Merge pull request #67 from chrisjonesBSU/graphene

Add graphene surface to library

hoomd_organics/library/__init__.py

@@ -20,3 +20,4 @@
     PolyEthylene,
 )
 from .simulations.tensile import Tensile
+from .surfaces import Graphene

hoomd_organics/library/surfaces.py

@@ -0,0 +1,46 @@
+"""Recipes to generate surfaces using mBuild."""
+
+from mbuild.compound import Compound
+from mbuild.lattice import Lattice
+
+
+class Graphene(Compound):
+    """Create a rectangular graphene layer or multiple layers.
+
+    Parameters
+    ----------
+    x_repeat : int, required
+        Number of times to repeat graphene lattice in the x-direciton.
+    y_repeat: int, required
+        Number of times to repeat graphene lattice in the y-direciton.
+    n_layers: int, optional, default 1
+        Number of times to repeat the complete layer in the normal direction.
+    periodicity : tuple of bools, length=3, optional, default=(True, True, False) # noqa: E501
+        Whether the Compound is periodic in the x, y, and z directions.
+        If None is provided, the periodicity is set to `(False, False, False)`
+        which is non-periodic in all directions.
+
+    Notes
+    -----
+    To create bonds along periodic boundaries of the layers in the x and y
+    directions, set `periodicity = (True, True, False)`
+
+    """
+
+    def __init__(
+        self, x_repeat, y_repeat, n_layers, periodicity=(True, True, False)
+    ):
+        super(Graphene, self).__init__(periodicity=periodicity)
+        spacings = [0.425, 0.246, 0.35]
+        points = [[1 / 6, 0, 0], [1 / 2, 0, 0], [0, 0.5, 0], [2 / 3, 1 / 2, 0]]
+        lattice = Lattice(
+            lattice_spacing=spacings,
+            angles=[90, 90, 90],
+            lattice_points={"A": points},
+        )
+        carbon = Compound(name="C")
+        layers = lattice.populate(
+            compound_dict={"A": carbon}, x=x_repeat, y=y_repeat, z=n_layers
+        )
+        self.add(layers)
+        self.freud_generate_bonds("C", "C", dmin=0.14, dmax=0.145)

hoomd_organics/tests/library/test_surfaces.py

@@ -0,0 +1,21 @@
+from hoomd_organics.library import Graphene
+
+
+class TestSurfaces:
+    def test_create_graphene_surface(self):
+        surface = Graphene(
+            x_repeat=2,
+            y_repeat=2,
+            n_layers=3,
+            periodicity=(False, False, False),
+        )
+        assert surface.n_particles == 4 * 2 * 2 * 3
+        assert surface.n_bonds == 54
+
+    def test_graphene_with_periodicity(self):
+        surface = Graphene(
+            x_repeat=2, y_repeat=2, n_layers=3, periodicity=(True, True, False)
+        )
+        assert surface.n_particles == 4 * 2 * 2 * 3
+        assert surface.periodicity == (True, True, False)
+        assert surface.n_bonds == 72