraph.vertexSet())
// inverseGraph.addVertex(curVertex);
// for (DefaultWeightedEdge curEdge : originalSimpleGraph.edgeSet()) {
// String sourceVertex = originalSimpleGraph.getEdgeSource(curEdge);
// String targetVertex = originalSimpleGraph.getEdgeTarget(curEdge);
// DefaultWeightedEdge newEdge = new DefaultWeightedEdge();
// inverseGraph.addEdge(sourceVertex, targetVertex, newEdge);
// inverseGraph.setEdgeWeight(newEdge, 1 / originalSimpleGraph.getEdgeWeight(curEdge));
// }
// 2. Initialize the map of vertices and the corresponding weights (distance from current vertex
// to the first vertex)
HashMap<String, Double> mapVertexShortestDistance = new HashMap<String, Double>();
// for (String thisOriginalVertex : inverseGraph.vertexSet())
for (String thisOriginalVertex : originalSimpleGraph.vertexSet())
mapVertexShortestDistance.put(thisOriginalVertex, 10E10);
// The weight of the first vertex is zero
mapVertexShortestDistance.put(thisVertex, 0.0);
// 3. Depth-first traversing, update the shortest-path values
Stack<String> bfiVertices =
new Stack<String>(); // Stack to store passed vertices in a breadth-first traversing
// The map of a weighted edge and the flag of having been visited
// HashMap<DefaultWeightedEdge, Boolean> mapEdgeVisited = new HashMap<DefaultWeightedEdge,
// Boolean>();
// for (DefaultWeightedEdge thisEdge : inverseGraph.edgeSet())
// mapEdgeVisited.put(thisEdge, false);
String currentVertex = thisVertex;
bfiVertices.push(currentVertex);
// System.out.println(bfiVertices.toString());
while (!bfiVertices.isEmpty()) {
// Operate the following codes for those edges started with current vertex
boolean hasNewEdge = false;
// for (DefaultWeightedEdge curEdge : inverseGraph.outgoingEdgesOf(currentVertex)) {
for (DefaultWeightedEdge curEdge : originalSimpleGraph.edgesOf(currentVertex)) {
// if (!mapEdgeVisited.get(curEdge)) { // Used for those edges that have not been treated
// yet
// 3.1. Mark current edge as already been visited
// mapEdgeVisited.put(curEdge, true);
// String nextVertex = inverseGraph.getEdgeTarget(curEdge);
String nextVertex = originalSimpleGraph.getEdgeTarget(curEdge);
// 3.2. Update shortest-path values
double curSD = mapVertexShortestDistance.get(currentVertex);
// double edgeWeight = inverseGraph.getEdgeWeight(curEdge);
double edgeWeight = originalSimpleGraph.getEdgeWeight(curEdge);
double newSD = curSD + edgeWeight;
if (mapVertexShortestDistance.get(nextVertex) > newSD) {
hasNewEdge = true;
mapVertexShortestDistance.put(nextVertex, newSD);
// 3.3. Push the target vertex of current edge into the stack
bfiVertices.push(nextVertex);
// System.out.println(bfiVertices.toString());
break;
// System.out.println("New shortest path [" + nextVertex + "]: " + newSD);
}
// }
}
if (!hasNewEdge) {
bfiVertices.pop();
}
if (!bfiVertices.isEmpty()) currentVertex = bfiVertices.peek();
}
// 4. Create shortest-path digraph of current vertex
// 4.1. Initialize the shortest-path digraph
Multigraph<String, DefaultEdge> shortestPathGraph =
new Multigraph<String, DefaultEdge>(DefaultEdge.class);
// 4.2. Add all qualified edges
// for (DefaultWeightedEdge curEdge : inverseGraph.edgeSet()) {
for (DefaultWeightedEdge curEdge : originalSimpleGraph.edgeSet()) {
// 4.2.1. Evaluate if current edge is suitable
// String sourceVertex = inverseGraph.getEdgeSource(curEdge);
// String targetVertex = inverseGraph.getEdgeTarget(curEdge);
String sourceVertex = originalSimpleGraph.getEdgeSource(curEdge);
String targetVertex = originalSimpleGraph.getEdgeTarget(curEdge);
// if (Math.abs(inverseGraph.getEdgeWeight(curEdge) -
if (originalSimpleGraph.getEdgeWeight(curEdge) > 1.0E-5) {
if (Math.abs(
originalSimpleGraph.getEdgeWeight(curEdge)
- (mapVertexShortestDistance.get(targetVertex)
- mapVertexShortestDistance.get(sourceVertex)))
< 1.0E-5) {
// 4.2.2. Add suitable edge that found just now
DefaultEdge newEdge = new DefaultEdge();
if (!shortestPathGraph.containsVertex(sourceVertex))
shortestPathGraph.addVertex(sourceVertex);
if (!shortestPathGraph.containsVertex(targetVertex))
shortestPathGraph.addVertex(targetVertex);
shortestPathGraph.addEdge(sourceVertex, targetVertex, newEdge);
}
}
}
return shortestPathGraph;
}
/**
* Reads the geometry and connectivity.
