add seed parameter

flowermd/base/system.py

@@ -626,6 +626,8 @@ class Pack(System):
         The space (nm) between the edge of the box and the molecules.
     overlap : float, default 0.2
         Minimum separation (nm) between particles of different molecules.
+    seed : int, default 12345
+        Random seed to be passed to PACKMOL.
 
 
     .. warning::
@@ -655,6 +657,7 @@ def __init__(
         packing_expand_factor=5,
         edge=0.2,
         overlap=0.2,
+        seed=12345,
         fix_orientation=False,
     ):
         if not isinstance(density, u.array.unyt_quantity):
@@ -668,10 +671,11 @@ def __init__(
         self.packing_expand_factor = packing_expand_factor
         self.edge = edge
         self.overlap = overlap
+        self.overlap = seed
         self.fix_orientation = fix_orientation
         super(Pack, self).__init__(molecules=molecules, base_units=base_units)
 
-    def _build_system(self):
+    def _build_system(self,**kwargs):
         mass_density = u.Unit("kg") / u.Unit("m**3")
         number_density = u.Unit("m**-3")
         if self.density.units.dimensions == mass_density.dimensions:
@@ -695,8 +699,10 @@ def _build_system(self):
             n_compounds=[1 for i in self.all_molecules],
             box=list(target_box * self.packing_expand_factor),
             overlap=self.overlap,
+            seed=self.seed,
             edge=self.edge,
             fix_orientation=self.fix_orientation,
+            **kwargs
         )
         return system
 

flowermd/tests/base/test_system.py

@@ -200,6 +200,32 @@ def test_pack_box(self, benzene_molecule):
         assert np.prod(low_density_system.box.lengths) > np.prod(
             high_density_system.box.lengths
         )
+
+    def test_pack_seed(self, benzene_molecule):
+        benzene_mol = benzene_molecule(n_mols=3)
+        default_seed = Pack(molecules=[benzene_mol], density=0.1)
+        change_seed = Pack(molecules=[benzene_mol], density=0.1, seed=12340)
+        assert np.prod(low_density_system.box.lengths) > np.prod(
+            high_density_system.box.lengths
+        )
+    #adding test for kwargs argument in system.py Pack class    
+    def test_pack_kwargs_attr(self, polyethylene):
+        polyethylene = polyethylene(lengths=5, num_mols=1)
+        system = Pack(
+            molecules=[polyethylene],
+            density=1.0,
+            compound,
+            n_compounds=None,
+            box=None,
+            density=None,
+            overlap=0.2,
+            seed=12345,
+            sidemax=100.0, edge=0.2, compound_ratio=None, aspect_ratio=None, fix_orientation=False, temp_file=None, update_port_locations=False, packmol_args=Non
+        )
+        assert system._ff_kwargs["r_cut"] == 2.5
+        assert system._ff_kwargs["nlist_buffer"] == 0.5
+        assert system._ff_kwargs["pppm_kwargs"]["resolution"] == (4, 4, 4)
+        assert system._ff_kwargs["pppm_kwargs"]["order"] == 3
 
     def test_mass(self, pps_molecule):
         pps_mol = pps_molecule(n_mols=20)