Fix Issue #5008 (#5012)

Fixes #5008 

Description of changes:
* Prevent users from adding angle/dihedral bonds with duplicate partners

src/python/espressomd/particle_data.py

@@ -617,6 +617,9 @@ def add_verified_bond(self, bond):
         if self.id in bond[1:]:
             raise Exception(
                 f"Bond partners {bond[1:]} include the particle {self.id} itself")
+        if len(set(bond[1:])) is not len(bond[1:]):
+            raise Exception(
+                f"Cannot add duplicate bond partners {bond[1:]} to particle {self.id}")
         self.call_method("add_bond",
                          bond_id=bond[0]._bond_id,
                          part_id=bond[1:])

testsuite/python/mpiio.py

@@ -64,13 +64,14 @@ def get_random_mock_particles():
                          v=np.random.rand(3),
                          bonds=[])
         # Up to 20 bonds; otherwise this test will take ages
-        for _ in range(random.randint(0, 20)):
+        while len(p.bonds) < 20:
             btype = random.randint(0, nbonds - 1)
             # Don't create loops, i.e. exclude "i" itself
             p1 = randint_different_from(0, npart, i)
             p2 = randint_different_from(0, npart, i)
-            # Don't add the same bond twice
-            if (btype, p1, p2) not in p.bonds:
+
+            # Don't add the same bond twice and don't use the same particle twice
+            if p1 != p2 and (btype, p1, p2) not in p.bonds:
                 p.bonds.append((btype, p1, p2))
         parts.append(p)
     return parts

testsuite/python/particle.py

@@ -440,6 +440,7 @@ def test_bonds(self):
 
         p1 = self.system.part.by_id(self.pid)
         p2 = self.system.part.add(pos=p1.pos)
+        p3 = self.system.part.add(pos=p1.pos)
         inactive_bond = espressomd.interactions.FeneBond(k=1, d_r_max=2)
         p2.add_bond([self.f1, p1])
         with self.assertRaisesRegex(RuntimeError, "already exists on particle"):
@@ -460,6 +461,22 @@ def test_bonds(self):
         with self.assertRaisesRegex(ValueError, "Bond partners have to be of type integer or ParticleHandle"):
             p2.delete_bond((self.f1, 'p1'))
 
+        active_pair_bond = espressomd.interactions.FeneBond(k=1, d_r_max=2)
+        self.system.bonded_inter.add(active_pair_bond)
+        with self.assertRaisesRegex(Exception, r"Bond partners \(17,\) include the particle 17 itself"):
+            p1.add_bond((active_pair_bond, p1))
+
+        active_angle_bond = espressomd.interactions.AngleCosine(bend=1, phi0=1)
+        self.system.bonded_inter.add(active_angle_bond)
+        with self.assertRaisesRegex(Exception, r"Cannot add duplicate bond partners \(17, 17\) to particle 18"):
+            p2.add_bond((active_angle_bond, p1, p1))
+
+        active_dihedral_bond = espressomd.interactions.Dihedral(
+            bend=1, mult=1, phase=1)
+        self.system.bonded_inter.add(active_dihedral_bond)
+        with self.assertRaisesRegex(Exception, r"Cannot add duplicate bond partners \(17, 17, 19\) to particle 18"):
+            p2.add_bond((active_dihedral_bond, p1, p1, p3))
+
     def test_zz_remove_all(self):
         for p in self.system.part.all():
             p.remove()