*
* @param filename the location of the gjf file
*/
public GJFfile(String filename) {
super(filename);
// read geometry
String name = "";
List<Atom> contents = new ArrayList<>();
SimpleWeightedGraph<Atom, DefaultWeightedEdge> connectivity =
new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
int blanks = 0;
boolean lastBlank = false;
boolean inGeometryBlock = false;
for (List<String> line : fileContents) {
// keep track of how many blanks we have seen
if (line.size() == 1 && line.get(0).length() == 0) {
if (lastBlank == false) {
blanks++;
lastBlank = true;
}
continue;
} else lastBlank = false;
// read the metadata
if (blanks == 1) {
for (String s : line) {
String[] fields = s.split("@");
if (fields.length != 3) continue;
String identifier = fields[1].toLowerCase();
String value = fields[2];
// System.out.println(s);
// System.out.println(identifier + " : " + value);
if (identifier.equals("o1")) O1Number = Integer.parseInt(value);
else if (identifier.equals("o2")) O2Number = Integer.parseInt(value);
else if (identifier.equals("n3")) N3Number = Integer.parseInt(value);
else if (identifier.equals("cl1")) Cl1Number = Integer.parseInt(value);
else if (identifier.equals("su2")) Su2Number = Integer.parseInt(value);
else if (identifier.equals("ol3")) Ol3Number = Integer.parseInt(value);
else if (identifier.equals("mem")) mem = Integer.parseInt(value);
else if (identifier.equals("nprocshared")) nprocshared = Integer.parseInt(value);
else if (identifier.equals("method")) method = value;
else if (identifier.equals("basis")) basis = value;
else System.out.println("unrecognized entry: " + s);
}
continue;
} else if (blanks != 2) continue;
// deal with the charge and multiplicity card (by ignoring it)
if (line.size() == 2 && inGeometryBlock == false) {
inGeometryBlock = true;
continue;
}
if (line.size() != 4 && inGeometryBlock == false)
throw new IllegalArgumentException(
"unexpected text in geometry block in " + filename + ":\n" + line.toString());
// create atom
// tinker atom types will be nonsense, of course
Atom newAtom =
new Atom(
line.get(0),
new Vector3D(
Double.parseDouble(line.get(1)),
Double.parseDouble(line.get(2)),
Double.parseDouble(line.get(3))),
1);
contents.add(newAtom);
connectivity.addVertex(newAtom);
}
// read connectivity
blanks = 0;
lastBlank = false;
for (List<String> line : fileContents) {
// read the fourth block of text
if (line.size() == 1 && line.get(0).length() == 0) {
if (lastBlank == false) {
blanks++;
lastBlank = true;
}
continue;
} else lastBlank = false;
// only read connectivity lines
if (blanks != 3) continue;
Atom fromAtom = contents.get(Integer.parseInt(line.get(0)) - 1);
for (int i = 1; i < line.size(); i += 2) {
int toAtomIndex = Integer.parseInt(line.get(i)) - 1;
Atom toAtom = contents.get(toAtomIndex);
double bondOrder = Double.parseDouble(line.get(i + 1));
DefaultWeightedEdge thisEdge = connectivity.addEdge(fromAtom, toAtom);
connectivity.setEdgeWeight(thisEdge, bondOrder);
}
}
// create the molecule
molecule = new Molecule(name, contents, connectivity, 0.0);
}
