Merge pull request #32 from KulaginVladimir/code-readability

Increase code readability
KulaginVladimir · Nov 22, 2024 · bc2041e · bc2041e
2 parents 16778e0 + df05fa1
commit bc2041e
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diff --git a/D_EUROFER/D_EUROFER.ipynb b/D_EUROFER/D_EUROFER.ipynb
diff --git a/D_EUROFER/reference_data/README.md b/D_EUROFER/reference_data/README.md
@@ -1,6 +1,6 @@
 ## Description of files
 
-- **143hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 143 h exposure of Eurofer without damaged-induced traps 
-- **DPA+48hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps 
-- **DPA+143hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 143 h exposure of Eurofer with damaged-induced traps 
-- **DPA+D+48hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps. Damaging was performed with already D-loaded sample.  
+- **143hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 143 h exposure of Eurofer without damaged-induced traps 
+- **DPA+48hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps 
+- **DPA+143hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 143 h exposure of Eurofer with damaged-induced traps 
+- **DPA+D+48hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps. Damaging was performed with already D-loaded sample.  
diff --git a/D_WO/D_WO.ipynb b/D_WO/D_WO.ipynb
diff --git a/D_damagedW/D_damagedW.ipynb b/D_damagedW/D_damagedW.ipynb
diff --git a/H_Ti/H_Ti.ipynb b/H_Ti/H_Ti.ipynb
@@ -24,53 +24,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Defining initial values\n",
-      "Defining variational problem\n",
-      "Defining source terms\n",
-      "Defining boundary conditions\n",
-      "Time stepping...\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "100.0 %        1.5e+03 s    Elapsed time so far: 8.5 s\n",
-      "Defining initial values\n",
-      "Defining variational problem\n",
-      "Defining source terms\n",
-      "Defining boundary conditions\n",
-      "Time stepping...\n",
-      "100.0 %        1.5e+03 s    Elapsed time so far: 6.0 s\n",
-      "Defining initial values\n",
-      "Defining variational problem\n",
-      "Defining source terms\n",
-      "Defining boundary conditions\n",
-      "Time stepping...\n",
-      "100.0 %        1.5e+03 s    Elapsed time so far: 5.2 s\n",
-      "Defining initial values\n",
-      "Defining variational problem\n",
-      "Defining source terms\n",
-      "Defining boundary conditions\n",
-      "Time stepping...\n",
-      "100.0 %        1.5e+03 s    Elapsed time so far: 5.2 s\n",
-      "Defining initial values\n",
-      "Defining variational problem\n",
-      "Defining source terms\n",
-      "Defining boundary conditions\n",
-      "Time stepping...\n",
-      "100.0 %        1.5e+03 s    Elapsed time so far: 4.9 s\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import festim as F\n",
     "import fenics as f\n",
     "import numpy as np\n",
     "import h_transport_materials as htm\n",
+    "import matplotlib.pyplot as plt\n",
     "\n",
     "################### PARAMETERS ###################\n",
     "N_A_const = 6.022e23  # Avogadro, mol^-1\n",
@@ -83,7 +45,7 @@
     "V = A * L  # Ti volume (1cm x 1.3cm x 1mm), m^-3\n",
     "\n",
     "# Ti properties\n",
-    "X_max = 3\n",
+    "X_max = 3  # maximum number of H atoms per a Ti atom in the bulk\n",
     "n_b = 9.4e4 * N_A_const  #  the number of atomic sites per unit of volume of Ti, m^-3\n",
     "n_surf = (\n",
     "    X_max * 2.16e-5 * N_A_const\n",
@@ -98,7 +60,7 @@
     "E_diff = D.act_energy.magnitude  # diffusion activation energy, eV\n",
     "\n",
     "E_des = F.kJmol_to_eV(1.17e5 / 1e3)  # activateion energy for desorption, eV\n",
-    "k_des = 1.08e8 * N_A_const  # frequency factor for the surface desorption\n",
+    "k_des = 1.08e8 * N_A_const / n_surf**2  # desorption rate, m^2 s^-1\n",
     "\n",
     "E_sb = F.kJmol_to_eV(\n",
     "    1.18e2\n",
@@ -114,14 +76,6 @@
     "V_ch = 2.95e-3  # the chamber volume, m^3\n",
     "P0 = 1.3e4  # the initial pressure, Pa\n",
     "\n",
-    "T_list = [\n",
-    "    450 + 273,\n",
-    "    500 + 273,\n",
-    "    550 + 273,\n",
-    "    600 + 273,\n",
-    "    650 + 273,\n",
-    "]  # reference data is given in deg C\n",
-    "\n",
     "\n",
     "################### FUNCTIONS ###################\n",
