moving *kwargs argument

cmelab · Jan 27, 2025 · 2eeb836 · 2eeb836
1 parent 5fa9efd
commit 2eeb836
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 13 deletions.
diff --git a/flowermd/base/system.py b/flowermd/base/system.py
@@ -659,6 +659,7 @@ def __init__(
         overlap=0.2,
         seed=12345,
         fix_orientation=False,
+        **kwargs
     ):
         if not isinstance(density, u.array.unyt_quantity):
             self.density = density * u.Unit("g") / u.Unit("cm**3")
@@ -671,11 +672,11 @@ def __init__(
         self.packing_expand_factor = packing_expand_factor
         self.edge = edge
         self.overlap = overlap
-        self.overlap = seed
+        self.seed = seed
         self.fix_orientation = fix_orientation
-        super(Pack, self).__init__(molecules=molecules, base_units=base_units)
+        super(Pack, self).__init__(molecules=molecules, base_units=base_units,**kwargs)
 
-    def _build_system(self, **kwargs):
+    def _build_system(self):
         mass_density = u.Unit("kg") / u.Unit("m**3")
         number_density = u.Unit("m**-3")
         if self.density.units.dimensions == mass_density.dimensions:
@@ -701,8 +702,7 @@ def _build_system(self, **kwargs):
             overlap=self.overlap,
             seed=self.seed,
             edge=self.edge,
-            fix_orientation=self.fix_orientation,
-            **kwargs,
+            fix_orientation=self.fix_orientation
         )
         return system
 

diff --git a/flowermd/tests/base/test_system.py b/flowermd/tests/base/test_system.py
@@ -205,9 +205,8 @@ 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
-        )
+        assert not np.array_equal(default_seed.xyz,change_seed.xyz)
+
     #adding test for kwargs argument in system.py Pack class
     def test_pack_kwargs_attr(self, polyethylene):
         polyethylene = polyethylene(lengths=5, num_mols=1)
@@ -220,12 +219,9 @@ def test_pack_kwargs_attr(self, polyethylene):
             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
+            sidemax=100.0, edge=0.2, compound_ratio=None, aspect_ratio=None, fix_orientation=False, temp_file=None, update_port_locations=False, packmol_args=None
         )
-        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
+        assert 
 
     def test_mass(self, pps_molecule):
         pps_mol = pps_molecule(n_mols=20)