Migration to freud Version 3#

Version 3 of the freud library introduces a few breaking changes to make the API more intuitive and facilitate future development. This guide explains how to alter scripts which use freud v2 APIs so they can be used with freud v3.

Overview of API Changes#

Goal

v2 API

v3 API

Use default RDF normalization.

freud.density.RDF(..., normalize=False)

freud.density.RDF(..., normalization_mode='exact')

Normalize small system RDFs to 1.

freud.density.RDF(..., normalize=True)

freud.density.RDF(..., normalization_mode='finite_size')

Color voronoi diagram by number of cell sides.

voro.plot(..., color_by_sides=True)

voro.plot(..., color_by='sides')

Get vectors corresponding to neighbor pairs.

points[nlist.point_indices] - points[nlist.query_point_indices]

nlist.vectors

Create a custom neighborlist from arrays.

freud.locality.NeighborList.from_arrays(..., distances=...)

freud.locality.NeighborList.from_arrays(..., vectors=...)

Compare environments of all particle pairs with EnvironmentCluster.

env_cluster.compute(..., global_search=True)

env_cluster.compute(..., neighbors=all_pairs_nlist, ...)

Use EnvironmentMotifMatch with a set of neighbors

freud.environment.EnvironmentMotifMatch().compute(..., neighbors=...)

freud.environment.EnvironmentMotifMatch().compute(..., env_neighbors=...)

Use EnvironmentCluster with a set of neighbors that define the cluster

freud.environment.EnvironmentCluster().compute(..., neighbors=...)

freud.environment.EnvironmentCluster().compute(..., cluster_neighbors=...)

Compute nematic order parameter.

freud.order.Nematic(u=director).compute(orientations=quaternions)

freud.order.Nematic().compute(orientations=orientation_vectors)

Find translational order in 2D systems.

Use freud.order.Translational or freud.order.Hexatic.

Use freud.order.Hexatic.