freud.density module is intended to compute a variety of quantities that relate spatial distributions of particles with other particles. In this notebook, we demonstrate
freud’s local density calculation, which can be used to characterize the particle distributions in some systems. In this example, we consider a toy example of calculating the particle density in the vicinity of a set of other points. This can be visualized as, for example, billiard balls on a table with certain
regions of the table being stickier than others. In practice, this method could be used for analyzing, e.g, binary systems to determine how densely one species packs close to the surface of the other.
import numpy as np import freud import matplotlib.pyplot as plt from matplotlib import patches
# Define some helper plotting functions. def add_patches(ax, points, radius=1, fill=False, color="#1f77b4", ls="solid", lw=None): """Add set of points as patches with radius to the provided axis""" for pt in points: p = patches.Circle(pt, fill=fill, linestyle=ls, radius=radius, facecolor=color, edgecolor=color, lw=lw) ax.add_patch(p) def plot_lattice(box, points, radius=1, ls="solid", lw=None): """Helper function for plotting points on a lattice.""" fig, ax = plt.subplots(1, 1, figsize=(9, 9)) box.plot(ax=ax) add_patches(ax, points, radius, ls=ls, lw=lw) return fig, ax
Let us consider a set of regions on a square lattice.
area = 2 radius = np.sqrt(area/np.pi) spot_area = area*100 spot_radius = np.sqrt(spot_area/np.pi) num = 6 scale = num*4 uc = freud.data.UnitCell(freud.Box.square(1), [[0.5, 0.5, 0]]) box, spot_centers = uc.generate_system(num, scale=scale) fig, ax = plot_lattice(box, spot_centers, spot_radius, ls="dashed", lw=2.5) plt.tick_params(axis="both", which="both", labelsize=14) plt.show()
Now let’s add a set of points to this box. Points are added by drawing from a normal distribution centered at each of the regions above. For demonstration, we will assume that each region has some relative “attractiveness,” which is represented by the covariance in the normal distributions used to draw points. Specifically, as we go up and to the right, the covariance increases proportional to the distance from the lower right corner of the box.
points =  fractional_distances_to_corner = np.linalg.norm(box.make_fractional(spot_centers), axis=-1) cov_basis = 20 * fractional_distances_to_corner for i, p in enumerate(spot_centers): np.random.seed(i) cov = cov_basis[i]*np.diag([1, 1, 0]) points.append( np.random.multivariate_normal(p, cov, size=(50,))) points = box.wrap(np.concatenate(points))
fig, ax = plot_lattice(box, spot_centers, spot_radius, ls="dashed", lw=2.5) plt.tick_params(axis="both", which="both", labelsize=14) add_patches(ax, points, radius, True, 'k', lw=None) plt.show()
We see that the density decreases as we move up and to the right. In order to compute the actual densities, we can leverage the
LocalDensity class. The class allows you to specify a set of query points around which the number of other points is computed. These other points can, but need not be, distinct from the query points. In our case, we want to use the blue regions as our query points with the small black dots as our data points.
When we construct the
LocalDensity class, there are two arguments. The first is the radius from the query points within which particles should be included in the query point’s counter. The second is the circumsphere diameter of the data points, not the query points. This distinction is critical for getting appropriate density values, since these values are used to actually check cutoffs and calculate the density.
density = freud.density.LocalDensity(spot_radius, radius) density.compute(system=(box, points), query_points=spot_centers);
fig, axes = plt.subplots(1, 2, figsize=(14, 6)) for i, data in enumerate([density.num_neighbors, density.density]): poly = np.poly1d(np.polyfit(cov_basis, data, 1)) axes[i].tick_params(axis="both", which="both", labelsize=14) axes[i].scatter(cov_basis, data) x = np.linspace(*axes[i].get_xlim(), 30) axes[i].plot(x, poly(x), label="Best fit") axes[i].set_xlabel("Covariance", fontsize=16) axes.set_ylabel("Number of neighbors", fontsize=16); axes.set_ylabel("Density", fontsize=16); plt.show()
As expected, we see that increasing the variance in the number of points centered at a particular query point decreases the total density at that point. The trend is noisy since we are randomly sampling possible positions, but the general behavior is clear.