From 7d00de9edffc88143aff3b6cda469635a8ac11cb Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Wed, 19 Jun 2024 07:49:02 -0600
Subject: [PATCH] Add support for freud 3.0 (#93)

* fix parameter in cluster module

* update version to match what we are using on conda-forge

* use box module to get vectors

* update version
---
 cmeutils/__version__.py |  2 +-
 cmeutils/gsd_utils.py   | 16 +++++++++++++---
 environment-dev.yml     |  2 +-
 environment.yml         |  2 +-
 4 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/cmeutils/__version__.py b/cmeutils/__version__.py
index a82b376..67bc602 100644
--- a/cmeutils/__version__.py
+++ b/cmeutils/__version__.py
@@ -1 +1 @@
-__version__ = "1.1.1"
+__version__ = "1.3.0"
diff --git a/cmeutils/gsd_utils.py b/cmeutils/gsd_utils.py
index 88893d3..c3f414d 100644
--- a/cmeutils/gsd_utils.py
+++ b/cmeutils/gsd_utils.py
@@ -129,11 +129,21 @@ def get_molecule_cluster(gsd_file=None, snap=None, gsd_frame=-1):
     n_query_points = n_points = snap.particles.N
     query_point_indices = snap.bonds.group[:, 0]
     point_indices = snap.bonds.group[:, 1]
-    distances = system.box.compute_distances(
-        system.points[query_point_indices], system.points[point_indices]
+    box = freud.box.Box(
+        snap.configuration.box[0],
+        snap.configuration.box[1],
+        snap.configuration.box[2],
+    )
+    vectors = box.wrap(
+        snap.particles.position[query_point_indices]
+        - snap.particles.position[point_indices]
     )
     nlist = freud.NeighborList.from_arrays(
-        n_query_points, n_points, query_point_indices, point_indices, distances
+        num_query_points=n_query_points,
+        num_points=n_points,
+        query_point_indices=query_point_indices,
+        point_indices=point_indices,
+        vectors=vectors,
     )
     cluster = freud.cluster.Cluster()
     cluster.compute(system=system, neighbors=nlist)
diff --git a/environment-dev.yml b/environment-dev.yml
index 65c1156..7638253 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -2,7 +2,7 @@ name: cmeutils-dev
 channels:
   - conda-forge
 dependencies:
-  - freud =2.13.2
+  - freud >= 3.0
   - gmso >=0.11.2
   - fresnel >=0.13.5
   - gsd >=3.0
diff --git a/environment.yml b/environment.yml
index eafb255..a99670e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: cmeutils
 channels:
   - conda-forge
 dependencies:
-  - freud =2.13.2
+  - freud >= 3.0
   - gmso >=0.11.2
   - fresnel >=0.13.5
   - gsd >=3.0