Merge branch 'main' into 700-lammpswrite-updates

.pre-commit-config.yaml

@@ -21,13 +21,13 @@ repos:
     - id: black
       args: [--line-length=80]
 - repo: https://github.com/pycqa/isort
-  rev: 5.11.1
+  rev: 5.12.0
   hooks:
     - id: isort
       name: isort (python)
       args: [--profile=black, --line-length=80]
 - repo: https://github.com/pycqa/pydocstyle
-  rev: '6.1.1'
+  rev: '6.3.0'
   hooks:
     - id: pydocstyle
       exclude: ^(gmso/abc|gmso/core|gmso/tests/|docs/|devtools/|setup.py)

environment-dev.yml

@@ -5,7 +5,7 @@ dependencies:
   - python>=3.8
   - numpy
   - sympy
-  - unyt
+  - unyt<=2.9.2
   - boltons
   - lxml
   - pydantic>1.8

environment.yml

@@ -5,7 +5,7 @@ dependencies:
   - python>=3.8
   - numpy
   - sympy
-  - unyt
+  - unyt<=2.9.2
   - boltons
   - lxml
   - pydantic>1.8

gmso/core/box.py

@@ -169,7 +169,7 @@ def _unit_vectors_from_angles(self):
         #    and then the xy plane, with the z-axis
         box_vec = [[1, 0, 0], [cosg, sing, 0], [cosb, mat_coef_y, mat_coef_z]]
 
-        return u.unyt_array(box_vec, u.dimensionless, dtype=np.float)
+        return u.unyt_array(box_vec, u.dimensionless, dtype=float)
 
     def get_vectors(self):
         """Return the vectors of the box."""

gmso/core/forcefield.py

@@ -613,14 +613,16 @@ def _xml_from_gmso(self, filename, overwrite=False):
         )
 
         metadata = etree.SubElement(ff_el, "FFMetaData")
-        if not self.scaling_factors.get("electrostatics14Scale") is None:
+        if self.scaling_factors.get("electrostatics14Scale") is not None:
             metadata.attrib["electrostatics14Scale"] = str(
                 self.scaling_factors.get("electrostatics14Scale")
             )
-        if not self.scaling_factors.get("nonBonded14Scale") is None:
+        if self.scaling_factors.get("nonBonded14Scale") is not None:
             metadata.attrib["nonBonded14Scale"] = str(
                 self.scaling_factors.get("nonBonded14Scale")
             )
+        if self.combining_rule is not None:
+            metadata.attrib["combiningRule"] = str(self.combining_rule)
 
         # ToDo: ParameterUnitsDefintions and DefaultUnits
         if self.units:

gmso/external/convert_mbuild.py

@@ -28,6 +28,7 @@ def from_mbuild(
     search_method=element_by_symbol,
     parse_label=True,
     custom_groups=None,
+    infer_elements=False,
 ):
     """Convert an mbuild.Compound to a gmso.Topology.
 
@@ -75,6 +76,9 @@ def from_mbuild(
         matching name on the way down from compound.children. Only the first match
         while moving downwards will be assigned to the site. If parse_label=False,
         this argument does nothing.
+    infer_elements : bool, default=False
+        Allows the reader to try to load element info from the mbuild Particle.name
+        instead of only from the populated Particle.element
 
     Returns
     -------
@@ -104,7 +108,9 @@ def from_mbuild(
 
     # Use site map to apply Compound info to Topology.
     for part in compound.particles():
-        site = _parse_site(site_map, part, search_method)
+        site = _parse_site(
+            site_map, part, search_method, infer_element=infer_elements
+        )
         top.add_site(site)
 
     for b1, b2 in compound.bonds():
@@ -247,10 +253,14 @@ def _parse_particle(particle_map, site):
     return particle
 
 
-def _parse_site(site_map, particle, search_method):
-    """Parse information for a gmso.Site from a mBuild.Compound adn add it to the site map."""
+def _parse_site(site_map, particle, search_method, infer_element=False):
+    """Parse information for a gmso.Site from a mBuild.Compound and add it to the site map."""
     pos = particle.xyz[0] * u.nm
-    ele = search_method(particle.element.symbol) if particle.element else None
+    if particle.element:
+        ele = search_method(particle.element.symbol)
+    else:
+        ele = search_method(particle.name) if infer_element else None
+
     charge = particle.charge * u.elementary_charge if particle.charge else None
     mass = particle.mass * u.amu if particle.mass else None
 

gmso/formats/xyz.py

@@ -40,7 +40,7 @@ def read_xyz(filename):
                     "were expected, but at least one fewer was found."
                 )
                 raise ValueError(msg.format(n_atoms))
-            tmp = np.array(line[1:4], dtype=np.float) * u.angstrom
+            tmp = np.array(line[1:4], dtype=float) * u.angstrom
             coords[row] = tmp.in_units(u.nanometer)
             site = Atom(name=line[0], position=coords[row])
             top.add_site(site)

gmso/parameterization/foyer_utils.py

@@ -60,7 +60,7 @@ def get_topology_graph(
                 if atomdata_populator
                 else {}
             )
-            if atom.name.startswith("_"):
+            if atom.name.startswith("_") or not atom.element:
                 top_graph.add_atom(
                     name=atom.name,
                     index=j,  # Assumes order is preserved
@@ -70,7 +70,6 @@ def get_topology_graph(
                     molecule=atom.molecule.name if atom.molecule else None,
                     **kwargs,
                 )
-
             else:
                 top_graph.add_atom(
                     name=atom.name,

gmso/tests/base_test.py

@@ -649,3 +649,23 @@ def hierarchical_top(self, hierarchical_compound):
         top = from_mbuild(hierarchical_compound)  # Create GMSO topology
         top.identify_connections()
         return top
+
+    @pytest.fixture
+    def ethane_gomc(self):
+        ethane_gomc = mb.load("CC", smiles=True)
+        ethane_gomc.name = "ETH"
+
+        return ethane_gomc
+
+    @pytest.fixture
+    def ethanol_gomc(self):
+        ethanol_gomc = mb.load("CCO", smiles=True)
+        ethanol_gomc.name = "ETO"
+
+        return ethanol_gomc
+
+    @pytest.fixture
+    def methane_ua_gomc(self):
+        methane_ua_gomc = mb.Compound(name="_CH4")
+
+        return methane_ua_gomc