Ol-Opx-SplV4.ipynb

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     "text": [
      "Welcome! This notebook calculates the oxygen fugacity of a sample using the olivine-orthopyroxene-spinel geo-oxybarometer, and the temperature of Fe-Mg equilibration between olivine and spinel using the olivine-spinel geothermometer. To use this notebook, enter the pressure (in bars) of sample formation, as well as the wt.% values of the listed oxide phases for spinel, orthopyroxene, and olivine.\n",
      "\n",
      "The oxygen fugacity results include:\n",
      "\n",
      "logfO2 = absolute log fO2\n",
      "\n",
      "dQFM fO2 = fO2 relative to the Quartz-Fayalite-Magnetite buffer, with values from Frost (1991)\n",
      "\n",
      "dIW fO2 = fO2 relative to the Iron-Wustite buffer, with values from Euster and Wones (1962)\n",
      "\n",
      "dNNO fO2 = fO2 relative to the Nickle-Nickle-Oxide buffer, with values from Huebner and Sato (1970)\n",
      "\n",
      "The geothermometry and geobarometry calculations in this notebook are based on work by Jianping et al. (1995), Myers and Eugster (1983), Sack and Ghiorso (1989, 1991a, 1991b), Wood (1990), Wood and Nell (1991). For a review on oxybarometers, including the olivine-orthopyroxene-spinel barometer used here, check out the paper by Herd (2008). References to the corresponding papers can be found at the bottom of this screen.\n",
      "\n",
      "To cite this notebook in publications please use the following citation: [will be added once final version is ready and Zenodo citation created]\n",
      "\n",
      "If you encounter issues using this notebook, or have suggestions for how it could be improved, please email benaroya@ualberta.ca\n",
      "\n"
     ]
    },
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       "Button(button_style='info', description='Olivine-Pyroxene-Spinel geobarometer', layout=Layout(height='auto', w…"
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       "AppLayout(children=(Output(layout=Layout(grid_area='footer')), VBox(children=(FloatText(value=0.0, description…"
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   "source": [
    "#OL-Opx-Spl\n",
    "\n",
    "#EOF\n",
    "import thermoengine as thermo\n",
    "from thermoengine import phases\n",
    "from thermoengine import model\n",
    "import numpy as np\n",
    "import math\n",
    "import ipywidgets as widgets\n",
    "from scipy import optimize as optim\n",
    "from ipywidgets import AppLayout, Button, Layout\n",
    "from ipywidgets import Accordion, HBox, VBox, Label\n",
    "from ipywidgets import Button, Output\n",
    "from ctypes import cdll\n",
    "from ctypes import util\n",
    "from rubicon.objc import ObjCClass, objc_method\n",
    "cdll.LoadLibrary(util.find_library('phaseobjc'))\n",
    "\n",
    "\n",
    "def create_expanded_button(description, button_style):\n",
    "    \"\"\"Helper function to create a button widget with a description and style.\"\"\"\n",
    "    button = Button(description=description, button_style=button_style)\n",
    "    button.layout.height = 'auto'\n",
    "    button.layout.width = 'auto'\n",
    "    return button\n",
    "\n",
    "\n",
    "\n",
    "# Create the main widget\n",
    "window = widgets.VBox()\n",
    "\n",
    "# Create a list of column names\n",
    "column_names = ['Spinel', 'Orthopyroxene', 'Olivine']\n",
    "\n",
    "# Create a list of empty strings to store the data\n",
    "data = [['' for _ in range(3)] for _ in range(10)]\n",
    "\n",
    "# Create a function to update the data list when the user clicks the \"Submit\" button\n",
    "def update_data(b):\n",
    "      for i in range(10):\n",
    "    # Get the data from each entry widget and update the corresponding element in the data list\n",
    "        data[i][0] = entries[i][0].value\n",
    "        data[i][1] = entries[i][1].value\n",
    "        data[i][2] = entries[i][2].value\n",
    "\n",
    "# Create a function to clear the data when the user clicks the \"Clear\" button\n",
    "def clear_data(b):\n",
    "      for i in range(10):\n",
    "        # Clear the data in each entry widget and update the corresponding element in the data list\n",
    "        entries[i][0].value = ''\n",
    "        entries[i][1].value = ''\n",
    "        entries[i][2].value = ''\n",
    "        data[i][0] = ''\n",
    "        data[i][1] = ''\n",
    "        data[i][2] = ''\n",
    "\n",
    "# Create a label for each column\n",
    "labels = []\n",
    "for i, name in enumerate(column_names):\n",
    "      label = widgets.Label(value=name)\n",
