{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 3a. Calculate <i>f</i><sub>O<sub>2</sub></sub> from melt S<sub>T</sub> for a single melt composition from a dataframe using default options"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Python set-up\n",
    "You need to install VolFe once on your machine, if you haven't yet. Then we need to import a few Python packages (including VolFe)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Install VolFe on your machine. Don't remove the # from this line!\n",
    "# pip install VolFe # Remove the first # in this line if you have not installed VolFe on your machine before.\n",
    "\n",
    "# import python packages\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import VolFe as vf"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Define the inputs\n",
    "\n",
    "At a minimum to run an S-2-<i>f</i><sub>O<sub>2</sub></sub> calculation, we need a dataframe of the melt composition and Fe in the melt [note 1], and temperature:\n",
    "\n",
    "- Sample is just the name for this analysis.\n",
    "\n",
    "- Temperature is in °C.\n",
    "\n",
    "- Volatile-free melt composition is in wt% oxides [note 2]. All these oxides must be present in the dataframe, so set them to 0. if you have no data for them (although see [note 1] around FeO<sub>T</sub>).\n",
    "\n",
    "- H2O is all hydrogen in the melt reported as H<sub>2</sub>O in wt% [note 3]. \n",
    "\n",
    "- CO2ppm is all carbon in the melt reported as CO<sub>2</sub> in ppm [note 3].\n",
    "\n",
    "- STppm is all sulfur in the melt reported as S in ppm [note 3].\n",
    "\n",
    "- Xppm is all \"X\" in the melt reported as \"X\" in ppm [note 3]. \"X\" is an unreactive melt species whose identity can be changed - this is explored Example 1d.\n",
    "\n",
    "[note 1] In this example we specify Fe in the melt as FeO<sub>T</sub> - other options are possible, such as Fe<sub>2</sub>O<sub>3,T</sub> or FeO and Fe<sub>2</sub>O<sub>3</sub>.\n",
    "\n",
    "[note 2] It does not matter what the non-volatile oxides sum too - they are renormalised to 100 wt% minus the total of the volatiles (i.e., H<sub>2</sub>O + CO<sub>2</sub> + S<sub>T</sub> + \"X\").\n",
    "\n",
    "[note 3] The volatile concentrations are absolute for the melt = i.e., the non-volatile melt composition is normalised to 100 wt% minus the volatiles. The volatiles are not added to the oxides and then renormalised.\n",
    "\n",
    "The following composition is analysis Sari15-04-34 from Brounce et al. (2014), with a temperature chosen as 1200 °C. We'll run at <i>P<sup>v</sup></i><sub>sat</sub> (based on the volatile content) for now so we don't have to specify a <i>P</i>."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "         Sample     T_C   SiO2  TiO2  Al2O3  FeOT   MnO  MgO    CaO  Na2O  \\\n",
      "0  Sari15-04-34  1200.0  46.94  0.65   16.0  8.92  0.15  7.3  13.94  1.61   \n",
      "\n",
      "    K2O  P2O5   H2O  CO2ppm    STppm  Xppm  \n",
      "0  0.26  0.07  3.83  1109.0  1614.12   0.0  \n"
     ]
    }
   ],
   "source": [
    "# Define the melt composition and T as a dictionary.\n",
    "my_analysis = {'Sample':'Sari15-04-34',\n",
    "           'T_C': 1200., # Temperature in 'C\n",
    "           'SiO2': 46.94, # wt%\n",
    "           'TiO2': 0.65, # wt%\n",
    "           'Al2O3': 16.0, # wt%\n",
    "           'FeOT': 8.92, # wt%\n",
    "           'MnO': 0.15, # wt%\n",
    "           'MgO': 7.3, # wt%\n",
    "           'CaO': 13.94, # wt%\n",
    "           'Na2O': 1.61, # wt%\n",
    "           'K2O': 0.26, # wt%\n",
    "           'P2O5': 0.07, # wt%\n",
    "           'H2O': 3.83, # wt%\n",
    "           'CO2ppm': 1109., # ppm\n",
    "           'STppm': 1614.12, # ppm\n",
    "           'Xppm': 0.} # ppm\n",
    "\t\t\t\t\t\t\t\t\t\t\t\t\t\n",
    "# Turn the dictionary into a pandas dataframe, setting the index to 0.\n",
    "my_analysis = pd.DataFrame(my_analysis, index=[0])\n",
    "\n",
    "# Show the DataFrame.\n",
