Class Network3D

Object

AbstractCollection<Node3D>

AbstractList<Node3D>

Network<Node3D>

Network3D

All Implemented Interfaces:

Iterable<Node3D>, Collection<Node3D>, Iterator<Node3D>, List<Node3D>, SequencedCollection<Node3D>

Direct Known Subclasses:

Network3DGWT

public abstract class Network3D
extends Network<Node3D>

Graphical representation of generic population geometries in 3D. A network corresponds to a (possibly ephemeral) collection and configuration of nodes.

Author:

Christoph Hauert

Nested Class Summary

Nested classes/interfaces inherited from class Network

Network.LayoutListener, Network.Status

Field Summary

Fields

Modifier and Type	Field	Description
private final Vector3D	attraction	Helper variable to store intermediate results when considering the potential energy resulting from the attraction between neighbouring nodes.
private static final double	IR	The inverse size of the baseline 3D universe.
private static final double	IR2	The inverse squared size of the baseline 3D universe, 1/R<sup>2</sup>.
private static final double	MIN_DISTANCE2	Smallest admissible squared center-to-center distance during layout calculations.
private final Vector3D	repulsion	Helper variable to store intermediate results when considering the potential energy resulting from the repulsion between nodes.
private static final double	SHELL_THICKNESS_SCALE	Fraction of the nominal nearest-neighbour spacing used as radial shell thickness.
static final double	UNIVERSE_RADIUS	The baseline size of the 3D universe.
private final Vector3D	vec	Temporary storage for the directional vector connecting two nodes.

Fields inherited from class Network

accuracy, engine, fLinks, geometry, GOLDEN_ANGLE, HARD_CORE_STIFFNESS, initialAdjust, isRunning, layoutProgress, layoutTimeout, listener, MAX_LINK_COUNT, MIN_DISTANCE, MIN_SCALED_DISTANCE, nLinks, nNodes, nodes, norm, potential, prevAdjust, prevPotential, radius, rng, status, timestamp

Fields inherited from class AbstractList

modCount

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	Network3D(EvoLudo engine, AbstractGeometry geometry)	Create a new network in 3D for the given engine and geometry.

Method Summary

Modifier and Type	Method	Description
protected double	attraction(int nodeidx)	Calculate the potential energy based on attraction to its neighbours for the node with index nodeidx.
private static ArrayList<double[]>	createFibonacciShells(int nNodes)	Create a deterministic ball composed of concentric phyllotactic shells.
boolean	equals(Object obj)
void	finishLayout()	Prepare graph for display: shift center of mass into origin rescale size of graph find number of links
private static double	fractional(double value)	Return the fractional part of value.
Node3D	get(int index)
int	hashCode()
void	initNodes(double pnorm, double nnorm, double unitradius)	Generate the initial placement of all nodes.
private static int[]	nodesPerShell(double maxR, int nShells, int sNodes)	Apportion the non-central nodes across concentric shells in proportion to shell volume using the largest-remainder method.
private double	pairDistance(Node3D from, Node3D to, int fromidx, int toidx)	Set vec to the directional vector from from to to and return the corresponding center-to-center distance.
double	relax(int nodeidx)	Relax the potential energy a single node with index nodeidx by adjusting its position.
double	relax(int nodeidx, double dt)	Relaxes the network node with index nodeidx.
protected double	repulsion(int nodeidx)	Calculate the potential energy based on repulsion for the node with index nodeidx.
Node3D[]	toArray()
private static double	volumeMeanRadius(double iR, double oR)	Compute the radius that best represents the shell volume between two boundaries.

Methods inherited from class Network

cancelLayout, clear, collectEdges, collectLinks, completeLayout, contains, doLayout, doLayoutPrep, getConvergenceAccuracy, getGeometry, getLayoutTimout, getNLinks, getRadius, getStatus, getTimestamp, getUnitRadius, hasNext, indexOf, isStatus, iterator, lastIndexOf, linkNodes, next, reset, sampleIndices, scaledNodeRadius, scaleRadiusTo, set, setLayoutListener, setLayoutTimout, setRadius, setStatus, shake, size, updateLayoutProgress

Methods inherited from class AbstractList

add, add, addAll, listIterator, listIterator, remove, removeRange, subList

Methods inherited from class AbstractCollection

addAll, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toString

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface Iterable

forEach

Methods inherited from interface Iterator

forEachRemaining, remove

Methods inherited from interface List

addAll, addFirst, addLast, containsAll, getFirst, getLast, isEmpty, remove, removeAll, removeFirst, removeLast, replaceAll, retainAll, reversed, sort, spliterator, toArray

Field Details

SHELL_THICKNESS_SCALE

private static final double SHELL_THICKNESS_SCALE

Fraction of the nominal nearest-neighbour spacing used as radial shell thickness. Values below one create more shells than a strict packing estimate, which makes the seed look more organic while still filling the volume.

See Also:

• Constant Field Values

attraction

private final Vector3D attraction

Helper variable to store intermediate results when considering the potential energy resulting from the attraction between neighbouring nodes.

repulsion

private final Vector3D repulsion

Helper variable to store intermediate results when considering the potential energy resulting from the repulsion between nodes.

vec

private final Vector3D vec

Temporary storage for the directional vector connecting two nodes.

UNIVERSE_RADIUS

public static final double UNIVERSE_RADIUS

The baseline size of the 3D universe.

See Also:

• Constant Field Values

IR

private static final double IR

The inverse size of the baseline 3D universe. Convenience constant.