    "      labels.append(label)\n",
    "  \n",
    "# Create a list of row names\n",
    "row_names = [\"SiO2\", \"TiO2\", \"Al2O3\", \"Cr2O3\", \"FeO\", \"MnO\", \"MgO\", \"CaO\", \"Fe2O3-spinel/ Na2O-orthopyroxene/ P2O5-olivine\", \"V2O3-spinel only, ignore other entry boxes\"]\n",
    "\n",
    "# Create a label for each row\n",
    "row_labels = []\n",
    "for i in range(10):\n",
    "  rlabel = widgets.Label(value=row_names[i])\n",
    "  row_labels.append(rlabel)\n",
    "\n",
    "# Create an entry widget for each cell in the grid\n",
    "entries = []\n",
    "for i in range(10):\n",
    "  row = []\n",
    "  for j in range(3):\n",
    "    entry = widgets.Text(placeholder='Enter value')\n",
    "    row.append(entry)\n",
    "  entries.append(row)\n",
    "\n",
    "for i in range(10):\n",
    "  for j in range(3):\n",
    "    entries[i][j].placeholder = column_names[j]\n",
    "\n",
    "\n",
    "# Create a grid to hold the entry widgets\n",
    "grid = widgets.VBox(children=[], layout=widgets.Layout(grid_template_columns=\"repeat(4, 1fr)\", grid_template_rows=\"repeat(11, 1fr)\"))\n",
    "\n",
    "# Create a \"Clear\" button\n",
    "clear_button = widgets.Button(description=\"Clear\", button_style='warning')\n",
    "clear_button.on_click(clear_data)\n",
    "\n",
    "# Create a \"Continue\" button\n",
    "continue_button = widgets.Button(description=\"Continue\", button_style='info')\n",
    "\n",
    "\n",
    "# Add the row labels and entries to the grid\n",
    "for i in range(10):\n",
    "  # Add the row label to the first column of the current row\n",
    "  grid.children = (*grid.children, widgets.Label(value=row_names[i]))\n",
    "  # Add the entries to the remaining columns of the current row\n",
    "  for j in range(3):\n",
    "    grid.children = (*grid.children, entries[i][j])\n",
    "\n",
    "#Entry widget for pressure \n",
    "entry = widgets.Text(description='P in bars:')\n",
    "\n",
    "#List of empty strings to store the data\n",
    "pressure_data = ['']\n",
    "\n",
    "def update_pressure_data(b):\n",
    "  # Get the value from the entry widget\n",
    "  pressure_data[0] = entry.value\n",
    "  # Update the pressure_data list with the entry value\n",
    "  pressure_data[0] = entry.value\n",
    "\n",
    "# Set up a callback function to update the data list when the button is clicked\n",
    "continue_button.on_click(update_pressure_data)\n",
    "\n",
    "# Add the grid and buttons to the main widget\n",
    "children = [entry] + [grid] + [continue_button] + [clear_button]\n",
    "window.children = children\n",
    "\n",
    "# Create the FloatText widget\n",
    "y_widget = widgets.FloatText(description='T°C', disabled=True, layout=widgets.Layout(width='200px', height='50px'))\n",
    "\n",
    "# Create the FloatText widget\n",
    "x_widget = widgets.FloatText(description='log fO2', disabled=True, layout=widgets.Layout(width='200px', height='50px'))\n",
    "\n",
    "# Create the FloatText widget\n",
    "z_widget = widgets.FloatText(description='dQFM fO2', disabled=True, layout=widgets.Layout(width='200px', height='50px'))\n",
    "\n",
    "# Create the FloatText widget\n",
    "aa_widget = widgets.FloatText(description='dIW fO2', disabled=True, layout=widgets.Layout(width='200px', height='50px'))\n",
    "\n",
    "# Create the FloatText widget\n",
    "ab_widget = widgets.FloatText(description='dNNO fO2', disabled=True, layout=widgets.Layout(width='200px', height='50px'))\n",
    "\n",
    "\n",
    "\n",
    "# Create a VBox widget to hold the x and y widgets\n",
    "result_box = widgets.VBox([y_widget, x_widget, z_widget, aa_widget, ab_widget])\n",
    "\n",
    "print(\"Welcome! This notebook calculates the oxygen fugacity of a sample using the olivine-orthopyroxene-spinel geo-oxybarometer, and the temperature of Fe-Mg equilibration between olivine and spinel using the olivine-spinel geothermometer. To use this notebook, enter the pressure (in bars) of sample formation, as well as the wt.% values of the listed oxide phases for spinel, orthopyroxene, and olivine.\")\n",
    "print()\n",
    "print(\"The oxygen fugacity results include:\")\n",
    "print()\n",
    "print(\"logfO2 = absolute log fO2\")\n",
    "print()\n",
    "print(\"dQFM fO2 = fO2 relative to the Quartz-Fayalite-Magnetite buffer, with values from Frost (1991)\")\n",
    "print()\n",
    "print(\"dIW fO2 = fO2 relative to the Iron-Wustite buffer, with values from Euster and Wones (1962)\")\n",
    "print()\n",
    "print(\"dNNO fO2 = fO2 relative to the Nickle-Nickle-Oxide buffer, with values from Huebner and Sato (1970)\")\n",
