{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Pourbaix Diagram for Copper"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pyPourbaix as pb"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Like elucidated in the previous examples, let's define the nessecarry Reactants for the hydrogen evolution reaction $(\\text{HER})$ and oxygen evolution reaction $(\\text{OER})$."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "species = ('H|+1|,      state=aq,   dGf=0,              dHf=0,              Sm=0',\n",
    "           'H2,         state=g,    dGf=0,              dHf=0,              Sm=0',\n",
    "           'e|-1|,      state=e,    dGf=0,              dHf=0,              Sm=0',\n",
    "           'H2O,        state=l,    dGf=-2.37140E+05,   dHf=-2.85830E+05,   Sm=69.95',\n",
    "           'O2,         state=g,    dGf=0,              dHf=0,              Sm=205.137')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The Pourbaix diagram of Copper is slightly more compley than the Pourbaix diagram of Aluminium. It involves 3 solid phases, crystalline $\\text{Cu}^{0}(\\text{s})$, copper oxide $\\text{Cu}_2\\text{O}(\\text{s})$ and copper hydroxide $\\text{Cu}(\\text{OH})_2(\\text{s})$:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "species = ('H|+1|,      state=aq,   dGf=0,              dHf=0,              Sm=0',\n",
    "           'H2,         state=g,    dGf=0,              dHf=0,              Sm=0',\n",
    "           'e|-1|,      state=e,    dGf=0,              dHf=0,              Sm=0',\n",
    "           'H2O,        state=l,    dGf=-2.37140E+05,   dHf=-2.85830E+05,   Sm=69.95',\n",
    "           'O2,         state=g,    dGf=0,              dHf=0,              Sm=205.137',\n",
    "           'Cu|0|,      state=s,    dGf=0,              dHf=0,              Sm=33.15',\n",
    "           'Cu2O|0|,    state=s,    dGf=-147.9E+03,     dHf=0,              Sm=92.36',\n",
    "           'Cu(OH)2|0|, state=s,    dGf=-359.92E+03,    dHf=0,              Sm=87.0'\n",
    "           )\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will again consider two aqueous species, $\\text{Cu}^{2+}$ predominantly present at acidic $\\text{pH}$ and $\\text{Cu}(\\text{OH})_4^{2-}$ that is preferrentially stabilised in alkaline media."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "species = ('H|+1|,      state=aq,   dGf=0,              dHf=0,              Sm=0',\n",
    "           'H2,         state=g,    dGf=0,              dHf=0,              Sm=0',\n",
    "           'e|-1|,      state=e,    dGf=0,              dHf=0,              Sm=0',\n",
    "           'H2O,        state=l,    dGf=-2.37140E+05,   dHf=-2.85830E+05,   Sm=69.95',\n",
    "           'O2,         state=g,    dGf=0,              dHf=0,              Sm=205.137',\n",
    "           'Cu|0|,      state=s,    dGf=0,              dHf=0,              Sm=33.15',\n",
    "           'Cu2O|0|,    state=s,    dGf=-147.9E+03,     dHf=0,              Sm=92.36',\n",
    "           'Cu(OH)2|0|, state=s,    dGf=-359.92E+03,    dHf=0,              Sm=87.0',\n",
    "           'Cu|+2|,     state=aq,   dGf=65.04E+03,      dHf=0,              Sm=-98.0',\n",
    "           'Cu(OH)4|-2|,state=aq,   dGf=-657.48e+03,    dHf=0,              Sm=-175'\n",
    "           )\n",
    "\n",