     "def S0(T):\n",
@@ -143,7 +97,7 @@
     "        * P_H2(T, X)\n",
     "        / (2 * np.pi * M_H2 * F.k_B * T * e) ** 0.5\n",
     "    )\n",
-    "    J_des = 2 * k_des * (surf_conc / n_surf) ** 2 * f.exp(-E_des / F.k_B / T)\n",
+    "    J_des = 2 * k_des * surf_conc**2 * f.exp(-E_des / F.k_B / T)\n",
     "    return J_ads - J_des\n",
     "\n",
     "\n",
@@ -168,10 +122,22 @@
     "        X = 2 * (f.assemble(self.mobile.solution * self.mesh.dx) + surf) * A\n",
     "\n",
     "        # Normalised content parameter\n",
-    "        self.h_transport_problem.boundary_conditions[0].prms[\"X\"].assign(X)\n",
-    "\n",
-    "\n",
-    "################### MODEL ###################\n",
+    "        self.h_transport_problem.boundary_conditions[0].prms[\"X\"].assign(X)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can now define a function that will run a FESTIM model for different cases:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "def run_sim(T0):\n",
     "    Ti_model_impl = CustomSimulation()\n",
     "\n",
@@ -223,8 +189,68 @@
     "    Ti_model_impl.initialise()\n",
     "    Ti_model_impl.run()\n",
     "\n",
-    "    return derived_quantities\n",
-    "\n",
+    "    return derived_quantities"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We now run the FESTIM model for the five cases with different material temperatures:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Defining initial values\n",
+      "Defining variational problem\n",
+      "Defining source terms\n",
+      "Defining boundary conditions\n",
+      "Time stepping...\n",
+      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
+      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
+      "100.0 %        1.5e+03 s    Elapsed time so far: 8.0 s\n",
+      "Defining initial values\n",
+      "Defining variational problem\n",
+      "Defining source terms\n",
+      "Defining boundary conditions\n",
+      "Time stepping...\n",
+      "100.0 %        1.5e+03 s    Elapsed time so far: 5.8 s\n",
+      "Defining initial values\n",
+      "Defining variational problem\n",
+      "Defining source terms\n",
+      "Defining boundary conditions\n",
+      "Time stepping...\n",
+      "100.0 %        1.5e+03 s    Elapsed time so far: 5.2 s\n",
+      "Defining initial values\n",
+      "Defining variational problem\n",
+      "Defining source terms\n",
+      "Defining boundary conditions\n",
+      "Time stepping...\n",
+      "100.0 %        1.5e+03 s    Elapsed time so far: 5.3 s\n",
+      "Defining initial values\n",
+      "Defining variational problem\n",
+      "Defining source terms\n",
+      "Defining boundary conditions\n",
+      "Time stepping...\n",
+      "100.0 %        1.5e+03 s    Elapsed time so far: 5.4 s\n"
+     ]
+    }
+   ],
+   "source": [
+    "T_list = [\n",
+    "    450 + 273,\n",
+    "    500 + 273,\n",
+    "    550 + 273,\n",
+    "    600 + 273,\n",
+    "    650 + 273,\n",
+    "]  # reference data is given in deg C\n",
     "\n",
     "results = {}\n",
     "for T0 in T_list:\n",
@@ -247,7 +273,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -262,9 +288,6 @@
     }
    ],
    "source": [
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "\n",
     "def plot_inventory(T0, FESTIM_data):\n",
     "    retention = np.array(FESTIM_data[1].data) + np.array(\n",
     "        FESTIM_data[0].data\n",
@@ -315,7 +338,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -338,7 +361,6 @@
     }
    ],
    "source": [
-    "import matplotlib.pyplot as plt\n",
     "from pypalettes import load_cmap\n",
     "\n",
     "cmap = load_cmap(\"Sunset2\")\n",
@@ -354,6 +376,8 @@
     "    ),\n",
     "    \"font.size\": 8,\n",
     "    \"font.family\": \"Times New Roman\",\n",
+    "    \"axes.spines.right\": False,\n",
+    "    \"axes.spines.top\": False,\n",
     "}\n",
     "plt.rcParams.update(params)\n",
     "\n",
@@ -386,7 +410,6 @@
     "        va=\"center\",\n",
     "        color=cmap(i),\n",
     "    )\n",
-    "    axis.spines[[\"right\", \"top\"]].set_visible(False)\n",
     "\n",
     "(dummy_line,) = axs[0].plot([-1], [-1], color=\"black\", lw=1.5, label=\"FESTIM\")\n",
     "dummy_dot = axs[0].scatter([-1], [-1], color=\"black\", s=10, label=\"Exp.\")\n",