    "print()\n",
    "print(\"The geothermometry and geobarometry calculations in this notebook are based on work by Jianping et al. (1995), Myers and Eugster (1983), Sack and Ghiorso (1989, 1991a, 1991b), Wood (1990), Wood and Nell (1991). For a review on oxybarometers, including the olivine-orthopyroxene-spinel barometer used here, check out the paper by Herd (2008). References to the corresponding papers can be found at the bottom of this screen.\")\n",
    "print()\n",
    "print(\"To cite this notebook in publications please use the following citation: [will be added once final version is ready and Zenodo citation created]\")\n",
    "print()\n",
    "print(\"If you encounter issues using this notebook, or have suggestions for how it could be improved, please email benaroya@ualberta.ca\")\n",
    "print()\n",
    "# Create a function to be called when the \"Continue\" button is clicked\n",
    "\n",
    "title = create_expanded_button('Olivine-Pyroxene-Spinel geobarometer', 'info')\n",
    "display(title)\n",
    "\n",
    "def on_continue_clicked(b):\n",
    "    update_pressure_data(b)\n",
    "    #SPINEL CALCULATIONS\n",
    "    spl_SiO2 = entries[0][0].value\n",
    "    if spl_SiO2:\n",
    "        spl_SiO2 = float(spl_SiO2)\n",
    "        spl_SiO2_mole = spl_SiO2 / 60.0843\n",
    "        spl_SiO2_cations = spl_SiO2_mole * 1\n",
    "        spl_SiO2_oxygens = spl_SiO2_mole * 2\n",
    "        \n",
    "    spl_TiO2 = entries[1][0].value\n",
    "    if spl_TiO2:\n",
    "        spl_TiO2 = float(spl_TiO2)\n",
    "        spl_TiO2_mole = spl_TiO2 / 78.8658\n",
    "        spl_TiO2_cations = spl_TiO2_mole * 1   \n",
    "        spl_TiO2_oxygens = spl_TiO2_mole * 2\n",
    "\n",
    "    spl_Al2O3 = entries[2][0].value\n",
    "    if spl_Al2O3:\n",
    "        spl_Al2O3 = float(spl_Al2O3)\n",
    "        spl_Al2O3_mole = spl_Al2O3 / 101.961276\n",
    "        spl_Al2O3_cations = spl_Al2O3_mole * 2   \n",
    "        spl_Al2O3_oxygens = spl_Al2O3_mole * 3\n",
    "\n",
    "    spl_Cr2O3 = entries[3][0].value\n",
    "    if spl_Cr2O3:\n",
    "        spl_Cr2O3 = float(spl_Cr2O3)\n",
    "        spl_Cr2O3_mole = spl_Cr2O3 / 151.9904\n",
    "        spl_Cr2O3_cations = spl_Cr2O3_mole * 2   \n",
    "        spl_Cr2O3_oxygens = spl_Cr2O3_mole * 3\n",
    "    \n",
    "    spl_FeO = entries[4][0].value\n",
    "    if spl_FeO:\n",
    "        spl_FeO = float(spl_FeO)\n",
    "        spl_FeO_mole = spl_FeO / 71.8444\n",
    "        spl_FeO_cations = spl_FeO_mole * 1   \n",
    "        spl_FeO_oxygens = spl_FeO_mole * 1\n",
    "\n",
    "    spl_MnO = entries[5][0].value\n",
    "    if spl_MnO:\n",
    "        spl_MnO = float(spl_MnO)\n",
    "        spl_MnO_mole = spl_MnO / 70.937449\n",
    "        spl_MnO_cations = spl_MnO_mole * 1   \n",
    "        spl_MnO_oxygens = spl_MnO_mole * 1\n",
    "\n",
    "    spl_MgO = entries[6][0].value\n",
    "    if spl_MgO:\n",
    "        spl_MgO = float(spl_MgO)\n",
    "        spl_MgO_mole = spl_MgO / 40.3044\n",
    "        spl_MgO_cations = spl_MgO_mole * 1   \n",
    "        spl_MgO_oxygens = spl_MgO_mole * 1   \n",
    "\n",
    "    spl_CaO = entries[7][0].value\n",
    "    if spl_CaO:\n",
    "        spl_CaO = float(spl_CaO)\n",
    "        spl_CaO_mole = spl_CaO / 56.0774\n",
    "        spl_CaO_cations = spl_CaO_mole * 1   \n",
    "        spl_CaO_oxygens = spl_CaO_mole * 1   \n",
    "\n",
    "    spl_Fe2O3 = entries[8][0].value\n",
    "    if spl_Fe2O3:\n",
    "        spl_Fe2O3 = float(spl_Fe2O3)\n",
    "        spl_Fe2O3_mole = spl_Fe2O3 / 159.6882\n",
    "        spl_Fe2O3_cations = spl_Fe2O3_mole * 2   \n",
    "        spl_Fe2O3_oxygens = spl_Fe2O3_mole * 3\n",
    "\n",
    "    spl_V2O3 = entries[9][0].value\n",
    "    if spl_V2O3:\n",
    "        spl_V2O3 = float(spl_V2O3)\n",
    "        spl_V2O3_mole = spl_V2O3 / 149.883\n",
    "        spl_V2O3_cations = spl_V2O3_mole * 2   \n",
    "        spl_V2O3_oxygens = spl_V2O3_mole * 3\n",
    "        \n",
    "    spl_Na2O = 0.0\n",
    "    \n",
    "    #ORTHOPYROXENE CALCULATIONS\n",
    "    opx_SiO2 = entries[0][1].value\n",
    "    if opx_SiO2:\n",
    "        opx_SiO2 = float(opx_SiO2)\n",
    "        opx_SiO2_mole = opx_SiO2 / 60.0843\n",
    "        opx_SiO2_cations = opx_SiO2_mole * 1\n",
    "        opx_SiO2_oxygens = opx_SiO2_mole * 2\n",
    "        \n",
    "    opx_TiO2 = entries[1][1].value\n",
    "    if opx_TiO2:\n",
    "        opx_TiO2 = float(opx_TiO2)\n",
    "        opx_TiO2_mole = opx_TiO2 / 78.8658\n",
    "        opx_TiO2_cations = opx_TiO2_mole * 1   \n",