    "db = pb.Database.from_default(species)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Having 5 rather that 4 stable constituents significantly increases the complexity of the final Pourbaix diagram. First of all, let's implement all $\\text{Cu}^{0}(\\text{s})$ oxidation reactions to form $\\text{Cu}^{2+}$, $\\text{Cu}_2\\text{O}(\\text{s})$ and $\\text{Cu}(\\text{OH})_4^{2-}$."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "reactions = ('2H|+1| + 2e|-1| -> H2',\n",
    "            'O2 + 4H|+1| + 4e|-1| -> 2H2O',\n",
    "            'Cu|0| -> Cu|+2| + 2e|-1|',\n",
    "            'Cu2O|0| + 2H|+1| + 2e|-1| -> 2Cu|0| + H2O',\n",
    "            'Cu(OH)4|-2| + 4H|+1| + 2e|-1| -> Cu|0| + 4H2O'\n",
    "            )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The $\\text{Cu}(\\text{I})$ copper oxide $\\text{Cu}_2\\text{O}(\\text{s})$ furthermore features 3 potential and $\\text{pH}$-dependent transitions to the aqueous species $\\text{Cu}^{2+}$ and $\\text{Cu}(\\text{OH})_4^{2-}$ as well as the $\\text{Cu}(\\text{II})$ copper hydroxide $\\text{Cu}(\\text{OH})_2(\\text{s})$:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "reactions = ('2H|+1| + 2e|-1| -> H2',\n",
    "            'O2 + 4H|+1| + 4e|-1| -> 2H2O',\n",
    "            'Cu|0| -> Cu|+2| + 2e|-1|',\n",
    "            'Cu2O|0| + 2H|+1| + 2e|-1| -> 2Cu|0| + H2O',\n",
    "            'Cu(OH)4|-2| + 4H|+1| + 2e|-1| -> Cu|0| + 4H2O',\n",
    "            '2Cu|+2| + H2O + 2e|-1| -> Cu2O|0| + 2H|+1|',\n",
    "            '2Cu(OH)4|-2| + 6H|+1| + 2e|-1| -> Cu2O|0| + 7H2O',\n",
    "            '2Cu(OH)2|0| + 2H|+1| + 2e|-1| -> Cu2O|0| + 3H2O'\n",
    "            )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Lastly, 2 potential-independent hydrolysis reactions mark the transitions between the 3 $\\text{Cu}(\\text{II})$ species $\\text{Cu}^{2+}$, $\\text{Cu}(\\text{OH})_2(\\text{s})$ and $\\text{Cu}(\\text{OH})_4^{2-}$:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "reactions = ('2H|+1| + 2e|-1| -> H2',\n",
    "            'O2 + 4H|+1| + 4e|-1| -> 2H2O',\n",
    "            'Cu|0| -> Cu|+2| + 2e|-1|',\n",
    "            'Cu2O|0| + 2H|+1| + 2e|-1| -> 2Cu|0| + H2O',\n",
    "            'Cu(OH)4|-2| + 4H|+1| + 2e|-1| -> Cu|0| + 4H2O',\n",
    "            '2Cu|+2| + H2O + 2e|-1| -> Cu2O|0| + 2H|+1|',\n",
    "            '2Cu(OH)4|-2| + 6H|+1| + 2e|-1| -> Cu2O|0| + 7H2O',\n",
    "            '2Cu(OH)2|0| + 2H|+1| + 2e|-1| -> Cu2O|0| + 3H2O',\n",
    "            'Cu(OH)2|0| + 2H|+1| -> Cu|+2| + 2H2O',\n",
    "            'Cu(OH)4|-2| + 2H|+1| -> Cu(OH)2|0| + 2H2O'\n",
    "            )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note that 1 additional solid species added a total of 3 reactions to the Pourbaix diagram. By this time, setting up the reactive system should come natural:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "Cu_system = pb.System()\n",
    "Cu_system.set_database(db)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As the transition of $\\text{Cu}^{0}(\\text{s})$ to $\\text{Cu}(\\text{OH})_4^{2-}$ is only visible at strongly alkaline pH, we will pick a borad $\\text{pH}$ interval of $[0, \\ 18]$."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "Cu_system.pHs = (0, 18)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will continue defining the reference electrode of our system. How about we pick the copper suphate electrode (CSE) this time, that sounds appropriate considering we want to generate a Pourbaix diagram of the element copper."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "Cu_system.reference_electrode = (\"CSE\",0.241)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's quickly define the electrode potential boundaries as well as all elements to be plotted. We will also set the activity of aqueous species to $\\{\\text{Cu}\\}_{\\text{aq}} = 1\\cdot10^{-3}$."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "Cu_system.electrode_potentials = (-1.5, 2)\n",
