revised load_xyz function (#1140)

* revised load_xyz function

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

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

mbuild/formats/xyz.py

@@ -44,6 +44,7 @@ def read_xyz(filename, compound=None):
 
     guessed_elements = set()
 
+    compound_list = []
     with open(filename, "r") as xyz_file:
         n_atoms = int(xyz_file.readline())
         xyz_file.readline()
@@ -74,7 +75,7 @@ def read_xyz(filename, compound=None):
                 element = None
 
             particle = mb.Compound(pos=coords[row], name=name, element=element)
-            compound.add(particle)
+            compound_list.append(particle)
 
         # Verify we have read the last line by ensuring the next line in blank
         line = xyz_file.readline().split()
@@ -86,6 +87,8 @@ def read_xyz(filename, compound=None):
             )
             raise MBuildError(msg.format(n_atoms))
 
+    compound.add(compound_list)
+
     return compound
 
 

mbuild/packing.py

@@ -888,9 +888,12 @@ def _create_topology(container, comp_to_add, n_compounds):
     container : mb.Compound
         Compound with added compounds from PACKMOL.
     """
+    container_list = []
     for comp, m_compound in zip(comp_to_add, n_compounds):
         for _ in range(m_compound):
-            container.add(clone(comp))
+            container_list.append(clone(comp))
+
+    container.add(container_list)
     return container