    "        opx_TiO2_oxygens = opx_TiO2_mole * 2\n",
    "\n",
    "    opx_Al2O3 = entries[2][1].value\n",
    "    if opx_Al2O3:\n",
    "        opx_Al2O3 = float(opx_Al2O3)\n",
    "        opx_Al2O3_mole = opx_Al2O3 / 101.961276\n",
    "        opx_Al2O3_cations = opx_Al2O3_mole * 2   \n",
    "        opx_Al2O3_oxygens = opx_Al2O3_mole * 3\n",
    "\n",
    "    opx_Cr2O3 = entries[3][1].value\n",
    "    if opx_Cr2O3:\n",
    "        opx_Cr2O3 = float(opx_Cr2O3)\n",
    "        opx_Cr2O3_mole = opx_Cr2O3 / 151.9904\n",
    "        opx_Cr2O3_cations = opx_Cr2O3_mole * 2   \n",
    "        opx_Cr2O3_oxygens = opx_Cr2O3_mole * 3\n",
    "    \n",
    "    opx_FeO = entries[4][1].value\n",
    "    if opx_FeO:\n",
    "        opx_FeO = float(opx_FeO)\n",
    "        opx_FeO_mole = opx_FeO / 71.8444\n",
    "        opx_FeO_cations = opx_FeO_mole * 1   \n",
    "        opx_FeO_oxygens = opx_FeO_mole * 1\n",
    "\n",
    "    opx_MnO = entries[5][1].value\n",
    "    if opx_MnO:\n",
    "        opx_MnO = float(opx_MnO)\n",
    "        opx_MnO_mole = opx_MnO / 70.937449\n",
    "        opx_MnO_cations = opx_MnO_mole * 1   \n",
    "        opx_MnO_oxygens = opx_MnO_mole * 1\n",
    "\n",
    "    opx_MgO = entries[6][1].value\n",
    "    if opx_MgO:\n",
    "        opx_MgO = float(opx_MgO)\n",
    "        opx_MgO_mole = opx_MgO / 40.3044\n",
    "        opx_MgO_cations = opx_MgO_mole * 1   \n",
    "        opx_MgO_oxygens = opx_MgO_mole * 1   \n",
    "\n",
    "    opx_CaO = entries[7][1].value\n",
    "    if opx_CaO:\n",
    "        opx_CaO = float(opx_CaO)\n",
    "        opx_CaO_mole = opx_CaO / 56.0774\n",
    "        opx_CaO_cations = opx_CaO_mole * 1   \n",
    "        opx_CaO_oxygens = opx_CaO_mole * 1   \n",
    "\n",
    "    opx_Na2O = entries[8][1].value\n",
    "    if opx_Na2O:\n",
    "        opx_Na2O = float(opx_Na2O)\n",
    "        opx_Na2O_mole = opx_Na2O / 61.97894\n",
    "        opx_Na2O_cations = opx_Na2O_mole * 2   \n",
    "        opx_Na2O_oxygens = opx_Na2O_mole * 1    \n",
    "    \n",
    "    #OLIVINE CALCULATIONS\n",
    "    ol_SiO2 = entries[0][2].value\n",
    "    if ol_SiO2:\n",
    "        ol_SiO2 = float(ol_SiO2)\n",
    "        ol_SiO2_mole = ol_SiO2 / 60.0843\n",
    "        ol_SiO2_cations = ol_SiO2_mole * 1\n",
    "        ol_SiO2_oxygens = ol_SiO2_mole * 2\n",
    "        \n",
    "    ol_TiO2 = entries[1][2].value\n",
    "    if ol_TiO2:\n",
    "        ol_TiO2 = float(ol_TiO2)\n",
    "        ol_TiO2_mole = ol_TiO2 / 78.8658\n",
    "        ol_TiO2_cations = ol_TiO2_mole * 1   \n",
    "        ol_TiO2_oxygens = ol_TiO2_mole * 2\n",
    "\n",
    "    ol_Al2O3 = entries[2][2].value\n",
    "    if ol_Al2O3:\n",
    "        ol_Al2O3 = float(ol_Al2O3)\n",
    "        ol_Al2O3_mole = ol_Al2O3 / 101.961276\n",
    "        ol_Al2O3_cations = ol_Al2O3_mole * 2   \n",
    "        ol_Al2O3_oxygens = ol_Al2O3_mole * 3\n",
    "\n",
    "    ol_Cr2O3 = entries[3][2].value\n",
    "    if ol_Cr2O3:\n",
    "        ol_Cr2O3 = float(ol_Cr2O3)\n",
    "        ol_Cr2O3_mole = ol_Cr2O3 / 151.9904\n",
    "        ol_Cr2O3_cations = ol_Cr2O3_mole * 2   \n",
    "        ol_Cr2O3_oxygens = ol_Cr2O3_mole * 3\n",
    "    \n",
    "    ol_FeO = entries[4][2].value\n",
    "    if ol_FeO:\n",
    "        ol_FeO = float(ol_FeO)\n",
    "        ol_FeO_mole = ol_FeO / 71.8444\n",
    "        ol_FeO_cations = ol_FeO_mole * 1   \n",
    "        ol_FeO_oxygens = ol_FeO_mole * 1\n",
    "\n",
    "    ol_MnO = entries[5][2].value\n",
    "    if ol_MnO:\n",
    "        ol_MnO = float(ol_MnO)\n",
    "        ol_MnO_mole = ol_MnO / 70.937449\n",
    "        ol_MnO_cations = ol_MnO_mole * 1   \n",
    "        ol_MnO_oxygens = ol_MnO_mole * 1\n",
    "\n",
    "    ol_MgO = entries[6][2].value\n",
    "    if ol_MgO:\n",
    "        ol_MgO = float(ol_MgO)\n",
    "        ol_MgO_mole = ol_MgO / 40.3044\n",
    "        ol_MgO_cations = ol_MgO_mole * 1   \n",
    "        ol_MgO_oxygens = ol_MgO_mole * 1   \n",
    "\n",
    "    ol_CaO = entries[7][2].value\n",
    "    if ol_CaO:\n",
    "        ol_CaO = float(ol_CaO)\n",
    "        ol_CaO_mole = ol_CaO / 56.0774\n",
    "        ol_CaO_cations = ol_CaO_mole * 1   \n",
    "        ol_CaO_oxygens = ol_CaO_mole * 1   \n",
    "\n",
    "    ol_P2O5 = entries[8][2].value\n",
    "    if ol_P2O5:\n",
    "        ol_P2O5 = float(ol_P2O5)\n",
    "        ol_P2O5_mole = ol_P2O5 / 141.944522\n",
    "        ol_P2O5_cations = ol_P2O5_mole * 2   \n",
    "        ol_P2O5_oxygens = ol_P2O5_mole * 5\n",
    "        \n",
