fix parameter in cluster module

cmelab · May 28, 2024 · 743ad56 · 743ad56
1 parent e32fb61
commit 743ad56
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/cmeutils/gsd_utils.py b/cmeutils/gsd_utils.py
@@ -129,11 +129,16 @@ 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]
+    vectors = (
+        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
@@ -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
@@ -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