default mass and charge of Compound to None

mbuild/compound.py

@@ -91,11 +91,11 @@ class Compound(object):
         The type of Compound.
     pos : np.ndarray, shape=(3,), dtype=float, optional, default=[0, 0, 0]
         The position of the Compound in Cartestian space
-    mass : float, optional, default=0.0
+    mass : float, optional, default=None
         The mass of the compound. If none is set, then will try to
         infer the mass from a compound's element attribute.
         If neither `mass` or `element` are specified, then the
-        mass will be zero.
+        mass will be None.
     charge : float, optional, default=0.0
         Currently not used. Likely removed in next release.
     periodicity : tuple of bools, length=3, optional, default=None
@@ -147,8 +147,8 @@ def __init__(
         subcompounds=None,
         name=None,
         pos=None,
-        mass=0.0,
-        charge=0.0,
+        mass=None,
+        charge=None,
         periodicity=None,
         box=None,
         element=None,
@@ -202,7 +202,7 @@ def __init__(
                 raise MBuildError(
                     "Can't set the mass of a Compound with subcompounds. "
                 )
-            self._charge = 0.0
+            self._charge = None
             self._mass = mass
             self.add(subcompounds)
         else:
@@ -358,17 +358,22 @@ def mass(self):
         if self._contains_only_ports():
             return self._particle_mass(self)
         else:
+            particle_masses = [self._particle_mass(p) for p in self.particles()]
+            if None in particle_masses:
+                warn(
+                    f"Some particle in this Compound has not had their mass set."
+                )
             return sum([self._particle_mass(p) for p in self.particles()])
 
     @staticmethod
     def _particle_mass(particle):
-        if particle._mass:
+        if particle._mass is not None:
             return particle._mass
         else:
             if particle.element:
                 return particle.element.mass
             else:
-                return 0
+                return None
 
     @mass.setter
     def mass(self, value):
@@ -386,7 +391,13 @@ def mass(self, value):
     @property
     def charge(self):
         """Get the charge of the Compound."""
-        return sum([particle._charge for particle in self.particles()])
+        return sum(
+            [
+                particle._charge
+                for particle in self.particles()
+                if particle._charge is not None
+            ]
+        )
 
     @charge.setter
     def charge(self, value):
@@ -673,7 +684,7 @@ def add(
                 "Only objects that inherit from mbuild.Compound can be added "
                 f"to Compounds. You tried to add '{new_child}'."
             )
-        if self._mass != 0.0 and not isinstance(new_child, Port):
+        if self._mass is not None and not isinstance(new_child, Port):
             warn(
                 f"{self} has a pre-defined mass of {self._mass}, "
                 "which will be reset to zero now that it contains children "

mbuild/packing.py

@@ -772,9 +772,10 @@ def _validate_mass(compound, n_compounds):
     found_zero_mass = False
     total_mass = 0
     for c, n in zip(compound, n_compounds):
-        comp_masses = [c._particle_mass(p) for p in c.particles()]
-        if 0.0 in comp_masses:
+        comp_masses = np.array([c._particle_mass(p) for p in c.particles()])
+        if 0.0 in comp_masses or None in comp_masses:
             found_zero_mass = True
+        comp_masses[comp_masses == None] = 0.0
         total_mass += np.sum(comp_masses) * n
 
     if total_mass == 0:
@@ -788,7 +789,7 @@ def _validate_mass(compound, n_compounds):
     if found_zero_mass:
         warnings.warn(
             "Some of the compounds or subcompounds in `compound` "
-            "have a mass of zero. This may have an effect on "
+            "have a mass of zero/None. This may have an effect on "
             "density calculations"
         )
     return total_mass

mbuild/tests/test_compound.py

@@ -396,7 +396,7 @@ def test_init_mass(self):
         assert bead_overwrite.mass == 1.0
 
         bead_no_mass = mb.Compound(name="A")
-        assert bead_no_mass.mass == 0.0
+        assert bead_no_mass.mass == None
 
     def test_init_with_bad_mass(self):
         with pytest.raises(MBuildError):