2024-11-18-myradex-with-cython-example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "2925fee9-3a23-4f00-9906-2253a18be481",
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "\n",
    "import numpy as np\n",
    "import matplotlib as mpl\n",
    "import matplotlib.pyplot as plt\n",
    "import pandas as pd\n",
    "pd.options.display.max_columns = 30\n",
    "import os\n",
    "import sys\n",
    "for std, __std__ in [\n",
    "    (sys.stdout, sys.__stdout__),\n",
    "    (sys.stderr, sys.__stderr__)]:\n",
    "    if getattr(std, \"_original_stdstream_copy\", None) is not None:\n",
    "        os.dup2(std._original_stdstream_copy, __std__.fileno())\n",
    "        std._original_stdstream_copy = None\n",
    "\n",
    "myRadexPath = os.path.expanduser('~/_c/my_radex')\n",
    "if myRadexPath not in sys.path:\n",
    "    sys.path.append(myRadexPath)\n",
    "\n",
    "import myRadex"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ee2740fa-c1e4-455f-91cd-c8bb68c10161",
   "metadata": {},
   "source": [
    "# Try with e-CH3OH"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "05ee5762-2896-4b0b-90f2-db51b5dde513",
   "metadata": {},
   "outputs": [],
   "source": [
    "a = myRadex.MyRadexModel(\n",
    "    dir_transition_rates=myRadexPath,\n",
    "    filename_molecule='e-ch3oh.dat')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ad0ec080-a1fc-499d-87a1-516631a725f2",
   "metadata": {},
   "source": [
    "## Solve with the ODE solver"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "b349c868-9c31-4ef3-8ce8-e5f48d76e751",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\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>iup</th>\n",
       "      <th>ilow</th>\n",
       "      <th>Eup</th>\n",
       "      <th>freq</th>\n",
       "      <th>lam</th>\n",
       "      <th>Tex</th>\n",
       "      <th>tau</th>\n",
       "      <th>Tr</th>\n",
       "      <th>fup</th>\n",
       "      <th>flow</th>\n",
       "      <th>flux_Kkms</th>\n",
       "      <th>flux_int</th>\n",
       "      <th>flux_Jy</th>\n",
       "      <th>beta</th>\n",
       "      <th>Jnu</th>\n",
       "      <th>gup</th>\n",
       "      <th>glow</th>\n",
       "      <th>Aul</th>\n",
       "      <th>Bul</th>\n",
       "      <th>Blu</th>\n",
       "      <th>n_crit</th>\n",
       "      <th>n_crit_old</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>80.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>175.526266</td>\n",
       "      <td>2.925982e+09</td>\n",
       "      <td>102458.749917</td>\n",
       "      <td>-0.041756</td>\n",
       "      <td>-8.661517e-07</td>\n",
       "      <td>2.474330e-06</td>\n",
       "      <td>5.745532e-08</td>\n",
       "      <td>1.791949e-09</td>\n",
       "      <td>2.633843e-06</td>\n",
       "      <td>8.497011e-19</td>\n",
       "      <td>1.560019e-08</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>7.131517e-18</td>\n",
       "      <td>23.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>3.882245e-11</td>\n",
       "      <td>1.051050e+08</td>\n",
       "      <td>1.151150e+08</td>\n",
       "      <td>0.081247</td>\n",
       "      <td>12.132016</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>15.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>36.334831</td>\n",
       "      <td>3.387356e+09</td>\n",
       "      <td>88503.380808</td>\n",
       "      <td>-0.078057</td>\n",
       "      <td>-2.458924e-06</td>\n",
       "      <td>7.058133e-06</td>\n",
       "      <td>6.804175e-03</td>\n",
       "      <td>6.592548e-04</td>\n",
       "      <td>7.513150e-06</td>\n",
       "      <td>3.760677e-18</td>\n",
       "      <td>5.964039e-08</td>\n",
       "      <td>1.000001</td>\n",
       "      <td>9.464363e-18</td>\n",
       "      <td>9.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1.593096e-15</td>\n",
       "      <td>2.779809e+03</td>\n",
       "      <td>3.574040e+03</td>\n",
       "      <td>0.000004</td>\n",
       "      <td>0.000797</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>97.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>215.895422</td>\n",
       "      <td>7.283364e+09</td>\n",
       "      <td>41161.262570</td>\n",
