Update tutorial

SMTG-Bham · Aug 13, 2024 · b04b9bf · b04b9bf
1 parent bdbdebb
commit b04b9bf
Showing 1 changed file with 19 additions and 21 deletions.
diff --git a/examples/fermisolver_tutorial.ipynb b/examples/fermisolver_tutorial.ipynb
@@ -24,8 +24,8 @@
    "cell_type": "code",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2024-08-11T16:35:19.573318Z",
-     "start_time": "2024-08-11T16:35:00.021051Z"
+     "end_time": "2024-08-12T20:08:34.735725Z",
+     "start_time": "2024-08-12T20:07:56.127239Z"
     }
    },
    "source": [
@@ -58,12 +58,10 @@
     "# defect thermodynamics and the electronic structure of the bulk material. The\n",
     "# chempots argument can be supplied to overwrite any chempots associated with\n",
     "# the defect thermodynamics object, but regardless chempots must be supplied\n",
-    "fs = FermiSolver(defect_thermodynamics=defect_thermo,\n",
-    "                      bulk_dos=vasprun_path,\n",
-    "                      chempots=chempots, backend=\"doped\")\n",
-    "py_fs = FermiSolver(defect_thermodynamics=defect_thermo,\n",
-    "                             bulk_dos=vasprun_path,\n",
-    "                             chempots=chempots, backend=\"py-sc-fermi\")\n",
+    "fs = FermiSolver(defect_thermodynamics=defect_thermo, bulk_dos=vasprun_path,\n",
+    "                 chempots=chempots, backend=\"doped\")  # default backend\n",
+    "py_fs = FermiSolver(defect_thermodynamics=defect_thermo, bulk_dos=vasprun_path,\n",
+    "                    chempots=chempots, backend=\"py-sc-fermi\")\n",
     "\n",
     "print(chempots)"
    ],
@@ -89,8 +87,8 @@
    "cell_type": "code",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2024-08-11T16:35:21.589410Z",
-     "start_time": "2024-08-11T16:35:19.574526Z"
+     "end_time": "2024-08-12T20:08:50.414395Z",
+     "start_time": "2024-08-12T20:08:42.207113Z"
     }
    },
    "source": [
@@ -186,19 +184,19 @@
    "cell_type": "code",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2024-08-11T16:35:34.843558Z",
-     "start_time": "2024-08-11T16:35:21.590392Z"
+     "end_time": "2024-08-13T02:32:58.939074Z",
+     "start_time": "2024-08-13T02:32:43.860988Z"
     }
    },
    "source": [
     "# scan between the Cd and Te rich limits to see how the defect concentrations\n",
     "# change as a function of chemical potential\n",
     "mu_df = py_fs.interpolate_chempots(limits = [\"Cd-rich\", \"Te-rich\"], \n",
-    "                                           n_points=20, annealing_temperature=1000, quenching_temperature = 300,\n",
-    "                                           processes=4)\n",
+    "                                   n_points=20, annealing_temperature=1000, \n",
+    "                                   quenching_temperature = 300)\n",
     "mu_df_doped = fs.interpolate_chempots(limits = [\"Cd-rich\", \"Te-rich\"],\n",
-    "                                                    n_points=20, annealing_temperature=1000, quenching_temperature=300,\n",
-    "                                                    processes=4)\n",
+    "                                      n_points=20, annealing_temperature=1000,\n",
+    "                                      quenching_temperature=300)\n",
     "\n",
     "# we'll keep the py-sc-fermi and doped comparison going\n",
     "mu_df[\"backend\"] = \"py-sc-fermi\"\n",
@@ -212,19 +210,19 @@
     "    for defect in unique_defects:\n",
     "        defect_df = mu_df.loc[defect]\n",
     "        defect_df_backend = defect_df[defect_df[\"backend\"] == backend]\n",
-    "        ax.plot(defect_df_backend[\"Cd\"], \n",
+    "        ax.plot(defect_df_backend[\"μ_Cd\"], \n",
     "            defect_df_backend[\"Concentration (cm^-3)\"], \n",
     "            label=format_defect_name(defect, include_site_info_in_name=True, wout_charge=True), \n",
     "            color=defect_colors[defect], \n",
     "            marker=\"o\" if backend == \"doped\" else \"x\",\n",
     "            alpha = 0.1)\n",
-    "    ax.plot(defect_df_backend[\"Cd\"], \n",
+    "    ax.plot(defect_df_backend[\"μ_Cd\"], \n",
     "            defect_df_backend[\"Holes (cm^-3)\"], \n",
     "            marker=\"o\" if backend == \"doped\" else \"x\", \n",
     "            linestyle=\"--\", \n",
     "            alpha = 0.75,\n",
     "            color = \"#999999\")\n",
-    "    ax.plot(defect_df_backend[\"Cd\"], \n",
+    "    ax.plot(defect_df_backend[\"μ_Cd\"], \n",
     "            defect_df_backend[\"Electrons (cm^-3)\"], \n",
     "            marker=\"o\" if backend == \"doped\" else \"x\", \n",
     "            linestyle=\"--\",\n",
@@ -259,7 +257,7 @@
      "output_type": "display_data"
     }
    ],
-   "execution_count": 3
+   "execution_count": 5
   },
   {
    "cell_type": "markdown",
@@ -631,7 +629,7 @@
     "    n_points=50,                # n_points in each dimension when scanning over the chemical potential grid\n",
     "    annealing_temperature=1000, # the temperature at which to anneal the system\n",
     "    quenching_temperature=300,  # the temperature at which to quench the system\n",
-    "    processes=4)                # the number of processes to use when scanning over the chemical potential grid"
+    ")"
    ]
   },
   {