code: public double[][] buildBondMatrix() {
          int i, j, k, m;
          for (i = 0; i < nodeNumber; i++) {
              for (j = 1; j <= layerNumber; j++) {
                  bondMatrix[i][j - 1] = 0.0;
                  for (k = 0; k < nodeNumber; k++) {
                      if (j == 1) {
                          if (apspMatrix[i][k] == j) {
                              bondMatrix[i][j - 1] += adjaMatrix[i][k];
                          }
                      } else {
                          if (apspMatrix[i][k] == j) {
                              for (m = 0; m < nodeNumber; m++) {
                                  if (apspMatrix[i][m] == (j - 1)) {
                                      bondMatrix[i][j - 1] += adjaMatrix[k][m];
                                  }
                              }
                          }
                      }
                  }
              }
          }
          return bondMatrix;
      }
docs: Build bond matrix.
  
  @return bond matrix.