       "      <td>0.177529</td>\n",
       "      <td>4.996843e-08</td>\n",
       "      <td>-1.222975e-07</td>\n",
       "      <td>6.653506e-10</td>\n",
       "      <td>4.353429e-09</td>\n",
       "      <td>-1.301816e-07</td>\n",
       "      <td>-6.477496e-19</td>\n",
       "      <td>-4.777607e-09</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>4.081381e-17</td>\n",
       "      <td>23.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>4.672324e-10</td>\n",
       "      <td>8.201483e+07</td>\n",
       "      <td>8.982576e+07</td>\n",
       "      <td>0.985907</td>\n",
       "      <td>186.892960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>31.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>71.002121</td>\n",
       "      <td>9.400854e+09</td>\n",
       "      <td>31889.917448</td>\n",
       "      <td>0.127315</td>\n",
       "      <td>1.031230e-05</td>\n",
       "      <td>-2.541626e-05</td>\n",
       "      <td>2.278948e-05</td>\n",
       "      <td>9.140470e-04</td>\n",
       "      <td>-2.705477e-05</td>\n",
       "      <td>-2.894724e-16</td>\n",
       "      <td>-1.654151e-06</td>\n",
       "      <td>0.999995</td>\n",
       "      <td>6.728572e-17</td>\n",
       "      <td>13.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>1.105666e-12</td>\n",
       "      <td>9.025629e+04</td>\n",
       "      <td>7.822212e+04</td>\n",
       "      <td>0.002469</td>\n",
       "      <td>0.480722</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>47.0</td>\n",
       "      <td>46.0</td>\n",
       "      <td>109.969910</td>\n",
       "      <td>9.936142e+09</td>\n",
       "      <td>30171.917632</td>\n",
       "      <td>-0.080149</td>\n",
       "      <td>-8.619618e-04</td>\n",
       "      <td>2.548682e-03</td>\n",
       "      <td>5.044694e-05</td>\n",
       "      <td>1.185815e-07</td>\n",
       "      <td>2.712988e-03</td>\n",
       "      <td>3.427383e-14</td>\n",
       "      <td>1.853020e-04</td>\n",
       "      <td>1.000431</td>\n",
       "      <td>7.518612e-17</td>\n",
       "      <td>19.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>1.668626e-09</td>\n",
       "      <td>1.153616e+08</td>\n",
       "      <td>1.289335e+08</td>\n",
       "      <td>3.439019</td>\n",
       "      <td>575.636328</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>6.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>20.089619</td>\n",
       "      <td>1.217858e+10</td>\n",
       "      <td>24616.364103</td>\n",
       "      <td>0.348474</td>\n",
       "      <td>5.911957e+00</td>\n",
       "      <td>-2.282249e+00</td>\n",
       "      <td>2.923116e-02</td>\n",
       "      <td>2.187644e-01</td>\n",
       "      <td>-2.429379e+00</td>\n",
       "      <td>-5.651283e-11</td>\n",
       "      <td>-2.492789e-01</td>\n",
       "      <td>0.168691</td>\n",
       "      <td>2.371889e-17</td>\n",
       "      <td>5.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.346957e-09</td>\n",
       "      <td>3.133959e+08</td>\n",
       "      <td>2.238542e+08</td>\n",
       "      <td>3.296727</td>\n",
       "      <td>370.540893</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>133.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>291.455583</td>\n",
       "      <td>1.490525e+10</td>\n",
       "      <td>20113.216373</td>\n",
       "      <td>0.292291</td>\n",
       "      <td>2.522090e-11</td>\n",
       "      <td>-5.799401e-11</td>\n",
       "      <td>9.227052e-12</td>\n",
       "      <td>1.138941e-10</td>\n",
       "      <td>-6.173271e-11</td>\n",
       "      <td>-2.632657e-21</td>\n",
       "      <td>-9.488345e-12</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.615789e-16</td>\n",
       "      <td>29.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>8.520992e-11</td>\n",
       "      <td>1.745131e+06</td>\n",
       "      <td>1.632542e+06</td>\n",
       "      <td>0.199765</td>\n",
       "      <td>23.029708</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>29.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>70.550345</td>\n",
       "      <td>1.561732e+10</td>\n",
       "      <td>19196.150147</td>\n",
       "      <td>-0.186404</td>\n",
