iteration_issue.py

    def _single_frame(self):
        self._i = self._i + 1
        iframe = self._ts.frame
        i_ref = self.atoms.positions - self.atoms.center_of_mass()
        # diagonal entries need not be calculated due to metric(x,x) == 0 in
        # theory, _ts not updated properly. Possible savings by setting a
        # cutoff for significant decimal places to sparsify matrix
        for j, ts in enumerate(self._u.trajectory[self.start:self.stop:self.step]):
            self._ts = ts
            if self._ts.frame >= iframe:
                if self._i == j:
                    self.dist_matrix[self._i, self._i] = 0
                else:
                    j_ref = self.atoms.positions-self.atoms.center_of_mass()
                    dist = self._metric(i_ref, j_ref, weights=self._weights)
                    self.dist_matrix[self._i, j] = (dist if dist > self._cutoff
                                                    else 0)
                    self.dist_matrix[j, self._i] = self.dist_matrix[self._i, j]
        self._ts = self._u.trajectory[iframe]