Add primitives if missing

autode/opt/coordinates/cartesian.py

@@ -89,3 +89,9 @@ def to(self, value: str) -> OptCoordinates:
             raise ValueError(
                 f"Cannot convert Cartesian coordinates to {value}"
             )
+
+    @property
+    def expected_number_of_dof(self) -> int:
+        """Expected number of degrees of freedom for the system"""
+        n_atoms = len(self.flatten()) // 3
+        return 3 * n_atoms - 6

autode/opt/coordinates/dic.py

@@ -69,7 +69,7 @@ def _calc_U(primitives: PIC, x: "CartesianCoordinates") -> np.ndarray:
         # of 3N - 6 non-redundant internals for a system of N atoms
         idxs = np.where(np.abs(lambd) > 1e-10)[0]
 
-        if len(idxs) < (len(x.flatten()) - 6):
+        if len(idxs) < x.expected_number_of_dof:
             raise RuntimeError(
                 "Failed to create a complete set of delocalised internal "
                 f"coordinates. {len(idxs)} < 3 N_atoms - 6. Likely due to "

autode/opt/optimisers/crfo.py

@@ -117,8 +117,20 @@ def _build_internal_coordinates(self):
             )
 
         cartesian_coords = CartesianCoordinates(self._species.coordinates)
+        primitives = self._primitives
+
+        if len(primitives) < cartesian_coords.expected_number_of_dof:
+            logger.info(
+                "Had an incomplete set of primitives. Adding "
+                "additional distances"
+            )
+            for i, j in itertools.combinations(
+                range(self._species.n_atoms), 2
+            ):
+                primitives.append(Distance(i, j))
+
         self._coords = DICWithConstraints.from_cartesian(
-            x=cartesian_coords, primitives=self._primitives
+            x=cartesian_coords, primitives=primitives
         )
         self._coords.zero_lagrangian_multipliers()
         return None