    "    #NORMALIZATION CALCULATIONS\n",
    "    #spl_total_oxygens = spl_SiO2_oxygens + spl_TiO2_oxygens + spl_Al2O3_oxygens + spl_Cr2O3_oxygens + spl_FeO_oxygens +spl_MnO_oxygens + spl_MgO_oxygens + spl_CaO_oxygens + spl_Fe2O3_oxygens + spl_V2O3_oxygens\n",
    "    #spl_oxygen_factor = 4 / spl_total_oxygens\n",
    "    #spl_SiO2_cations_normalized = spl_SiO2_cations * spl_oxygen_factor\n",
    "    #spl_TiO2_cations_normalized = spl_TiO2_cations * spl_oxygen_factor\n",
    "    #spl_Al2O3_cations_normalized = spl_Al2O3_cations * spl_oxygen_factor\n",
    "    #spl_Cr2O3_cations_normalized = spl_Cr2O3_cations * spl_oxygen_factor\n",
    "    #spl_FeO_cations_normalized = spl_FeO_cations * spl_oxygen_factor\n",
    "    #spl_MnO_cations_normalized = spl_MnO_cations * spl_oxygen_factor\n",
    "    #spl_MgO_cations_normalized = spl_MgO_cations * spl_oxygen_factor\n",
    "    #spl_CaO_cations_normalized = spl_CaO_cations * spl_oxygen_factor\n",
    "    #spl_Fe2O3_cations_normalized = spl_Fe2O3_cations * spl_oxygen_factor\n",
    "    #spl_V2O3_cations_normalized = spl_V2O3_cations * spl_oxygen_factor\n",
    "    #spl_total_cations_normalized = spl_SiO2_cations_normalized + spl_TiO2_cations_normalized + spl_Al2O3_cations_normalized + spl_Cr2O3_cations_normalized + spl_FeO_cations_normalized + spl_MnO_cations_normalized + spl_MgO_cations_normalized + spl_CaO_cations_normalized + spl_Fe2O3_cations_normalized + spl_V2O3_cations_normalized\n",
    "\n",
    "    spl_total_cations = spl_SiO2_cations + spl_TiO2_cations + spl_Al2O3_cations + spl_Cr2O3_cations + spl_FeO_cations +spl_MnO_cations + spl_MgO_cations + spl_CaO_cations + spl_Fe2O3_cations + spl_V2O3_cations\n",
    "    spl_oxygen_factor = 4 / spl_total_cations\n",
    "    spl_SiO2_cations_normalized = spl_SiO2_cations * spl_oxygen_factor\n",
    "    spl_TiO2_cations_normalized = spl_TiO2_cations * spl_oxygen_factor\n",
    "    spl_Al2O3_cations_normalized = spl_Al2O3_cations * spl_oxygen_factor\n",
    "    spl_Cr2O3_cations_normalized = spl_Cr2O3_cations * spl_oxygen_factor\n",
    "    spl_FeO_cations_normalized = spl_FeO_cations * spl_oxygen_factor\n",
    "    spl_MnO_cations_normalized = spl_MnO_cations * spl_oxygen_factor\n",
    "    spl_MgO_cations_normalized = spl_MgO_cations * spl_oxygen_factor\n",
    "    spl_CaO_cations_normalized = spl_CaO_cations * spl_oxygen_factor\n",
    "    spl_Fe2O3_cations_normalized = spl_Fe2O3_cations * spl_oxygen_factor\n",
    "    spl_V2O3_cations_normalized = spl_V2O3_cations * spl_oxygen_factor\n",
    "    spl_total_cations_normalized = spl_SiO2_cations_normalized + spl_TiO2_cations_normalized + spl_Al2O3_cations_normalized + spl_Cr2O3_cations_normalized + spl_FeO_cations_normalized + spl_MnO_cations_normalized + spl_MgO_cations_normalized + spl_CaO_cations_normalized + spl_Fe2O3_cations_normalized + spl_V2O3_cations_normalized    \n",
    "    \n",
    "    opx_total_valences = (4 * (opx_SiO2_cations + opx_TiO2_cations)) + (3 * (opx_Al2O3_cations + opx_Cr2O3_cations)) + (2 * (opx_MgO_cations + opx_CaO_cations + opx_MnO_cations + opx_FeO_cations)) + (opx_Na2O_cations)\n",
    "    opx_normalization_factor = 12 / opx_total_valences\n",
    "    opx_SiO2_cations_normalized = opx_SiO2_cations * opx_normalization_factor\n",
    "    opx_TiO2_cations_normalized = opx_TiO2_cations * opx_normalization_factor\n",
    "    opx_Al2O3_cations_normalized = opx_Al2O3_cations * opx_normalization_factor\n",
    "    opx_Cr2O3_cations_normalized = opx_Cr2O3_cations * opx_normalization_factor\n",
    "    opx_FeO_cations_normalized = opx_FeO_cations * opx_normalization_factor\n",
    "    opx_MnO_cations_normalized = opx_MnO_cations * opx_normalization_factor\n",
    "    opx_MgO_cations_normalized = opx_MgO_cations * opx_normalization_factor\n",
    "    opx_CaO_cations_normalized = opx_CaO_cations * opx_normalization_factor\n",
    "    opx_Na2O_cations_normalized = opx_Na2O_cations * opx_normalization_factor\n",
    "    opx_total_cations_normalized = opx_SiO2_cations_normalized + opx_TiO2_cations_normalized + opx_Al2O3_cations_normalized + opx_Cr2O3_cations_normalized + opx_FeO_cations_normalized + opx_MnO_cations_normalized + opx_MgO_cations_normalized + opx_CaO_cations_normalized + opx_Na2O_cations_normalized\n",
    "    \n",
    "    ol_total_cations = ol_SiO2_cations + ol_TiO2_cations + ol_Al2O3_cations + ol_Cr2O3_cations + ol_FeO_cations + ol_MnO_cations + ol_MgO_cations + ol_CaO_cations\n",
    "    ol_total_valences = (5 * (ol_P2O5_oxygens)) + (4 * (ol_SiO2_oxygens + ol_TiO2_oxygens)) + (3 * (ol_Al2O3_oxygens + ol_Cr2O3_oxygens)) + (2 * (ol_MgO_oxygens + ol_CaO_oxygens + ol_MnO_oxygens + ol_FeO_oxygens))\n",
