Class PDEInitialize

Object

ODEInitialize

PDEInitialize

class PDEInitialize
extends ODEInitialize

Helper class responsible for initializing spatial density fields for PDE based simulations in the EvoLudo framework.

PDEInitialize encapsulates a particular initialization "type" (uniform, random, localized shapes, Gaussian, ring, etc.), a background density vector, an optional dependent-component index and an RNG for randomized initial configurations. It provides a single entry point init(double[][]) that fills a preallocated two-dimensional density array where each row corresponds to the state vector at a lattice site.

Concepts and inputs

• density - destination array of shape [space.getSize()][nDim]; each row receives the initial density vector for a spatial location.
• y0 - baseline initial state vector (peak or default densities) used for the selected initialization pattern.
• background - background density vector used for locations outside the initialized region (e.g. outside a circle or square).
• dependent - index of a dependent component (or -1 if none). When set, several initialization modes perform a correction and normalization so the dependent component and the total density are consistent (e.g. for frequency-based models).
• rng - random number generator used for RANDOM initializations.

Supported initialization types

The class supports the following patterns via the inner PDEInitialize.Type enum: UNIFORM, RANDOM, PERTURBATION, SQUARE, CIRCLE, GAUSSIAN (sombrero) and RING. The chosen type determines how y0 and background are applied across the lattice: globally, randomly, locally (centered square/circle), or using radially/gaussian-scaled profiles.

Usage

Construct an instance with the desired PDEInitialize.Type, background vector, dependent index and RNG (if needed), then call init(double[][]) to populate the simulation density array prior to starting integration or discrete updates.

See Also:

• AbstractGeometry
• PDEInitialize.Type
• init(double[][])

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	PDEInitialize.Type	Types of initial configurations.

Nested classes/interfaces inherited from class ODEInitialize

ODEInitialize.InitType

Field Summary

Fields

Modifier and Type	Field	Description
private final PDE	pde	Owning PDE model providing geometry and background data.

Constructor Summary

Constructors

Constructor	Description
PDEInitialize(PDE pde)	Create an initializer tied to the supplied PDE model.

Method Summary

Modifier and Type	Method	Description
(package private) void	apply(int x, int l, double[] y0, double[][] dest)	Applies the initialization for GeometryType.LINEAR.
(package private) void	apply(int x, int y, int l, double[] y0, double[][] dest)	Applies the initialization for GeometryType.SQUARE and variants.
(package private) void	apply(int x, int y, int z, int l, int lz, double[] y0, double[][] dest)	Applies the initialization for GeometryType.CUBE.
void	init(double[][] density)	Initialize the density array according to the configured type.
private void	initFunction(double[][] density, double[] y0, AbstractGeometry space)	Dispatch initialization based on the dimensionality of the geometry.
private void	initFunction1D(double[][] density, double[] y0, AbstractGeometry space)	Initialization for GeometryType.LINEAR geometries extracted to reduce complexity.
private void	initFunction2D(double[][] density, double[] y0, AbstractGeometry space)	Initialization for square/triangular/hexagonal lattice geometries extracted to reduce cognitive complexity.
private void	initFunction3D(double[][] density, double[] y0, AbstractGeometry space)	Initialization for GeometryType.CUBE geometries extracted to reduce complexity.
private void	initPerturbation(double[][] density, double[] y0, AbstractGeometry space)	Initialize a uniform background with a single perturbed site at the center.
private void	initRandom(double[][] density, double[] y0, AbstractGeometry space)	Initialize each site independently at random (normalized if needed).
private void	initUniform(double[][] density, double[] y0, AbstractGeometry space)	Initialize every lattice point with the same state.
private void	scaleDensity(double[] y0, double scale, double[] d)	Helper method to scale the density vector d by the scalar factor scale.

Methods inherited from class ODEInitialize

init, parse

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

pde

private final PDE pde

Owning PDE model providing geometry and background data.

Constructor Details

PDEInitialize

PDEInitialize(PDE pde)

Create an initializer tied to the supplied PDE model.

Parameters:

pde - owning PDE

Method Details

init

public void init(double[][] density)

Initialize the density array according to the configured type.

Parameters:

density - per-node trait densities to fill

initUniform

private void initUniform(double[][] density,
 double[] y0,
 AbstractGeometry space)

Initialize every lattice point with the same state.

Parameters:

density - per-node density buffer to populate

y0 - base state vector copied to each node

space - simulation geometry describing the lattice size

initPerturbation

private void initPerturbation(double[][] density,
 double[] y0,
 AbstractGeometry space)

Initialize a uniform background with a single perturbed site at the center.

Parameters:

density - per-node density buffer to populate

y0 - perturbed state vector applied to the central node

space - simulation geometry describing the lattice

initRandom

private void initRandom(double[][] density,
 double[] y0,
 AbstractGeometry space)

Initialize each site independently at random (normalized if needed).

Parameters:

density - per-node density buffer to populate

y0 - base amplitudes for random sampling

space - simulation geometry describing the lattice size

initFunction

private void initFunction(double[][] density,
 double[] y0,
 AbstractGeometry space)

Dispatch initialization based on the dimensionality of the geometry.

Parameters:

density - per-node density buffer to populate

y0 - peak density vector for the localized shapes

space - simulation geometry describing the lattice

initFunction3D

private void initFunction3D(double[][] density,
 double[] y0,
 AbstractGeometry space)

Initialization for GeometryType.CUBE geometries extracted to reduce complexity.

Parameters:

density - per-node density buffer to populate

y0 - peak density vector for the localized shape

space - simulation geometry describing the lattice

initFunction1D

private void initFunction1D(double[][] density,
 double[] y0,
 AbstractGeometry space)

Initialization for GeometryType.LINEAR geometries extracted to reduce complexity.

Parameters:

density - per-node density buffer to populate

y0 - peak density vector for the localized shape

space - simulation geometry describing the lattice

initFunction2D

private void initFunction2D(double[][] density,
 double[] y0,
 AbstractGeometry space)

Initialization for square/triangular/hexagonal lattice geometries extracted to reduce cognitive complexity.

Parameters:

density - per-node density buffer to populate

y0 - peak density vector for the localized shape

space - simulation geometry describing the lattice

apply

void apply(int x,
 int l,
 double[] y0,
 double[][] dest)

Applies the initialization for GeometryType.LINEAR.

Parameters:

x - the x coordinate

l - the linear length of the lattice

y0 - the initial state

dest - the destination array

apply

void apply(int x,
 int y,
 int l,
 double[] y0,
 double[][] dest)

Applies the initialization for GeometryType.SQUARE and variants.

Parameters:

x - the x coordinate

y - the y coordinate

l - the linear length of the lattice

y0 - the initial state

dest - the destination array

apply

void apply(int x,
 int y,
 int z,
 int l,
 int lz,
 double[] y0,
 double[][] dest)

Applies the initialization for GeometryType.CUBE.

Parameters:

x - the x coordinate

y - the y coordinate

z - the z coordinate

l - the linear length of the lattice

lz - the linear height of the lattice (lz == l except for NOVA)

y0 - the initial state

dest - the destination array

scaleDensity

private void scaleDensity(double[] y0,
 double scale,
 double[] d)

Helper method to scale the density vector d by the scalar factor scale. The scalar must lie in \((0, 1)\) such that the initial densities/frequencies represent the maximum.

Parameters:

y0 - the initial density vector

scale - the scaling factor

d - the location to store the scaled density