DOC: Updating disloc mobility docs to work with returned bulk

libAtoms · Sep 9, 2024 · f834c4f · f834c4f
1 parent 6a7f5f1
commit f834c4f
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/docs/applications/disloc_mobility.ipynb b/docs/applications/disloc_mobility.ipynb
@@ -225,7 +225,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Si_kink = Si_disloc.build_kink_cylinder(\n",
+    "Si_bulk, Si_kink = Si_disloc.build_kink_cylinder(\n",
     "                    radius=20,\n",
     "                    kink_map= [0] * 5 + [1] * 5\n",
     "                )\n",
@@ -247,7 +247,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Si_quad_kink = Si_quad.build_kink_quadrupole(\n",
+    "Si_quad_bulk, Si_quad_kink = Si_quad.build_kink_quadrupole(\n",
     "    glide_separation=8,\n",
     "    kink_map=[0]*5 + [1]*5\n",
     ")\n",
@@ -268,7 +268,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Si_quad_kink = Si_quad.build_minimal_kink_quadrupole(\n",
+    "Si_quad_bulk, Si_quad_kink = Si_quad.build_minimal_kink_quadrupole(\n",
     "    glide_separation=8,\n",
     "    n_kink=1\n",
     ")\n",
@@ -302,7 +302,7 @@
     "\n",
     "kink_map = [0, 0, 0, 1, 1, 1]\n",
     "\n",
-    "ref_bulk, glide_structs = Si_disloc.build_kink_glide_structs(kink_map, radius=40)\n",
+    "ref_bulk, glide_structs, struct_map = Si_disloc.build_kink_glide_structs(kink_map, radius=40)\n",
     "\n",
     "# glide_structs has a length of 2, as only two unique values in the kink map\n",
     "\n",
@@ -311,7 +311,7 @@
     "    opt = PreconLBFGS(struct)\n",
     "    opt.run(1e-1)\n",
     "\n",
-    "Si_kink = Si_disloc.build_kink_from_glide_cyls(ref_bulk, glide_structs, kink_map)\n",
+    "Si_bulk, Si_kink = Si_disloc.build_kink_from_glide_cyls(ref_bulk, glide_structs, kink_map, struct_map)\n",
     "\n",
     "Si_disloc.view_cyl(Si_kink)"
    ]