    "Cu_system.add_elements([\"O\",\"H\",\"Cu\"])\n",
    "Cu_system.set_aqueous_activity(\"Cu\",1e-3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "After adding so many different reactions to the reactive system, users might have lost track. Luckily, we can easily get an overview over the reactive system and generate a summary of all reactions added using the <code>print</code> command like so:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-----------------------------System-----------------------------\n",
      "Temperature : 298.15, Pressure : 1.0\n",
      "----------------------------------------------------------------\n",
      "\t1.0H₂ ⇄ 2.0H⁺¹ + 2.0e⁻¹\n",
      "\t2.0H₂O ⇄ 1.0O₂ + 4.0H⁺¹ + 4.0e⁻¹\n",
      "\t1.0Cu⁺² + 2.0e⁻¹ ⇄ 1.0Cu⁰\n",
      "\t2.0Cu⁰ + 1.0H₂O ⇄ 1.0Cu₂O⁰ + 2.0H⁺¹ + 2.0e⁻¹\n",
      "\t1.0Cu⁰ + 4.0H₂O ⇄ 1.0Cu(OH)₄⁻² + 4.0H⁺¹ + 2.0e⁻¹\n",
      "\t1.0Cu₂O⁰ + 2.0H⁺¹ ⇄ 2.0Cu⁺² + 1.0H₂O + 2.0e⁻¹\n",
      "\t1.0Cu₂O⁰ + 7.0H₂O ⇄ 2.0Cu(OH)₄⁻² + 6.0H⁺¹ + 2.0e⁻¹\n",
      "\t1.0Cu₂O⁰ + 3.0H₂O ⇄ 2.0Cu(OH)₂⁰ + 2.0H⁺¹ + 2.0e⁻¹\n",
      "\t1.0Cu⁺² + 2.0H₂O ⇄ 1.0Cu(OH)₂⁰ + 2.0H⁺¹\n",
      "\t1.0Cu(OH)₂⁰ + 2.0H₂O ⇄ 1.0Cu(OH)₄⁻² + 2.0H⁺¹\n",
      "----------------------------------------------------------------\n"
     ]
    }
   ],
   "source": [
    "Cu_system.add_reactions(reactions)\n",
    "print(Cu_system)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Likewise, we can inspect the database of species, together with all entered thermodynamic parameters:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "----------------------------Database----------------------------\n",
      "Species \t     dGf\t     dHf\t      Sm\n",
      "----------------------------------------------------------------\n",
      "H|+1|   \t     0.0\t     0.0\t     0.0\n",
      "H2      \t     0.0\t     0.0\t     0.0\n",
      "e|-1|   \t     0.0\t     0.0\t     0.0\n",
      "H2O     \t-237140.0\t-285830.0\t   69.95\n",
      "O2      \t     0.0\t     0.0\t 205.137\n",
      "Cu|0|   \t     0.0\t     0.0\t   33.15\n",
      "Cu2O|0| \t-147900.0\t     0.0\t   92.36\n",
      "Cu(OH)2|0|\t-359920.0\t     0.0\t    87.0\n",
      "Cu|+2|  \t 65040.0\t     0.0\t   -98.0\n",
      "Cu(OH)4|-2|\t-657480.0\t     0.0\t  -175.0\n",
      "----------------------------------------------------------------\n"
     ]
    }
   ],
   "source": [
    "print(db)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's generate and plot the diagram using th plotting backend <code>bokeh</code>:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "Cu_diagram = pb.PourbaixDiagram(Cu_system,HER=True,OER=True)\n",
    "Cu_diagram.solve()\n",
    "Cu_diagram.show(backend='bokeh',plot_regions=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It can be recognised that any of the $\\text{Cu}^{0}(\\text{s})$ oxidation reactions feature a potential greater than the hydrogen evolution line $\\text{E}_{\\text{H}^+/\\text{H}_2} = \\text{E}^0_{\\text{H}^+/\\text{H}_2} - 0.059\\times\\text{pH}$."
   ]
  }
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