fix relaxor spelling and add doc str

materialsvirtuallab · Dec 11, 2023 · c1b724e · c1b724e
1 parent 7ad8550
commit c1b724e
Showing 1 changed file with 17 additions and 16 deletions.
diff --git a/examples/LiFePO4-NEB.ipynb b/examples/LiFePO4-NEB.ipynb
@@ -152,10 +152,10 @@
     "%%time\n",
     "results = {}\n",
     "for UP_label, UP_cal in UP_cals.items():\n",
-    "    relaxor = RelaxCalc(UP_cal, optimizer=\"BFGS\", relax_cell=True, fmax=0.02)\n",
-    "    s_LFPO_relaxed = relaxor.calc(s_LFPO)['final_structure']\n",
+    "    relaxer = RelaxCalc(UP_cal, optimizer=\"BFGS\", relax_cell=True, fmax=0.02)\n",
+    "    supercell_LFPO_relaxed = relaxer.calc(s_LFPO)['final_structure']\n",
     "    results[UP_label] = {\n",
-    "        \"supercell_LFPO\": s_LFPO_relaxed\n",
+    "        \"supercell_LFPO\": supercell_LFPO_relaxed\n",
     "    }"
    ]
   },
@@ -185,19 +185,19 @@
    "source": [
     "%%time\n",
     "for UP_label, UP_cal in UP_cals.items():\n",
-    "    relaxor = RelaxCalc(UP_cal, optimizer=\"BFGS\", relax_cell=False, fmax=0.02)\n",
-    "    s_LFPO_relaxed = results[UP_label][\"supercell_LFPO\"]\n",
+    "    relaxer = RelaxCalc(UP_cal, optimizer=\"BFGS\", relax_cell=False, fmax=0.02)\n",
+    "    supercell_LFPO_relaxed = results[UP_label][\"supercell_LFPO\"]\n",
     "\n",
     "    # NEB path along b and c directions have the same starting image.\n",
-    "    s_LFPO_end_b = s_LFPO_relaxed.copy()\n",
+    "    s_LFPO_end_b = supercell_LFPO_relaxed.copy()\n",
     "    s_LFPO_end_b.remove_sites([11])\n",
-    "    s_LFPO_end_b_relaxed = relaxor.calc(s_LFPO_end_b)['final_structure']\n",
-    "    s_LFPO_end_c = s_LFPO_relaxed.copy()\n",
+    "    s_LFPO_end_b_relaxed = relaxer.calc(s_LFPO_end_b)['final_structure']\n",
+    "    s_LFPO_end_c = supercell_LFPO_relaxed.copy()\n",
     "    s_LFPO_end_c.remove_sites([4])\n",
-    "    s_LFPO_end_c_relaxed = relaxor.calc(s_LFPO_end_c)['final_structure']\n",
-    "    s_LFPO_start_bc = s_LFPO_relaxed.copy()\n",
+    "    s_LFPO_end_c_relaxed = relaxer.calc(s_LFPO_end_c)['final_structure']\n",
+    "    s_LFPO_start_bc = supercell_LFPO_relaxed.copy()\n",
     "    s_LFPO_start_bc.remove_sites([5])\n",
-    "    s_LFPO_start_bc_relaxed = relaxor.calc(s_LFPO_start_bc)['final_structure']\n",
+    "    s_LFPO_start_bc_relaxed = relaxer.calc(s_LFPO_start_bc)['final_structure']\n",
     "    results[UP_label].update(\n",
     "        {\n",
     "            \"supercell_LFPO_end_b\":s_LFPO_end_b_relaxed,\n",
@@ -627,13 +627,14 @@
     "\n",
     "\n",
     "def generate_path_cif_from_images(images: list, filename: str):\n",
-    "    images_struct = [AseAtomsAdaptor().get_structure(i) for i in images]\n",
+    "    \"\"\"Generate a cif file from a list of image atoms.\"\"\"\n",
+    "    image_structs = list(map(AseAtomsAdaptor().get_structure, images))\n",
     "    sites = set()\n",
-    "    lat = images_struct[0].lattice\n",
-    "    for site in chain(*(struct for struct in images_struct)):\n",
+    "    lat = image_structs[0].lattice\n",
+    "    for site in chain(*(struct for struct in image_structs)):\n",
     "        sites.add(PeriodicSite(site.species, site.frac_coords, lat))\n",
-    "    nebpath = Structure.from_sites(sorted(sites))\n",
-    "    nebpath.to(filename, \"cif\")"
+    "    neb_path = Structure.from_sites(sorted(sites))\n",
+    "    neb_path.to(filename, \"cif\")"
    ]
   },
   {