handle mix of rigid and non rigid

gmso/external/convert_hoomd.py

@@ -301,8 +301,10 @@ def _parse_particle_information(
     # Check for rigid molecules
     rigid_mols = any([site.molecule.isrigid for site in top.sites])
     if rigid_mols:
-        rigid_ids = [site.molecule.number for site in top.sites]
-        rigid_ids_set = set(rigid_ids)
+        rigid_ids = [
+            site.molecule.number if site.molecule.isrigid else -1 for site in top.sites
+        ]
+        rigid_ids_set = set([i for i in rigid_ids if i != -1])
         n_rigid = len(rigid_ids_set)
         rigid_charges = np.zeros(n_rigid) * charges.units
         rigid_masses = np.zeros(n_rigid) * masses.units
@@ -314,6 +316,8 @@ def _parse_particle_information(
         typeids = np.concatenate((np.array([0] * n_rigid), typeids + 1))
         # Update mass list and position list of Frame
         for idx, _id in enumerate(rigid_ids_set):
+            if _id == 1:
+                continue
             group_indices = np.where(np.array(rigid_ids) == _id)[0]
             group_positions = xyz[group_indices]
             group_masses = masses[group_indices]

gmso/tests/test_hoomd.py

@@ -106,6 +106,29 @@ def test_rigid_bodies(self):
         ):
             assert np.array_equal(np.array(group1), np.array(group2) + 2)
 
+    def test_rigid_bodies_mix(self):
+        ethane = mb.lib.molecules.Ethane()
+        ethane.name = "ethane"
+        benzene = mb.load("c1ccccc1", smiles=True)
+        benzene.name = "benzene"
+        box = mb.fill_box([benzene, ethane], n_compounds=[1, 1], box=[2, 2, 2])
+        top = from_mbuild(box)
+        for site in top.sites:
+            if site.molecule.name == "benzene":
+                site.molecule.isrigid = True
+
+        snapshot, refs = to_gsd_snapshot(top)
+        assert snapshot.particles.typeid[0] == 0
+        assert snapshot.particles.N == top.n_sites + 1
+        assert np.array_equal(
+            snapshot.particles.body[-ethane.n_particles :],
+            np.array([-1] * ethane.n_particles),
+        )
+        assert np.array_equal(
+            snapshot.particles.body[1 : benzene.n_particles + 1],
+            np.array([0] * benzene.n_particles),
+        )
+
     @pytest.mark.skipif(
         int(hoomd_version[0]) < 4, reason="Unsupported features in HOOMD 3"
     )