Populate Group information from mBuild Compounds (#683)

* [pre-commit.ci] pre-commit autoupdate (#673)

updates:
- [github.com/psf/black: 22.3.0 → 22.6.0](psf/black@22.3.0...22.6.0)

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

* Revert to older versions of forcefield

* Add import for xml_representation in parameteric potential"

* Added tests for generating a forcefield object from a GMSO topology

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Remove unused import

* pin unyt to version 2.8

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Populate group names with top level compound names if hierarchy doesn't exist

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

gmso/external/convert_mbuild.py

@@ -60,7 +60,7 @@ def from_mbuild(
         Valid functions are element_by_symbol, element_by_name,
         element_by_atomic_number, and element_by_mass, which can be imported
         from `gmso.core.element'
-    parse_label : bool, optional, default=False
+    parse_label : bool, optional, default=True
         Option to parse hierarchy info of the compound into system of top label,
         including, group, molecule and residue labels.
 
@@ -85,6 +85,7 @@ def from_mbuild(
         for child in compound.children:
             if not child.children:
                 site = _parse_site(site_map, child, search_method)
+                site.group = compound.name
                 top.add_site(site)
             else:
                 for particle in child.particles():
@@ -93,6 +94,7 @@ def from_mbuild(
                     top.add_site(site)
     else:
         site = _parse_site(site_map, compound, search_method)
+        site.group = compound.name
         top.add_site(site)
 
     for b1, b2 in compound.bonds():

gmso/tests/test_convert_mbuild.py

@@ -174,3 +174,12 @@ def test_hierarchical_structure(self, hierarchical_top):
             assert label in hierarchical_top.unique_site_labels(
                 "group", name_only=True
             )
+
+    @pytest.mark.skipif(not has_mbuild, reason="mBuild is not installed")
+    def test_group_2_level_compound(self):
+        mb_cpd = mb.Compound(name="_CH4", mass=12)
+        filled_box = mb.fill_box(mb_cpd, n_compounds=2, density=0.01)
+        filled_box.name = "group1"
+        top = from_mbuild(filled_box)
+        for site in top.sites:
+            assert site.group == filled_box.name