fixed freud bond issue (#1127)

* fixed freud bond issue

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update mbuild/compound.py

---------

Co-authored-by: Christopher Iacovella <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Co Quach <[email protected]>

Author: 4 people

mbuild/compound.py

@@ -1306,7 +1306,6 @@ def freud_generate_bonds(
         name_b,
         dmin,
         dmax,
-        exclude_ii=True,
     ):
         """Add Bonds between all pairs of types a/b within [dmin, dmax].
 
@@ -1320,8 +1319,6 @@ def freud_generate_bonds(
             The minimum distance (in nm) between Particles for considering a bond
         dmax : float
             The maximum distance (in nm) between Particles for considering a bond
-        exclude_ii : bool, optional, default=True
-            Whether or not to include neighbors with the same index.
 
         Notes
         -----
@@ -1367,7 +1364,21 @@ def freud_generate_bonds(
                 a_indices.append(i)
             if part.name == name_b:
                 b_indices.append(i)
-
+        # If we are looking to create bonds between the same species
+        # then the indices added to a_indices and b_indices will be identical.
+        # In this case we need to make sure that we don't try to bond a particle
+        # to itself  (i.e., excluded_ii = True).
+        # If we are looking for bonds between two different species,
+        # the indices we find for a and b will be distinct, with no overlap.
+        # However, the way the code is structured, we don't actually pass
+        # freud the indices, but rather a list of particle positions associated with each set of indices.
+        # As such, the indices that freud sees will be (0, len(a_indices)) and (0, len(b_indices)), even though
+        # they represent different actually particles. Thus, to get the right behavior we
+        # must not exclude particles with the same index, and thus exclude_ii = False.
+        if name_a == name_b:
+            exclude_ii = True
+        else:
+            exclude_ii = False
         aq = freud.locality.AABBQuery(freud_box, moved_positions[b_indices])
 
         nlist = aq.query(

mbuild/tests/test_compound.py

@@ -720,33 +720,49 @@ def test_freud_generated_bonds_periodicity(self, ch3):
         ch3_clone = mb.clone(ch3)
         ch3_clone.box = mb.Box(lengths=[max(bounding_box.lengths) + 1] * 3)
         ch3_clone.periodicity = (True, True, True)
-        ch3_clone.freud_generate_bonds(
-            "H", "H", dmin=0.01, dmax=0.2, exclude_ii=True
-        )
+        ch3_clone.freud_generate_bonds("H", "H", dmin=0.01, dmax=0.2)
         assert ch3_clone.n_bonds == 3 + 3
 
         ch3_clone2 = mb.clone(ch3)
         ch3_clone2.box = mb.Box(lengths=[max(bounding_box.lengths) + 1] * 3)
         ch3_clone2.periodicity = (True, True, False)
-        ch3_clone2.freud_generate_bonds(
-            "H", "H", dmin=0.01, dmax=0.2, exclude_ii=True
-        )
+        ch3_clone2.freud_generate_bonds("H", "H", dmin=0.01, dmax=0.2)
         assert ch3_clone2.n_bonds == 3 + 3
 
     @pytest.mark.skipif(not has_freud, reason="Freud not installed.")
     def test_freud_generate_bonds(self, ch3):
         bounding_box = ch3.get_boundingbox()
         ch3.box = mb.Box(lengths=[max(bounding_box.lengths) + 1] * 3)
-        ch3.freud_generate_bonds("H", "H", dmin=0.01, dmax=0.2, exclude_ii=True)
+        ch3.freud_generate_bonds("H", "H", dmin=0.01, dmax=0.2)
         assert ch3.n_bonds == 3 + 3
 
     @pytest.mark.skipif(not has_freud, reason="Freud not installed.")
     def test_freud_generate_bonds_expected(self, ch3):
         bounding_box = ch3.get_boundingbox()
         ch3.box = mb.Box(lengths=[max(bounding_box.lengths) + 1] * 3)
-        ch3.freud_generate_bonds("H", "H", dmin=0.01, dmax=0.1, exclude_ii=True)
+        ch3.freud_generate_bonds("H", "H", dmin=0.01, dmax=0.1)
         assert ch3.n_bonds == 3
 
+    @pytest.mark.skipif(not has_freud, reason="Freud not installed.")
+    def test_freud_generate_bonds_mixed(self):
+        carbon_atom = mb.Compound(name="C", element="C")
+
+        grid_pattern = mb.Grid3DPattern(2, 2, 2)
+
+        grid_pattern.scale([0.25, 0.25, 0.25])
+        carbon_list = grid_pattern.apply(carbon_atom)
+        co_system = mb.Compound(carbon_list)
+        co_system.box = mb.Box([1, 1, 1])
+        for i, child in enumerate(co_system.children):
+            if i % 2 == 0:
+                child.name = "O"
+                child.element = "O"
+
+        co_system.freud_generate_bonds(
+            name_a="C", name_b="O", dmin=0.0, dmax=0.16
+        )
+        assert co_system.n_bonds == 4
+
     def test_remove_from_box(self, ethane):
         n_ethanes = 5
         box = mb.fill_box(ethane, n_ethanes, [3, 3, 3])