    "    ol_normalization_factor = 8 / ol_total_valences\n",
    "    ol_SiO2_cations_normalized = ol_SiO2_cations * ol_normalization_factor\n",
    "    ol_TiO2_cations_normalized = ol_TiO2_cations * ol_normalization_factor\n",
    "    ol_Al2O3_cations_normalized = ol_Al2O3_cations * ol_normalization_factor\n",
    "    ol_Cr2O3_cations_normalized = ol_Cr2O3_cations * ol_normalization_factor\n",
    "    ol_FeO_cations_normalized = ol_FeO_cations * ol_normalization_factor\n",
    "    ol_MnO_cations_normalized = ol_MnO_cations * ol_normalization_factor\n",
    "    ol_MgO_cations_normalized = ol_MgO_cations * ol_normalization_factor\n",
    "    ol_CaO_cations_normalized = ol_CaO_cations * ol_normalization_factor\n",
    "    ol_P2O5_cations_normalized = ol_P2O5_cations * ol_normalization_factor\n",
    "    ol_total_cations_normalized = ol_SiO2_cations_normalized + ol_TiO2_cations_normalized + ol_Al2O3_cations_normalized + ol_Cr2O3_cations_normalized + ol_FeO_cations_normalized + ol_MnO_cations_normalized + ol_MgO_cations_normalized + ol_CaO_cations_normalized + ol_P2O5_cations_normalized\n",
    "\n",
    "    # Spinel-Olivine geothermometry\n",
    "    #molar fraction of Mg and Fe in olivine\n",
    "    ol_Mg_mole_fraction = ol_MgO_cations_normalized / (ol_MgO_cations_normalized + ol_FeO_cations_normalized)\n",
    "    ol_Fe_mole_fraction = ol_FeO_cations_normalized / (ol_MgO_cations_normalized + ol_FeO_cations_normalized)\n",
    "\n",
    "    #molar fraction of Mg, Fe, and Cr in spinel\n",
    "    spl_Mg_mole_fraction = spl_MgO_cations_normalized / (spl_MgO_cations_normalized + spl_FeO_cations_normalized)\n",
    "    spl_Fe_mole_fraction = spl_FeO_cations_normalized / (spl_MgO_cations_normalized + spl_FeO_cations_normalized)\n",
    "    spl_Fe3_mole_fraction = spl_Fe2O3_cations_normalized / (spl_Fe2O3_cations_normalized + spl_Cr2O3_cations_normalized + spl_Al2O3_cations_normalized)\n",
    "    spl_Cr_mole_fraction = spl_Cr2O3_cations_normalized / (spl_Fe2O3_cations_normalized + spl_Cr2O3_cations_normalized + spl_Al2O3_cations_normalized)\n",
    "\n",
    "    #natural log\n",
    "    math.e\n",
    "    e = math.e\n",
    "    math.log(e)\n",
    "\n",
    "    #base lnKd value\n",
    "    spl_ol_mole_fractions = ((ol_Mg_mole_fraction * spl_Fe_mole_fraction) / (ol_Fe_mole_fraction * spl_Mg_mole_fraction))\n",
    "    base_ln_Kd = math.log((spl_ol_mole_fractions))\n",
    "\n",
    "    #ln Kd 0 value\n",
    "    ln_Kd_zero = base_ln_Kd - (2 * spl_Fe3_mole_fraction)\n",
    "\n",
    "    #temperature calculation finally :)\n",
    "\n",
    "    temperature_kelvin = ((4299 * spl_Cr_mole_fraction) + 1283) / ((ln_Kd_zero + (1.469 * spl_Cr_mole_fraction) + 0.363))\n",
    "    temperature_celcius = temperature_kelvin - 273.15\n",
    "\n",
    "    #print(\"Temperature in Celcius using olivine-spinel geothermometer based on work by Jianping et al. (1995), Sack and Ghiorso, (1991), and Fabries (1987)\")\n",
    "    #print(temperature_celcius)\n",
    "\n",
    "    #OLIVINE-ORTHOPYROXENE-SPINEL OXYBAROMETRY SECTION\n",
    "    pressure_in_bars_initial = pressure_data[0]\n",
    "    pressure_in_bars = int(pressure_in_bars_initial)\n",
    "   \n",
    "    #spl_a = (math.log((spl_FeO_cations_normalized * (spl_Fe2O3_cations_normalized * spl_Fe2O3_cations_normalized))/4))\n",
    "    #spl_b = (1/temperature_kelvin) * (406 * (spl_Al2O3_cations_normalized * spl_Al2O3_cations_normalized))\n",
    "    #spl_c = (653 * spl_MgO_cations_normalized * spl_Al2O3_cations_normalized)\n",
    "    #spl_d = (299 * (spl_Cr2O3_cations_normalized * spl_Cr2O3_cations_normalized))\n",
    "    #spl_e = (199 * spl_Al2O3_cations_normalized * spl_Cr2O3_cations_normalized)\n",
    "    #spl_f = (346 * spl_MgO_cations_normalized * spl_Cr2O3_cations_normalized)\n",
    "    #intermediate_value_spinel_activity = spl_a + spl_b + spl_c + spl_d + spl_e + spl_f\n",
    "    #spinel_activity = 2 * (math.log10(intermediate_value_spinel_activity))\n",
    "    \n",
    "    Spl = ObjCClass('SpinelBerman')\n",
    "    obj = Spl.alloc().init()\n",
    "    print (obj.phaseName)\n",
    "    \n",
    "    modelDB = thermo.model.Database()\n",
    "    SplS = modelDB.get_phase('SplS')    \n",
    "    data = [spl_SiO2, spl_TiO2, spl_Al2O3, spl_Fe2O3, spl_FeO, spl_MnO, spl_MgO, spl_CaO, spl_Na2O, spl_Cr2O3]\n",
    "\n",
    "    oxide_names = ['SiO2', 'TiO2', 'Al2O3', 'Fe2O3', 'FeO', 'MnO', 'MgO', 'CaO', 'Na2O', 'Cr2O3']\n",
    "    def get_oxide_comp(data):\n",
    "        SplS_mol_oxides = thermo.chem.format_mol_oxide_comp(dict(zip(oxide_names, data)), convert_grams_to_moles=True)\n",
