public Organism doVariation(Generation parents, Generation offspring, Selection sel) {
GAParameters params = GAParameters.getParams();
Random rand = params.getRandom();
// pick a parent randomly
StructureOrg p = (StructureOrg) (sel.doSelection(parents, 1)[0]);
Cell pStruct = p.getCell();
// copy the parent's data into new structures
List<Site> pSites = pStruct.getSites();
List<Site> newSites = new LinkedList<Site>();
// perturbing the lattice parameters
double[][] strain = new double[3][3];
// initialize the strain matrix to the identity
// then add some zero mean Gaussian random variables
for (int i = 0; i < strain.length; i++)
for (int j = 0; j < strain.length; j++) {
strain[i][j] = rand.nextGaussian() * sigmaLattice;
// allow strain matrix perturbations to be only between -1 and 1
if (strain[i][j] > 1) strain[i][j] = 1;
if (strain[i][j] < -1) strain[i][j] = -1;
// add the identity
if (i == j) strain[i][j] += 1;
}
// modify the basis to make newBasis
double[][] newVectsD = new double[Constants.numDimensions][Constants.numDimensions];
for (int i = 0; i < Constants.numDimensions; i++)
for (int j = 0; j < Constants.numDimensions; j++)
newVectsD[i][j] = pStruct.getLatticeVectors().get(i).getCartesianComponents().get(j);
// newVects = MatrixMath.SquareMatrixMult(strain, newVects);
newVectsD = (new Matrix(strain)).times(new Matrix(newVectsD)).getArray();
List<Vect> newVects = new LinkedList<Vect>();
for (int i = 0; i < Constants.numDimensions; i++) newVects.add(new Vect(newVectsD[i]));
// perturb atomic positions
for (int i = 0; i < pSites.size(); i++) {
// perturb each site's location with probability mutRate
List<Double> fracCoords =
pSites.get(i).getCoords().getComponentsWRTBasis(pStruct.getLatticeVectors());
if (rand.nextDouble() < mutRate) {
// perturb by a Gaussian of stddev mutRadius along each axis
for (int k = 0; k < Constants.numDimensions; k++)
fracCoords.set(
k, GAUtils.renormZeroOne(fracCoords.get(k) + rand.nextGaussian() * sigmaAtoms));
}
newSites.add(new Site(pSites.get(i).getElement(), new Vect(fracCoords, newVects)));
}
// make the new offspring
StructureOrg result = new StructureOrg(new Cell(newVects, newSites));
GAOut.out().stdout("StructureMut created new StructureOrg:", GAOut.DEBUG, result.getID());
GAOut.out().stdout(result.toString(), GAOut.DEBUG, result.getID());
return result;
}
public String getLabel() {
return cell.getLabel();
}
public Composition getComposition() {
return cell.getComposition();
}
public double getEnergyPerAtom() {
return getTotalEnergy() / cell.getNumSites();
}