       "      <td>-1.331460e-06</td>\n",
       "      <td>4.214507e-06</td>\n",
       "      <td>9.140470e-04</td>\n",
       "      <td>1.420226e-05</td>\n",
       "      <td>4.486203e-06</td>\n",
       "      <td>2.200696e-16</td>\n",
       "      <td>7.569877e-07</td>\n",
       "      <td>1.000001</td>\n",
       "      <td>1.800036e-16</td>\n",
       "      <td>15.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>5.609782e-13</td>\n",
       "      <td>9.988074e+03</td>\n",
       "      <td>1.152470e+04</td>\n",
       "      <td>0.001144</td>\n",
       "      <td>0.207770</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>59.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>131.279610</td>\n",
       "      <td>1.834596e+10</td>\n",
       "      <td>16341.063138</td>\n",
       "      <td>0.889372</td>\n",
       "      <td>1.002352e-10</td>\n",
       "      <td>-1.759370e-10</td>\n",
       "      <td>1.254484e-08</td>\n",
       "      <td>3.773521e-08</td>\n",
       "      <td>-1.872792e-10</td>\n",
       "      <td>-1.489265e-20</td>\n",
       "      <td>-4.360808e-11</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>2.353414e-16</td>\n",
       "      <td>17.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>2.896289e-12</td>\n",
       "      <td>3.181092e+04</td>\n",
       "      <td>2.846240e+04</td>\n",
       "      <td>0.006776</td>\n",
       "      <td>52.659800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>9.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>28.011516</td>\n",
       "      <td>1.996738e+10</td>\n",
       "      <td>15014.113923</td>\n",
       "      <td>0.459775</td>\n",
       "      <td>2.753554e-01</td>\n",
       "      <td>-5.095736e-01</td>\n",
       "      <td>1.805096e-03</td>\n",
       "      <td>2.031178e-02</td>\n",
       "      <td>-5.424243e-01</td>\n",
       "      <td>-5.561137e-11</td>\n",
       "      <td>-1.496159e-01</td>\n",
       "      <td>0.874135</td>\n",
       "      <td>2.433652e-16</td>\n",
       "      <td>5.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1.713363e-08</td>\n",
       "      <td>1.459627e+08</td>\n",
       "      <td>1.042591e+08</td>\n",
       "      <td>41.056119</td>\n",
       "      <td>3186.618017</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     iup   ilow         Eup          freq            lam       Tex  \\\n",
       "0   80.0   79.0  175.526266  2.925982e+09  102458.749917 -0.041756   \n",
       "1   15.0   14.0   36.334831  3.387356e+09   88503.380808 -0.078057   \n",
       "2   97.0   96.0  215.895422  7.283364e+09   41161.262570  0.177529   \n",
       "3   31.0   29.0   71.002121  9.400854e+09   31889.917448  0.127315   \n",
       "4   47.0   46.0  109.969910  9.936142e+09   30171.917632 -0.080149   \n",
       "5    6.0    5.0   20.089619  1.217858e+10   24616.364103  0.348474   \n",
       "6  133.0  132.0  291.455583  1.490525e+10   20113.216373  0.292291   \n",
       "7   29.0   28.0   70.550345  1.561732e+10   19196.150147 -0.186404   \n",
       "8   59.0   57.0  131.279610  1.834596e+10   16341.063138  0.889372   \n",
       "9    9.0    8.0   28.011516  1.996738e+10   15014.113923  0.459775   \n",
       "\n",
       "            tau            Tr           fup          flow     flux_Kkms  \\\n",
       "0 -8.661517e-07  2.474330e-06  5.745532e-08  1.791949e-09  2.633843e-06   \n",
       "1 -2.458924e-06  7.058133e-06  6.804175e-03  6.592548e-04  7.513150e-06   \n",
       "2  4.996843e-08 -1.222975e-07  6.653506e-10  4.353429e-09 -1.301816e-07   \n",
       "3  1.031230e-05 -2.541626e-05  2.278948e-05  9.140470e-04 -2.705477e-05   \n",
       "4 -8.619618e-04  2.548682e-03  5.044694e-05  1.185815e-07  2.712988e-03   \n",
       "5  5.911957e+00 -2.282249e+00  2.923116e-02  2.187644e-01 -2.429379e+00   \n",
       "6  2.522090e-11 -5.799401e-11  9.227052e-12  1.138941e-10 -6.173271e-11   \n",
       "7 -1.331460e-06  4.214507e-06  9.140470e-04  1.420226e-05  4.486203e-06   \n",
       "8  1.002352e-10 -1.759370e-10  1.254484e-08  3.773521e-08 -1.872792e-10   \n",
       "9  2.753554e-01 -5.095736e-01  1.805096e-03  2.031178e-02 -5.424243e-01   \n",
       "\n",
       "       flux_int       flux_Jy      beta           Jnu   gup  glow  \\\n",
