fix charge array in np.concatenate call

gmso/external/convert_hoomd.py

@@ -285,16 +285,14 @@ def _parse_particle_information(
         for site in top.sites
     ]
     masses = np.zeros(top.n_sites)
-    # charges = np.zeros(top.n_sites)
-    charges = list()
+    charges = np.zeros(top.n_sites)
     for idx, site in enumerate(top.sites):
         masses[idx] = (
             site.mass.to_value(base_units["mass"])
             if site.mass
             else 1 * base_units["mass"]
         )
-        # charges[idx] = site.charge if site.charge else 0 * u.elementary_charge
-        charges.append(site.charge if site.charge else 0 * u.elementary_charge)
+        charges[idx] = site.charge if site.charge else 0 * u.elementary_charge
 
     unique_types = sorted(list(set(types)))
     typeids = np.array([unique_types.index(t) for t in types])
@@ -313,7 +311,7 @@ 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):
-            group_indices = np.where(rigid_ids == _id)[0]
+            group_indices = np.where(np.array(rigid_ids) == _id)[0]
             group_positions = xyz[group_indices]
             group_masses = masses[group_indices]
             com_xyz = np.sum(group_positions.T * group_masses, axis=1) / sum(
@@ -324,7 +322,7 @@ def _parse_particle_information(
         # Append rigid center mass and xyz to front
         masses = np.concatenate((rigid_masses, masses))
         xyz = np.concatenate((rigid_xyz, xyz))
-        charges = np.concatenate((np.zeros(n_rigid), np.array(charges)))
+        charges = np.concatenate((np.zeros(n_rigid), charges))
         rigid_id_tags = np.concatenate((np.arange(n_rigid), np.array(rigid_ids)))
     else:
         n_rigid = 0

gmso/tests/test_hoomd.py

@@ -82,7 +82,7 @@ def test_rigid_bodies(self):
         assert np.array_equal(
             snapshot.particles.body[10:], np.array([1] * ethane.n_particles)
         )
-        assert snapshot.particles.mass[0] == ethane.mass
+        assert np.allclose(snapshot.particles.mass[0], ethane.mass, atol=1e-2)
 
     @pytest.mark.skipif(
         int(hoomd_version[0]) < 4, reason="Unsupported features in HOOMD 3"