slight tweaks

glotzerlab · Feb 13, 2024 · 3aca60e · 3aca60e
1 parent e0c2d29
commit 3aca60e
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Showing 2 changed files with 17 additions and 19 deletions.
diff --git a/environment.yml b/environment.yml
@@ -4,12 +4,12 @@ dependencies:
   - bokeh
   - fresnel>=0.12
   - freud
-  - gsd
+  - gsd<3
   - hoomd=2.*
   - ipywidgets>=7
   - jupyterlab>=3
   - lammps
-  - matplotlib>=3
+  - matplotlib>=3,<3.7
   - mdanalysis>=2
   - mdtraj
   - nbconvert>=6

diff --git a/module_intros/locality.Filter.ipynb b/module_intros/locality.Filter.ipynb
@@ -54,7 +54,7 @@
     {
      "data": {
       "text/plain": [
-       "<freud.locality.NeighborList at 0x7f0769d6b0c0>"
+       "<freud.locality.NeighborList at 0x7f3671512840>"
       ]
      },
      "execution_count": 1,
@@ -102,7 +102,7 @@
     {
      "data": {
       "text/plain": [
-       "<freud.locality.NeighborList at 0x7f08241e9fc0>"
+       "<freud.locality.NeighborList at 0x7f371c162600>"
       ]
      },
      "execution_count": 2,
@@ -138,7 +138,7 @@
     {
      "data": {
       "text/plain": [
-       "<freud.locality.NeighborList at 0x7f0769d82640>"
+       "<freud.locality.NeighborList at 0x7f371e34fa80>"
       ]
      },
      "execution_count": 3,
@@ -153,11 +153,9 @@
     "M = 15\n",
     "query_point_indices = np.arange(N).repeat(M)\n",
     "point_indices = np.random.randint(low=0, high=N, size=M * N)\n",
-    "distances = np.linalg.norm(\n",
-    "    box.wrap(points[point_indices, :] - points[query_point_indices, :]), axis=-1\n",
-    ")\n",
+    "vectors = box.wrap(points[point_indices, :] - points[query_point_indices, :])\n",
     "nlist = freud.locality.NeighborList.from_arrays(\n",
-    "    N, N, query_point_indices, point_indices, distances\n",
+    "    N, N, query_point_indices, point_indices, vectors\n",
     ")\n",
     "\n",
     "# call compute\n",
@@ -184,7 +182,7 @@
     {
      "data": {
       "text/plain": [
-       "<freud.locality.NeighborList at 0x7f0769d6b200>"
+       "<freud.locality.NeighborList at 0x7f36707510c0>"
       ]
      },
      "execution_count": 4,
@@ -310,22 +308,22 @@
    "id": "24fc48ae",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: Query point indices 0, 1, 2, 3, 4 do not have full neighbor shells.\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
-       "<freud.locality.FilterSANN at 0x7f083f9f51d0>"
+       "<freud.locality.FilterSANN at 0x7f371e352520>"
       ]
      },
      "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "WARNING: Query point indices 0, 1, 2, 3, 4 do not have full neighbor shells.\n"
+     ]
     }
    ],
    "source": [
@@ -404,7 +402,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,