       "0  8.497011e-19  1.560019e-08  1.000000  7.131517e-18  23.0  21.0   \n",
       "1  3.760677e-18  5.964039e-08  1.000001  9.464363e-18   9.0   7.0   \n",
       "2 -6.477496e-19 -4.777607e-09  1.000000  4.081381e-17  23.0  21.0   \n",
       "3 -2.894724e-16 -1.654151e-06  0.999995  6.728572e-17  13.0  15.0   \n",
       "4  3.427383e-14  1.853020e-04  1.000431  7.518612e-17  19.0  17.0   \n",
       "5 -5.651283e-11 -2.492789e-01  0.168691  2.371889e-17   5.0   7.0   \n",
       "6 -2.632657e-21 -9.488345e-12  1.000000  1.615789e-16  29.0  31.0   \n",
       "7  2.200696e-16  7.569877e-07  1.000001  1.800036e-16  15.0  13.0   \n",
       "8 -1.489265e-20 -4.360808e-11  1.000000  2.353414e-16  17.0  19.0   \n",
       "9 -5.561137e-11 -1.496159e-01  0.874135  2.433652e-16   5.0   7.0   \n",
       "\n",
       "            Aul           Bul           Blu     n_crit   n_crit_old  \n",
       "0  3.882245e-11  1.051050e+08  1.151150e+08   0.081247    12.132016  \n",
       "1  1.593096e-15  2.779809e+03  3.574040e+03   0.000004     0.000797  \n",
       "2  4.672324e-10  8.201483e+07  8.982576e+07   0.985907   186.892960  \n",
       "3  1.105666e-12  9.025629e+04  7.822212e+04   0.002469     0.480722  \n",
       "4  1.668626e-09  1.153616e+08  1.289335e+08   3.439019   575.636328  \n",
       "5  8.346957e-09  3.133959e+08  2.238542e+08   3.296727   370.540893  \n",
       "6  8.520992e-11  1.745131e+06  1.632542e+06   0.199765    23.029708  \n",
       "7  5.609782e-13  9.988074e+03  1.152470e+04   0.001144     0.207770  \n",
       "8  2.896289e-12  3.181092e+04  2.846240e+04   0.006776    52.659800  \n",
       "9  1.713363e-08  1.459627e+08  1.042591e+08  41.056119  3186.618017  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.run_one_params(\n",
    "    Tkin=30.0, dv_CGS=1e5, Ncol_X_CGS=1e15,\n",
    "    oH2_density_CGS=3e4, pH2_densty_CGS=1e4, solve_method='ODE', geotype='')\n",
    "df = pd.DataFrame(data=a.data_transitions, columns=a.column_names)\n",
    "df.head(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b17d2139-c946-41d8-9aa8-1811e8c65c43",
   "metadata": {},
   "source": [
    "## Solve with the Newton solver"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "934590e6-7b15-4c21-81f6-1f2b70c2d70d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\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>iup</th>\n",
       "      <th>ilow</th>\n",
       "      <th>Eup</th>\n",
       "      <th>freq</th>\n",
       "      <th>lam</th>\n",
       "      <th>Tex</th>\n",
       "      <th>tau</th>\n",
       "      <th>Tr</th>\n",
       "      <th>fup</th>\n",
       "      <th>flow</th>\n",
       "      <th>flux_Kkms</th>\n",
       "      <th>flux_int</th>\n",
       "      <th>flux_Jy</th>\n",
       "      <th>beta</th>\n",
       "      <th>Jnu</th>\n",
       "      <th>gup</th>\n",
       "      <th>glow</th>\n",
       "      <th>Aul</th>\n",
       "      <th>Bul</th>\n",
       "      <th>Blu</th>\n",
       "      <th>n_crit</th>\n",
       "      <th>n_crit_old</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>80.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>175.526266</td>\n",
       "      <td>2.925982e+09</td>\n",
       "      <td>102458.749917</td>\n",
       "      <td>-0.041756</td>\n",
       "      <td>-8.661514e-07</td>\n",
       "      <td>2.474329e-06</td>\n",
       "      <td>5.745531e-08</td>\n",
       "      <td>1.791956e-09</td>\n",
       "      <td>2.633842e-06</td>\n",
       "      <td>8.497009e-19</td>\n",
       "      <td>1.560018e-08</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>7.131517e-18</td>\n",
       "      <td>23.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>3.882245e-11</td>\n",
       "      <td>1.051050e+08</td>\n",
       "      <td>1.151150e+08</td>\n",
       "      <td>0.081247</td>\n",
       "      <td>12.132016</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>15.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>36.334831</td>\n",
       "      <td>3.387356e+09</td>\n",
       "      <td>88503.380808</td>\n",
       "      <td>-0.078056</td>\n",
       "      <td>-2.458937e-06</td>\n",
       "      <td>7.058170e-06</td>\n",
       "      <td>6.804199e-03</td>\n",
