New defect example ipynb

WMD-group · Mar 30, 2023 · 58c2f20 · 58c2f20
1 parent 86cb26b
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diff --git a/DefectCon_example.ipynb b/DefectCon_example.ipynb
@@ -0,0 +1,68 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from materials\n",
+    "import numpy as np\n",
+    "\n",
+    "from plot_potential import plot_potential\n",
+    "\n",
+    "T = np.linspace(600,1200,100)    # K\n",
+    "P = np.array( np.logspace(1,7,100),ndmin=2).transpose() # Pa\n",
+    "\n",
+    "#D_mu_S8 = 1/8*(S8.mu_kJ(T, P) - alpha_S.mu_kJ(T, P))\n",
+    "mu_S2 = 1/2*S2.mu_kJ(T, P)\n",
+    "mu_Ss = 1/8 *alpha_S.mu_kJ(T, P)\n",
+    "mu_S8 = 1/8 * S8.mu_kJ(T, P)\n",
+    "D_mu = 1/2 * S2.mu_kJ(T, P) - 1/8 *alpha_S.mu_kJ(T, P)\n",
+    "#D_mu = 1/2* S2.mu_kJ(T, P) - 1/8 * S8.mu_kJ(T, P)\n",
+    "\n",
+    "E_Ss = (-.12378465E+04) - (-.12377738E+04) + (1) * (mu_Ss) * 0.0103636 + (+2)*(3.15+0.846)\n",
+    "E_S8 = (-.12378465E+04) - (-.12377738E+04) + (1) * (mu_S8) * 0.0103636 + (+2)*(3.15+0.846)\n",
+    "E_S2 = (-.12378465E+04) - (-.12377738E+04) + (1) * (mu_S2) * 0.0103636 + (+2)*(3.15+0.846)\n",
+    "kbt = (1.380649e-23) * T / (1.6e-19)\n",
+    "n_S2 = np.log10(1 * 64 * np.exp(-E_S2/kbt))\n",
+    "n_S8 = np.log10(1 * 64 * np.exp(-E_S8/kbt))\n",
+    "n_Ss = np.log10(1 * 64 * np.exp(-E_Ss/kbt))\n",
+    "\n",
+    "\n",
+    "n =(- D_mu * 1000 / ((1.380649e-23) * (6.0221408e+23) * T))\n",
+    "\n",
+    "D_mu_label = 'ln(n(V$_{S}$)/n(V$_{S(ref)}$))'\n",
+    "formation = 'V$_{S}$$^{+2}$ formation energy (eV)'\n",
+    "con_label= 'V$_{S}$$^{+2}$ Defect concentration (log10)'\n",
+    "scale_range = [0,35]\n",
+    "\n",
+    "#plot_potential(T,P,E_S2,formation,scale_range,filename='plots/FormationS2.png')\n",
+    "plot_potential(T,P,mu_Ss,con_label,scale_range,filename='plots/muSs_y.png')\n",
+    "plot_potential(T,P,E_S8,con_label,scale_range,filename='plots/E8.png')\n",
+    "plot_potential(T,P,n_S2,con_label,scale_range,filename='plots/ConcentrationS2_y.png')\n",
+    "plot_potential(T,P,n_S8,con_label,scale_range,filename='plots/ConcentrationS8_y.png')\n",
+    "plot_potential(T,P,n_Ss,con_label,scale_range,filename='plots/ConcentrationSs_y.png')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.16 64-bit",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.9.16"
+  },
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "397704579725e15f5c7cb49fe5f0341eb7531c82d19f2c29d197e8b64ab5776b"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/example.ipynb → Thermodynamics_example.ipynb b/example.ipynb → Thermodynamics_example.ipynb
diff --git a/docs/index.md b/docs/index.md
diff --git a/mkdocs.yml b/mkdocs.yml
diff --git a/scripts/defect_concentration.py b/scripts/defect_concentration.py
@@ -0,0 +1,41 @@
+def main():
+    from materials
+    import numpy as np
+
+    from plot_potential import plot_potential
+
+    T = np.linspace(600,1200,100)    # K
+    P = np.array( np.logspace(1,7,100),ndmin=2).transpose() # Pa
+
+    #D_mu_S8 = 1/8*(S8.mu_kJ(T, P) - alpha_S.mu_kJ(T, P))
+    mu_S2 = 1/2*S2.mu_kJ(T, P)
+    mu_Ss = 1/8 *alpha_S.mu_kJ(T, P)
+    mu_S8 = 1/8 * S8.mu_kJ(T, P)
+    D_mu = 1/2 * S2.mu_kJ(T, P) - 1/8 *alpha_S.mu_kJ(T, P)
+    #D_mu = 1/2* S2.mu_kJ(T, P) - 1/8 * S8.mu_kJ(T, P)
+
+    E_Ss = (-.12378465E+04) - (-.12377738E+04) + (1) * (mu_Ss) * 0.0103636 + (+2)*(3.15+0.846)
+    E_S8 = (-.12378465E+04) - (-.12377738E+04) + (1) * (mu_S8) * 0.0103636 + (+2)*(3.15+0.846)
+    E_S2 = (-.12378465E+04) - (-.12377738E+04) + (1) * (mu_S2) * 0.0103636 + (+2)*(3.15+0.846)
+    kbt = (1.380649e-23) * T / (1.6e-19)
+    n_S2 = np.log10(1 * 64 * np.exp(-E_S2/kbt))
+    n_S8 = np.log10(1 * 64 * np.exp(-E_S8/kbt))
+    n_Ss = np.log10(1 * 64 * np.exp(-E_Ss/kbt))
+
+
+    n =(- D_mu * 1000 / ((1.380649e-23) * (6.0221408e+23) * T))
+
+    D_mu_label = 'ln(n(V$_{S}$)/n(V$_{S(ref)}$))'
+    formation = 'V$_{S}$$^{+2}$ formation energy (eV)'
+    con_label= 'V$_{S}$$^{+2}$ Defect concentration (log10)'
+    scale_range = [0,35]
+
+    #plot_potential(T,P,E_S2,formation,scale_range,filename='plots/FormationS2.png')
+    plot_potential(T,P,mu_Ss,con_label,scale_range,filename='plots/muSs_y.png')
+    plot_potential(T,P,E_S8,con_label,scale_range,filename='plots/E8.png')
+    plot_potential(T,P,n_S2,con_label,scale_range,filename='plots/ConcentrationS2_y.png')
+    plot_potential(T,P,n_S8,con_label,scale_range,filename='plots/ConcentrationS8_y.png')
+    plot_potential(T,P,n_Ss,con_label,scale_range,filename='plots/ConcentrationSs_y.png')
+
+if __name__ == "__main__":
+    main()