    "print(my_analysis)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For this example we will use the default options in VolFe, which can be found below:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                            option\n",
      "type                              \n",
      "COH_species     yes_H2_CO_CH4_melt\n",
      "H2S_m                         True\n",
      "species X                       Ar\n",
      "Hspeciation                   none\n",
      "fO2                       Kress91A\n",
      "...                            ...\n",
      "error                          0.1\n",
      "print status                 False\n",
      "output csv                    True\n",
      "setup                        False\n",
      "high precision               False\n",
      "\n",
      "[78 rows x 1 columns]\n"
     ]
    }
   ],
   "source": [
    "# print default options in VolFe\n",
    "print(vf.default_models)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run the calculation\n",
    "\n",
    "### At <i>P<sup>v</sup></i><sub>sat</sub>\n",
    "\n",
    "And below runs the calculation - it outputs a dataframe of the full results. So in this example, the sample would be sulfide-saturated but doesn't have enough sulfur to be anhydrite saturated."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sample</th>\n",
       "      <th>T ('C)</th>\n",
       "      <th>H2OT-eq_wtpc</th>\n",
       "      <th>CO2T-eq_ppmw</th>\n",
       "      <th>ST_ppmw</th>\n",
       "      <th>X_ppmw</th>\n",
       "      <th>P (bar) sulf</th>\n",
       "      <th>S2- SCSS</th>\n",
       "      <th>sulfide saturated?</th>\n",
       "      <th>DFMQ-sulfide</th>\n",
       "      <th>...</th>\n",
       "      <th>KHOSg opt</th>\n",
       "      <th>KOSg opt</th>\n",
       "      <th>KOSg2 opt</th>\n",
       "      <th>KCOg opt</th>\n",
       "      <th>KCOHg opt</th>\n",
       "      <th>KOCSg opt</th>\n",
       "      <th>KCOs opt</th>\n",
       "      <th>carbonylsulfide opt</th>\n",
       "      <th>density opt</th>\n",
       "      <th>Date</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Sari15-04-34</td>\n",
       "      <td>1200.0</td>\n",
       "      <td>3.83</td>\n",
       "      <td>1109.0</td>\n",
       "      <td>1614.12</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3209.679276</td>\n",
       "      <td>1071.669795</td>\n",
       "      <td>True</td>\n",
       "      <td>0.905944</td>\n",
       "      <td>...</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>ONeill22</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Moussallam19</td>\n",
       "      <td>Holloway92</td>\n",
       "      <td>COS</td>\n",
       "      <td>DensityX</td>\n",
       "      <td>2025-02-02 12:10:37.752486</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1 rows × 67 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "0        sample  T ('C) H2OT-eq_wtpc CO2T-eq_ppmw  ST_ppmw X_ppmw  \\\n",
       "0  Sari15-04-34  1200.0         3.83       1109.0  1614.12    0.0   \n",
       "\n",
       "0 P (bar) sulf     S2- SCSS sulfide saturated? DFMQ-sulfide  ... KHOSg opt  \\\n",
       "0  3209.679276  1071.669795               True     0.905944  ...  Ohmoto97   \n",
       "\n",
       "0  KOSg opt KOSg2 opt  KCOg opt KCOHg opt     KOCSg opt    KCOs opt  \\\n",
       "0  Ohmoto97  ONeill22  Ohmoto97  Ohmoto97  Moussallam19  Holloway92   \n",
       "\n",
       "0 carbonylsulfide opt density opt                        Date  \n",
       "0                 COS    DensityX  2025-02-02 12:10:37.752486  \n",
       "\n",
       "[1 rows x 67 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# runs the calculation\n",
    "vf.calc_melt_S_oxybarometer(my_analysis)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### At specified <i>P</i>\n",
    "\n",
    "Alternatively, we can specify the pressure of the calculation by adding \"P_bar\" to the dataframe. \n",
    "\n",