    "        return SplS_mol_oxides\n",
    "    def validate_endmember_comp(moles_end, phase):\n",
    "        print(phase.props['phase_name'])\n",
    "        sum = 0.0\n",
    "               \n",
    "    SplS_mol_oxides = get_oxide_comp(data)\n",
    "    SplS_moles_end = SplS.calc_endmember_comp(mol_oxide_comp=SplS_mol_oxides, method='intrinsic', normalize=True)\n",
    "    validate_endmember_comp(SplS_moles_end, SplS)\n",
    "   \n",
    "    #calculating the number of components and species\n",
    "    nc = obj.numberOfSolutionComponents()\n",
    "    #print ('Number of components = ', nc)\n",
    "    ns = obj.numberOfSolutionSpecies()\n",
    "    #print ('Number of species = ', ns)\n",
    "\n",
    "    PhaseBase = ObjCClass('PhaseBase')\n",
    "    #print ('component name, formula, and molecular weight (g/mol)')\n",
    "    for i in range(0, nc):\n",
    "        component = obj.componentAtIndex_(i)\n",
    "\n",
    "    chromite = SplS_moles_end[0]\n",
    "    hercynite = SplS_moles_end[1]\n",
    "    magnetite = SplS_moles_end[2]\n",
    "    spinel = SplS_moles_end[3]\n",
    "    ulvospinel = SplS_moles_end[4]\n",
    "    \n",
    "    import ctypes\n",
    "    m = (ctypes.c_double*nc)()\n",
    "    ctypes.cast(m, ctypes.POINTER(ctypes.c_double))\n",
    "    m[0] = chromite\n",
    "    m[1] = hercynite\n",
    "    m[2] = magnetite\n",
    "    m[3] = spinel\n",
    "    m[4] = ulvospinel\n",
    "    \n",
    "    for i in range (0, nc):\n",
    "        component = obj.componentAtIndex_(2)\n",
    "        print ('moles of (', component.phaseName.ljust(20), ') = ', m[2])\n",
    "\n",
    "    t = temperature_kelvin\n",
    "    p = pressure_in_bars\n",
    "    activity = obj.getActivityFromMolesOfComponents_andT_andP_(m, t, p)\n",
    "    potential = obj.getChemicalPotentialFromMolesOfComponents_andT_andP_(m, t, p)  \n",
    "    print (component.phaseName, activity.valueAtIndex_(3), potential.valueAtIndex_(3))\n",
    "    activity_of_magnetite_component = activity.valueAtIndex_(3)\n",
    "    print(activity_of_magnetite_component)\n",
    "    spinel_activity = 2 * (math.log10(activity_of_magnetite_component))\n",
    "    print(spinel_activity)\n",
    "    spinel_barometer_calculation = spinel_activity\n",
    "\n",
    "\n",
    "    #Orthopyroxene calculation section\n",
    "    opx_Al_IV = 2 - opx_SiO2_cations_normalized\n",
    "    opx_Al_VI = opx_Al2O3_cations_normalized - opx_Al_IV\n",
    "    M1_site = opx_Al_VI + opx_Cr2O3_cations_normalized + opx_TiO2_cations_normalized\n",
    "    M2_site = opx_CaO_cations_normalized + opx_MnO_cations_normalized\n",
    "    M1_site_Mg_Fe = M1_site + (opx_MgO_cations_normalized /2) + (opx_FeO_cations_normalized /2)\n",
    "    \n",
    "    M1_Fe_fraction = (opx_FeO_cations_normalized/2) /  M1_site_Mg_Fe\n",
    "    \n",
    "    M2_site_Mg_Fe = M2_site + (opx_MgO_cations_normalized /2) + (opx_FeO_cations_normalized /2)\n",
    "    \n",
    "    M2_Fe_fraction = (opx_FeO_cations_normalized/2) /  M2_site_Mg_Fe\n",
    "    \n",
    "    opx_M_sites =  (M1_Fe_fraction) *  (M2_Fe_fraction)\n",
    "    opx_barometer_calculation = (3 * math.log10(opx_M_sites))\n",
    "\n",
    "    #Olivine calculation section\n",
    "\n",
    "    ol_barometer_intermediate_calculation = ((2620/temperature_kelvin) * (ol_Mg_mole_fraction * ol_Mg_mole_fraction))\n",
    "    ol_barometer_calculation = ((12 * (math.log10(ol_Fe_mole_fraction))) - (ol_barometer_intermediate_calculation))\n",
    "\n",
    "    logfo2calc = ((-24441.9 / temperature_kelvin) + (8.29)) \n",
    "    pressure_in_bars_initial = pressure_data[0]\n",
    "    pressure_in_bars = int(pressure_in_bars_initial)\n",
    "    log_calc_with_pressure = -logfo2calc + (220/temperature_kelvin) + (0.35) - ((0.0369 * pressure_in_bars)/temperature_kelvin)\n",
    "    calc_with_pressure = ((220/temperature_kelvin) + (0.35) - ((0.0369 * pressure_in_bars)/temperature_kelvin)) - (ol_barometer_calculation) + (opx_barometer_calculation) + (spinel_barometer_calculation)\n",
    "\n",
    "    #log fo2 FINALLY!\n",
    "    #base log is the absolute log\n",
    "    base_log_fo2 = -1 * (log_calc_with_pressure - (ol_barometer_calculation) + (opx_barometer_calculation) + (spinel_barometer_calculation))\n",
    "    \n",
    "    #Frost 1991 values\n",
    "    Frost_QFM_buffer = (-25096.3/temperature_kelvin) + (8.735) + ((0.110*((pressure_in_bars - 1)))/temperature_kelvin)\n",
    "    \n",
    "    #Euster and Wones 1962 values for the Iron_Wustite buffer\n",
