correctly account for individually added bonds, angles, and dihedrals

src/create_bonds.cpp

@@ -342,6 +342,7 @@ void CreateBonds::single_bond()
     bond_atom[m][num_bond[m]] = batom2;
     num_bond[m]++;
   }
+  ++atom->nbonds;
 
   if (force->newton_bond) return;
 
@@ -389,6 +390,7 @@ void CreateBonds::single_angle()
     angle_atom3[m][num_angle[m]] = aatom3;
     num_angle[m]++;
   }
+  ++atom->nangles;
 
   if (force->newton_bond) return;
 
@@ -452,6 +454,7 @@ void CreateBonds::single_dihedral()
     dihedral_atom4[m][num_dihedral[m]] = datom4;
     num_dihedral[m]++;
   }
+  ++atom->ndihedrals;
 
   if (force->newton_bond) return;