    "The calculation is not iterative yet (work in progress) which means you also have to specify Fe<sup>3+</sup>/Fe<sub>T</sub> of the melt so it can calculate S<sup>2-</sup>CSS and S<sup>6+</sup>CAS... \n",
    "\n",
    "Note that if this is below <i>P<sup>v</sup></i><sub>sat</sub> for the volatile content, the melt composition is metastable because a vapor would be present, lowering the volatile content of the melt."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sample</th>\n",
       "      <th>T ('C)</th>\n",
       "      <th>H2OT-eq_wtpc</th>\n",
       "      <th>CO2T-eq_ppmw</th>\n",
       "      <th>ST_ppmw</th>\n",
       "      <th>X_ppmw</th>\n",
       "      <th>P (bar) sulf</th>\n",
       "      <th>S2- SCSS</th>\n",
       "      <th>sulfide saturated?</th>\n",
       "      <th>DFMQ-sulfide</th>\n",
       "      <th>...</th>\n",
       "      <th>KHOSg opt</th>\n",
       "      <th>KOSg opt</th>\n",
       "      <th>KOSg2 opt</th>\n",
       "      <th>KCOg opt</th>\n",
       "      <th>KCOHg opt</th>\n",
       "      <th>KOCSg opt</th>\n",
       "      <th>KCOs opt</th>\n",
       "      <th>carbonylsulfide opt</th>\n",
       "      <th>density opt</th>\n",
       "      <th>Date</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Sari15-04-34</td>\n",
       "      <td>1200.0</td>\n",
       "      <td>3.83</td>\n",
       "      <td>1109.0</td>\n",
       "      <td>1614.12</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1000.0</td>\n",
       "      <td>930.456494</td>\n",
       "      <td>possible</td>\n",
       "      <td>1.158861</td>\n",
       "      <td>...</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>ONeill22</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Moussallam19</td>\n",
       "      <td>Holloway92</td>\n",
       "      <td>COS</td>\n",
       "      <td>DensityX</td>\n",
       "      <td>2025-02-02 09:58:12.197469</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1 rows × 67 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "0        sample  T ('C) H2OT-eq_wtpc CO2T-eq_ppmw  ST_ppmw X_ppmw  \\\n",
       "0  Sari15-04-34  1200.0         3.83       1109.0  1614.12    0.0   \n",
       "\n",
       "0 P (bar) sulf    S2- SCSS sulfide saturated? DFMQ-sulfide  ... KHOSg opt  \\\n",
       "0       1000.0  930.456494           possible     1.158861  ...  Ohmoto97   \n",
       "\n",
       "0  KOSg opt KOSg2 opt  KCOg opt KCOHg opt     KOCSg opt    KCOs opt  \\\n",
       "0  Ohmoto97  ONeill22  Ohmoto97  Ohmoto97  Moussallam19  Holloway92   \n",
       "\n",
       "0 carbonylsulfide opt density opt                        Date  \n",
       "0                 COS    DensityX  2025-02-02 09:58:12.197469  \n",
       "\n",
       "[1 rows x 67 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Define the melt composition, P, and T as a dictionary.\n",
    "my_analysis = {'Sample':'Sari15-04-34',\n",
    "           'T_C': 1200., # Temperature in 'C\n",
    "           'SiO2': 46.94, # wt%\n",
    "           'TiO2': 0.65, # wt%\n",
    "           'Al2O3': 16.0, # wt%\n",
    "           'FeOT': 8.92, # wt%\n",
    "           'MnO': 0.15, # wt%\n",
    "           'MgO': 7.3, # wt%\n",
    "           'CaO': 13.94, # wt%\n",
    "           'Na2O': 1.61, # wt%\n",
    "           'K2O': 0.26, # wt%\n",
    "           'P2O5': 0.07, # wt%\n",
    "           'H2O': 3.83, # wt%\n",
    "           'CO2ppm': 1109., # ppm\n",
    "           'STppm': 1614.12, # ppm\n",
    "           'Xppm': 0., # ppm\n",
    "           'P_bar': 1000., # bar\n",
    "           'Fe3FeT': 0.1} \n",
    "\t\t\t\t\t\t\t\t\t\t\t\t\t\n",
    "# Turn the dictionary into a pandas dataframe, setting the index to 0.\n",
    "my_analysis = pd.DataFrame(my_analysis, index=[0])\n",
    "\n",
    "# runs the calculation\n",
    "vf.calc_melt_S_oxybarometer(my_analysis)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Specifying sulfide composition\n",
    "\n",
    "The sulfide composition (i.e., fractions of Fe, Ni, and Cu) change the S<sup>2-</sup>CSS, which is incoporated into some parameterisations of S<sup>2-</sup>CSS (see Wieser & Gleeson, 2023, for an overview). \n",
