// set up matrix of desired edge lengths using L*d[i][j]
private DenseDoubleMatrix2D calcLMatrix(DenseDoubleMatrix2D distMatrix, double optDist) {
int nNodes = distMatrix.rows();
DenseDoubleMatrix2D lMatrix = new DenseDoubleMatrix2D(nNodes, nNodes);
for (int i = 0; i < nNodes; i++) {
for (int j = 0; j < nNodes; j++) {
lMatrix.setQuick(i, j, (optDist * distMatrix.getQuick(i, j)));
}
}
return lMatrix;
}
// set up matrix of spring forces between pairs using K/(d[i][j]^2)
private DenseDoubleMatrix2D calcKMatrix(DenseDoubleMatrix2D distMatrix, double spring) {
int nNodes = distMatrix.rows();
DenseDoubleMatrix2D kMatrix = new DenseDoubleMatrix2D(nNodes, nNodes);
for (int i = 0; i < nNodes; i++) {
for (int j = 0; j < nNodes; j++) {
double distMVal = distMatrix.getQuick(i, j);
kMatrix.setQuick(i, j, (spring / (distMVal * distMVal)));
}
}
return kMatrix;
}