    "    EW62_IW_buffer = (-27215/temperature_kelvin) + (6.57) + ((0.056*((pressure_in_bars - 1)))/temperature_kelvin)\n",
    "    \n",
    "    #Huebner and Sato 1970 values for the nickle nickle oxide buffer\n",
    "    HS70_NNO_buffer = (-24930/temperature_kelvin) + (9.36) + ((0.046*((pressure_in_bars - 1)))/temperature_kelvin)\n",
    "    \n",
    "    dqfm_log_fo2 = base_log_fo2 - Frost_QFM_buffer\n",
    "    diw_log_fo2 = base_log_fo2 - EW62_IW_buffer\n",
    "    dnno_log_fo2 = base_log_fo2 - HS70_NNO_buffer\n",
    "    \n",
    "    log_fo2_QFM = base_log_fo2\n",
    "    print(dqfm_log_fo2)\n",
    "    #widget values\n",
    "    x_widget.value = log_fo2_QFM\n",
    "    y_widget.value = temperature_celcius\n",
    "    z_widget.value = dqfm_log_fo2\n",
    "    aa_widget.value = diw_log_fo2\n",
    "    ab_widget.value = dnno_log_fo2\n",
    "    \n",
    "pass\n",
    "continue_button.on_click(on_continue_clicked)\n",
    "\n",
    "# create an output widget\n",
    "output = widgets.Output()\n",
    "\n",
    "# display the widget\n",
    "output\n",
    "\n",
    "# add some print statements\n",
    "with output:\n",
    "    print(\"\")\n",
    "    print(\"References: \")\n",
    "    print(\"\")\n",
    "    print(\"Herd, C.D.K., 2008. Basalts as Probes of Planetary Interior Redox State. Reviews in Mineralogy and Geochemistry 68, 527–553. https://doi.org/10.2138/rmg.2008.68.19\")\n",
    "    print(\"\")\n",
    "    print(\"Jianping, L., Kornprobst, J., Vielzeuf, D., Fabriès, J., 1995. An improved experimental calibration of the olivine-spinel geothermometer. Chin. J. of Geochem. 14, 68–77. https://doi.org/10.1007/BF02840385\")\n",
    "    print(\"\")\n",
    "    print(\"Myers, J., Eugster, H.P., 1983. The system Fe-Si-O: Oxygen buffer calibrations to 1,500K. Contr. Mineral. and Petrol. 82, 75–90. https://doi.org/10.1007/BF00371177\")\n",
    "    print(\"\")\n",
    "    #print(\"Sack, R.O., Ghiorso, M.S., 1994a. Thermodynamics of multicomponent pyroxenes: I. Formulation of a general model. Contr. Mineral. and Petrol. 116, 277–286. https://doi.org/10.1007/BF00306497\")\n",
    "    #print(\"\")\n",
    "    #print(\"Sack, R.O., Ghiorso, M.S., 1994b. Thermodynamics of multicomponent pyroxenes: II. Phase relations in the quadrilateral. Contr. Mineral. and Petrol. 116, 287–300. https://doi.org/10.1007/BF00306498\")\n",
    "    #print(\"\")\n",
    "    #print(\"Sack, R.O., Ghiorso, M.S., 1994c. Thermodynamics of multicomponent pyroxenes: III. Calibration of Fe2+(Mg)-1, TiAl2(MgSi2)-1, TiFe23+(MgSi2)-1, AlFe3+(MgSi)-1, NaAl(CaMg)-1, Al2(MgSi)-1 and Ca(Mg)-1 exchange reactions between pyroxenes and silicate melts. Contr. Mineral. and Petrol. 118, 271–296. https://doi.org/10.1007/BF00306648\")\n",
    "    #print(\"\")\n",
    "    print(\"Sack, R.O., Ghiorso, M.S., 1991a. Chromian spinels as petrogenetic indicators: Thermodynamics and petrological applications. American Mineralogist 76, 827–847.\")\n",
    "    print(\"\")\n",
    "    print(\"Sack, R.O., Ghiorso, M.S., 1991b. An internally consistent model for the thermodynamic properties of Fe−Mg-titanomagnetite-aluminate spinels. Contr. Mineral. and Petrol. 106, 474–505. https://doi.org/10.1007/BF00321989\")\n",
    "    print(\"\")\n",
    "    print(\"Sack, R.O., Ghiorso, M.S., 1989. Importance of considerations of mixing properties in establishing an internally consistent thermodynamic database: thermochemistry of minerals in the system Mg2SiO4-Fe2SiO4-SiO2. Contr. Mineral. and Petrol. 102, 41–68. https://doi.org/10.1007/BF01160190\")\n",
    "    print(\"\")\n",
    "    print(\"Wood, B.J., 1990. An experimental test of the spinel peridotite oxygen barometer. Journal of Geophysical Research: Solid Earth 95, 15845–15851. https://doi.org/10.1029/JB095iB10p15845\")\n",
    "    print(\"\")\n",
    "    print(\"Wood, B.J., Nell, J., 1991. High-temperature electrical conductivity of the lower-mantle phase (Mg, Fe)O. Nature 351, 309–311. https://doi.org/10.1038/351309a0\")\n",
    "\n",
    "\n",
    "# Create the AppLayout\n",
    "app = AppLayout(header=None,\n",
    "                left_sidebar=None,\n",
    "                center=window,\n",
    "                right_sidebar=result_box,\n",
    "                footer=output,\n",
    "                pane_widths=[10, 10, 10],\n",
    "                pane_heights=[2, 5, '2000px'])\n",
    "\n",
    "# Display the AppLayout\n",
    "app\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a22066c9-062b-4dcd-aada-07f0f6896593",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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