See Also:

• Constant Field Values

IR2

private static final double IR2

The inverse squared size of the baseline 3D universe, 1/R<sup>2</sup>. Convenience constant.

See Also:

• Constant Field Values

MIN_DISTANCE2

private static final double MIN_DISTANCE2

Smallest admissible squared center-to-center distance during layout calculations.

See Also:

• Constant Field Values

Constructor Details

Network3D

protected Network3D(EvoLudo engine,
 AbstractGeometry geometry)

Create a new network in 3D for the given engine and geometry.

Parameters:

engine - the pacemaker for running the model

geometry - the structure of the population

Method Details

initNodes

public void initNodes(double pnorm,
 double nnorm,
 double unitradius)

Description copied from class: Network

Generate the initial placement of all nodes. The size of nodes scales with their total number of incoming and outgoing links in heterogeneous networks.

Specified by:

initNodes in class Network<Node3D>

Parameters:

pnorm - the maximal radius of a node

nnorm - the minimal radius of a node

unitradius - the reference radius of a node

createFibonacciShells

private static ArrayList<double[]> createFibonacciShells(int nNodes)

Create a deterministic ball composed of concentric phyllotactic shells. Node zero is kept at the origin, while the remaining nodes are distributed over spherical shells with populations proportional to shell volume.

Parameters:

nNodes - the number of nodes to distribute

Returns:

the shell positions sorted from the center to the boundary

nodesPerShell

private static int[] nodesPerShell(double maxR,
 int nShells,
 int sNodes)

Apportion the non-central nodes across concentric shells in proportion to shell volume using the largest-remainder method.

Parameters:

maxR - the radius of the seed ball

nShells - the number of shells

sNodes - the number of nodes on shells

Returns:

the number of nodes placed on each shell

volumeMeanRadius

private static double volumeMeanRadius(double iR,
 double oR)

Compute the radius that best represents the shell volume between two boundaries. This uses the radius averaged with respect to volume density.

Parameters:

iR - the inner shell boundary

oR - the outer shell boundary

Returns:

the representative shell radius

relax

public double relax(int nodeidx)

Description copied from class: Network

Relax the potential energy a single node with index nodeidx by adjusting its position. The potential energy increases proportional to D where D denotes the distance to its neighbours and decreases proportional to 1/D<sup>2</sup> where D refers to the distance from all other nodes.

Specified by:

relax in class Network<Node3D>

Parameters:

nodeidx - the index of the node to relax

Returns:

the change in potential energy

relax

public double relax(int nodeidx,
 double dt)

Description copied from class: Network

Relaxes the network node with index nodeidx. The attraction and repulsion forces act on the node for a time interval dt, which limits the changes in the position of the node.

Specified by:

relax in class Network<Node3D>

Parameters:

nodeidx - the index of the node to relax

dt - the time interval

Returns:

the change in potential energy

See Also:

• Network.relax(int)

repulsion

protected double repulsion(int nodeidx)

Description copied from class: Network

Calculate the potential energy based on repulsion for the node with index nodeidx. Return the net repulsion (overall direction and magnitude) acting on it in Network.repulsion(int). Implementations may include additional short-range penalties here, for example to discourage overlap between nodes with finite size.

Note:

To prevent disjoint parts of a network (and unstructured populations, in particular) to continue to fly apart, the repulsion changes sign, i.e. turns into attraction, once the distance between nodes exceeds the radius of the universe.

Specified by:

repulsion in class Network<Node3D>

Parameters:

nodeidx - the index of the node to relax

Returns:

the potential energy of the node

attraction

protected double attraction(int nodeidx)

Description copied from class: Network

Calculate the potential energy based on attraction to its neighbours for the node with index nodeidx. Return the net attraction (overall direction and magnitude) acting on it in Network.attraction(int).

Specified by:

attraction in class Network<Node3D>

Parameters:

nodeidx - the index of the node to relax

Returns:

the potential energy of the node

pairDistance

private double pairDistance(Node3D from,
 Node3D to,
 int fromidx,
 int toidx)

Set vec to the directional vector from from to to and return the corresponding center-to-center distance. Coincident nodes are separated by a deterministic fallback direction to keep layouting stable and reproducible.

Parameters:

from - the source node

to - the target node

fromidx - the index of the source node

toidx - the index of the target node

Returns:

the center-to-center distance

fractional

private static double fractional(double value)

Return the fractional part of value.

Parameters:

value - the value to reduce to its fractional part

Returns:

the fractional part in the interval [0,1)

finishLayout

public void finishLayout()

Prepare graph for display:

1. shift center of mass into origin
2. rescale size of graph
3. find number of links

Specified by:

finishLayout in class Network<Node3D>

toArray

public Node3D[] toArray()

Specified by:

toArray in interface Collection<Node3D>

Specified by:

toArray in interface List<Node3D>

Overrides:

toArray in class AbstractCollection<Node3D>

get

public Node3D get(int index)

Specified by:

get in interface List<Node3D>

Specified by:

get in class AbstractList<Node3D>

equals

public boolean equals(Object obj)

Specified by:

equals in interface Collection<Node3D>

Specified by:

equals in interface List<Node3D>

Overrides:

equals in class Network<Node3D>

hashCode

public int hashCode()

Specified by:

hashCode in interface Collection<Node3D>

Specified by:

hashCode in interface List<Node3D>

Overrides:

hashCode in class Network<Node3D>