<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
 def get_structure_with_nodes(self, find_min=True, min_dist=0.5, tol=0.2, threshold_frac=None, threshold_abs=None):
 """ Get the modified structure with the possible interstitial sites added. The species is set as a DummySpecie X. Args: find_min (bool):
 True to find local minimum else maximum, otherwise find local maximum. min_dist (float):
 The minimum distance (in Angstrom) that a predicted site needs to be from existing atoms. A min_dist with value <= 0 returns all sites without distance checking. tol (float):
 A distance tolerance of nodes clustering that sites too closed to other predicted sites will be merged. PBC is taken into account. threshold_frac (float):
 optional fraction of extrema, which returns `threshold_frac * tot_num_extrema` extrema fractional coordinates based on highest/lowest intensity. E.g. set 0.2 to insert DummySpecie atom at the extrema with 20% highest or lowest intensity. Value range: 0 <= threshold_frac <= 1 Note that threshold_abs and threshold_frac should not set in the same time. threshold_abs (float):
 optional filter. When searching for local minima, intensity <= threshold_abs returns; when searching for local maxima, intensity >= threshold_abs returns. Note that threshold_abs and threshold_frac should not set in the same time. Returns: structure (Structure) """


        structure = self.structure.copy()
        self.get_local_extrema(find_min=find_min, threshold_frac=threshold_frac,
                               threshold_abs=threshold_abs)

        self.remove_collisions(min_dist)
        self.cluster_nodes(tol=tol)
        for fc in self.extrema_coords:
            structure.append("X", fc)

        return structure