diff --git a/environment.yml b/environment.yml index b2b5f44..c7ef462 100644 --- 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 index e9095ea..ab47708 100644 --- a/module_intros/locality.Filter.ipynb +++ b/module_intros/locality.Filter.ipynb @@ -54,7 +54,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 1, @@ -102,7 +102,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -138,7 +138,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "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": [ - "" + "" ] }, "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": [ - "" + "" ] }, "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,