    "\n",
    "If nothing about the sulfide composition is specified, VolFe assumes the sulfide is pure FeS. However, the composition of the sulfide can be specified in the input dataframe using \"sulf_XFe\", \"sulf_XCu\", and \"sulf_XNi\" as the mole fractions of FeS, CuS, and NiS in the sulfide, as shown below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sample</th>\n",
       "      <th>T ('C)</th>\n",
       "      <th>H2OT-eq_wtpc</th>\n",
       "      <th>CO2T-eq_ppmw</th>\n",
       "      <th>ST_ppmw</th>\n",
       "      <th>X_ppmw</th>\n",
       "      <th>P (bar) sulf</th>\n",
       "      <th>S2- SCSS</th>\n",
       "      <th>sulfide saturated?</th>\n",
       "      <th>DFMQ-sulfide</th>\n",
       "      <th>...</th>\n",
       "      <th>KHOSg opt</th>\n",
       "      <th>KOSg opt</th>\n",
       "      <th>KOSg2 opt</th>\n",
       "      <th>KCOg opt</th>\n",
       "      <th>KCOHg opt</th>\n",
       "      <th>KOCSg opt</th>\n",
       "      <th>KCOs opt</th>\n",
       "      <th>carbonylsulfide opt</th>\n",
       "      <th>density opt</th>\n",
       "      <th>Date</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Sari15-04-34</td>\n",
       "      <td>1200.0</td>\n",
       "      <td>3.83</td>\n",
       "      <td>1109.0</td>\n",
       "      <td>1614.12</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3223.517523</td>\n",
       "      <td>867.284719</td>\n",
       "      <td>True</td>\n",
       "      <td>1.023231</td>\n",
       "      <td>...</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>ONeill22</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Ohmoto97</td>\n",
       "      <td>Moussallam19</td>\n",
       "      <td>Holloway92</td>\n",
       "      <td>COS</td>\n",
       "      <td>DensityX</td>\n",
       "      <td>2025-02-02 09:59:13.344561</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1 rows × 67 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "0        sample  T ('C) H2OT-eq_wtpc CO2T-eq_ppmw  ST_ppmw X_ppmw  \\\n",
       "0  Sari15-04-34  1200.0         3.83       1109.0  1614.12    0.0   \n",
       "\n",
       "0 P (bar) sulf    S2- SCSS sulfide saturated? DFMQ-sulfide  ... KHOSg opt  \\\n",
       "0  3223.517523  867.284719               True     1.023231  ...  Ohmoto97   \n",
       "\n",
       "0  KOSg opt KOSg2 opt  KCOg opt KCOHg opt     KOCSg opt    KCOs opt  \\\n",
       "0  Ohmoto97  ONeill22  Ohmoto97  Ohmoto97  Moussallam19  Holloway92   \n",
       "\n",
       "0 carbonylsulfide opt density opt                        Date  \n",
       "0                 COS    DensityX  2025-02-02 09:59:13.344561  \n",
       "\n",
       "[1 rows x 67 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Define the melt composition, sulfide composition, and T as a dictionary.\n",
    "my_analysis = {'Sample':'Sari15-04-34',\n",
    "           'T_C': 1200., # Temperature in 'C\n",
    "           'SiO2': 46.94, # wt%\n",
    "           'TiO2': 0.65, # wt%\n",
    "           'Al2O3': 16.0, # wt%\n",
    "           'FeOT': 8.92, # wt%\n",
    "           'MnO': 0.15, # wt%\n",
    "           'MgO': 7.3, # wt%\n",
    "           'CaO': 13.94, # wt%\n",
    "           'Na2O': 1.61, # wt%\n",
    "           'K2O': 0.26, # wt%\n",
    "           'P2O5': 0.07, # wt%\n",
    "           'H2O': 3.83, # wt%\n",
    "           'CO2ppm': 1109., # ppm\n",
    "           'STppm': 1614.12, # ppm\n",
    "           'Xppm': 0., # ppm\n",
    "           'sulf_XFe': 0.8,\n",
    "           'sulf_XCu': 0.15,\n",
    "           'sulf_XNi': 0.05}\n",
    "\t\t\t\t\t\t\t\t\t\t\t\t\t\n",
    "# Turn the dictionary into a pandas dataframe, setting the index to 0.\n",
    "my_analysis = pd.DataFrame(my_analysis, index=[0])\n",
    "\n",
    "# runs the calculation\n",
    "vf.calc_melt_S_oxybarometer(my_analysis)"
   ]
  }
 ],
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