diff --git a/MMS/MMS.ipynb b/MMS/MMS.ipynb
@@ -282,7 +282,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -305,7 +305,6 @@
     }
    ],
    "source": [
-    "import matplotlib.pyplot as plt\n",
     "from pypalettes import load_cmap\n",
     "\n",
     "cmap = load_cmap(\"Sunset2\", reverse=False)\n",

diff --git a/README.md b/README.md
@@ -14,9 +14,9 @@ The repository includes several validation cases and one verification test on th
 
 [2] [D adsorption on oxidised W](./D_WO): The case reproduces simulation results of [E. A. Hodille et al.](https://iopscience.iop.org/article/10.1088/1741-4326/ad2a29) on the D adsorption/desorption on/from oxidised W. The simulations are based on experiments performed by [A. Dunand et al.](https://iopscience.iop.org/article/10.1088/1741-4326/ac583a)
 
-[3] [D implantation in damaged W](./D_damagedW): The case reproduces simulation results of [E. A. Hodille et al.](https://iopscience.iop.org/article/10.1088/1741-4326/aa5aa5/meta) on the isothermal D implantation in self-damaged W, followed by isothermal desorption. The simulations are based on experiments performed by [S. Markelj et al.](https://www.sciencedirect.com/science/article/pii/S0022311515303470?via%3Dihub)
+[3] [D atom exposure of self-damaged W](./D_damagedW): The case reproduces simulation results of [E. A. Hodille et al.](https://iopscience.iop.org/article/10.1088/1741-4326/aa5aa5/meta) on the isothermal D implantation in self-damaged W, followed by isothermal desorption. The simulations are based on experiments performed by [S. Markelj et al.](https://www.sciencedirect.com/science/article/pii/S0022311515303470?via%3Dihub)
 
-[4] [D implantation in damaged EUROFER](./D_EUROFER): The case reproduces experimental results of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179122002228) on the D implantation in damaged EUROFER, followed by TDS measurements. The FESTIM model is mainly based on the simulations of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179123001333?via%3Dihub)
+[4] [D implantation in W-damaged EUROFER](./D_EUROFER): The case reproduces experimental results of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179122002228) on the D implantation in damaged EUROFER, followed by TDS measurements. The FESTIM model is mainly based on the simulations of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179123001333?via%3Dihub)
 
 [5] [MMS](./MMS) test