Merge branch 'main' into main

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.2 # Ruff version
+    rev: v0.9.3 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

flowermd/base/system.py

@@ -48,6 +48,8 @@ class System(ABC):
         Dictionary of base units to use for scaling.
         Dictionary keys are "length", "mass", and "energy". Values should be an
         unyt array of the desired base unit.
+    kwargs
+        See classes that inherit from System for kwargs
 
     Warnings
     --------
@@ -68,6 +70,7 @@ def __init__(
         self,
         molecules,
         base_units=dict(),
+        **kwargs,
     ):
         self._molecules = check_return_iterable(molecules)
         self.all_molecules = []
@@ -123,7 +126,7 @@ def __init__(
                 self.n_mol_types += 1
 
         # Create mBuild system
-        self.system = self._build_system()
+        self.system = self._build_system(**kwargs)
         # Create GMSO topology
         self.gmso_system = self._convert_to_gmso()
 
@@ -637,6 +640,10 @@ 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
+        Change seed to be passed to PACKMOL for different starting positions
+    kwargs
+        Arguments to be passed into mbuild.packing.fill_box
 
 
     .. warning::
@@ -666,7 +673,9 @@ def __init__(
         packing_expand_factor=5,
         edge=0.2,
         overlap=0.2,
+        seed=12345,
         fix_orientation=False,
+        **kwargs,
     ):
         if isinstance(density, (int, float)):
             warnings.warn(
@@ -678,10 +687,13 @@ def __init__(
         self.packing_expand_factor = packing_expand_factor
         self.edge = edge
         self.overlap = overlap
+        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):
+    def _build_system(self, **kwargs):
         mass_density = Units.kg_m3
         number_density = Units.n_m3
         if self.density.units.dimensions == mass_density.dimensions:
@@ -705,8 +717,10 @@ 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_molecule.py

@@ -207,8 +207,8 @@ def test_polymer_different_chain_lengths(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 53
-        assert len(polymer.molecules[0].children) == 3
-        assert len(polymer.molecules[1].children) == 4
+        assert len(polymer.molecules[0].labels["all-monomers"]) == 3
+        assert len(polymer.molecules[1].labels["all-monomers"]) == 4
 
     def test_polymer_different_num_mol(self, dimethylether_smiles):
         polymer = Polymer(
@@ -220,9 +220,9 @@ def test_polymer_different_num_mol(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 55
-        assert len(polymer.molecules[0].children) == 3
-        assert len(polymer.molecules[1].children) == 2
-        assert len(polymer.molecules[2].children) == 2
+        assert len(polymer.molecules[0].labels["all-monomers"]) == 3
+        assert len(polymer.molecules[1].labels["all-monomers"]) == 2
+        assert len(polymer.molecules[2].labels["all-monomers"]) == 2
 
     def test_polymer_unequal_num_mol_length(self, dimethylether_smiles):
         with pytest.raises(ValueError):

flowermd/tests/base/test_system.py

@@ -201,6 +201,33 @@ def test_pack_box(self, benzene_molecule):
             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 not np.array_equal(
+            default_seed.system.xyz, change_seed.system.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)
+        system1 = Pack(
+            molecules=[polyethylene],
+            density=1.0,
+            overlap=0.2,
+            seed=12345,
+            fix_orientation=True,
+        )
+        system2 = Pack(
+            molecules=[polyethylene],
+            density=1.0,
+            overlap=0.2,
+            seed=12345,
+            fix_orientation=False,
+        )
+        assert not np.array_equal(system1.system.xyz, system2.system.xyz)
+
     def test_mass(self, pps_molecule):
         pps_mol = pps_molecule(n_mols=20)
         system = Pack(molecules=[pps_mol], density=1.0)