       "      <td>6.592494e-04</td>\n",
       "      <td>7.513189e-06</td>\n",
       "      <td>3.760697e-18</td>\n",
       "      <td>5.964070e-08</td>\n",
       "      <td>1.000001</td>\n",
       "      <td>9.464363e-18</td>\n",
       "      <td>9.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1.593096e-15</td>\n",
       "      <td>2.779809e+03</td>\n",
       "      <td>3.574040e+03</td>\n",
       "      <td>0.000004</td>\n",
       "      <td>0.000797</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>97.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>215.895422</td>\n",
       "      <td>7.283364e+09</td>\n",
       "      <td>41161.262570</td>\n",
       "      <td>0.177530</td>\n",
       "      <td>4.996841e-08</td>\n",
       "      <td>-1.222974e-07</td>\n",
       "      <td>6.653519e-10</td>\n",
       "      <td>4.353429e-09</td>\n",
       "      <td>-1.301816e-07</td>\n",
       "      <td>-6.477493e-19</td>\n",
       "      <td>-4.777605e-09</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>4.081381e-17</td>\n",
       "      <td>23.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>4.672324e-10</td>\n",
       "      <td>8.201483e+07</td>\n",
       "      <td>8.982576e+07</td>\n",
       "      <td>0.985907</td>\n",
       "      <td>186.892960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>31.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>71.002121</td>\n",
       "      <td>9.400854e+09</td>\n",
       "      <td>31889.917448</td>\n",
       "      <td>0.127315</td>\n",
       "      <td>1.031231e-05</td>\n",
       "      <td>-2.541628e-05</td>\n",
       "      <td>2.278946e-05</td>\n",
       "      <td>9.140477e-04</td>\n",
       "      <td>-2.705479e-05</td>\n",
       "      <td>-2.894726e-16</td>\n",
       "      <td>-1.654152e-06</td>\n",
       "      <td>0.999995</td>\n",
       "      <td>6.728572e-17</td>\n",
       "      <td>13.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>1.105666e-12</td>\n",
       "      <td>9.025629e+04</td>\n",
       "      <td>7.822212e+04</td>\n",
       "      <td>0.002469</td>\n",
       "      <td>0.480722</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>47.0</td>\n",
       "      <td>46.0</td>\n",
       "      <td>109.969910</td>\n",
       "      <td>9.936142e+09</td>\n",
       "      <td>30171.917632</td>\n",
       "      <td>-0.080149</td>\n",
       "      <td>-8.619624e-04</td>\n",
       "      <td>2.548684e-03</td>\n",
       "      <td>5.044697e-05</td>\n",
       "      <td>1.185818e-07</td>\n",
       "      <td>2.712990e-03</td>\n",
       "      <td>3.427386e-14</td>\n",
       "      <td>1.853022e-04</td>\n",
       "      <td>1.000431</td>\n",
       "      <td>7.518612e-17</td>\n",
       "      <td>19.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>1.668626e-09</td>\n",
       "      <td>1.153616e+08</td>\n",
       "      <td>1.289335e+08</td>\n",
       "      <td>3.439019</td>\n",
       "      <td>575.636329</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>6.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>20.089619</td>\n",
       "      <td>1.217858e+10</td>\n",
       "      <td>24616.364103</td>\n",
       "      <td>0.348475</td>\n",
       "      <td>5.911951e+00</td>\n",
       "      <td>-2.282248e+00</td>\n",
       "      <td>2.923129e-02</td>\n",
       "      <td>2.187644e-01</td>\n",
       "      <td>-2.429378e+00</td>\n",
       "      <td>-5.651281e-11</td>\n",
       "      <td>-2.492788e-01</td>\n",
       "      <td>0.168691</td>\n",
       "      <td>2.371894e-17</td>\n",
       "      <td>5.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.346957e-09</td>\n",
       "      <td>3.133959e+08</td>\n",
       "      <td>2.238542e+08</td>\n",
       "      <td>3.296731</td>\n",
       "      <td>370.541274</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>133.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>291.455583</td>\n",
       "      <td>1.490525e+10</td>\n",
       "      <td>20113.216373</td>\n",
       "      <td>0.292290</td>\n",
       "      <td>2.522116e-11</td>\n",
       "      <td>-5.799437e-11</td>\n",
       "      <td>9.227090e-12</td>\n",
       "      <td>1.138952e-10</td>\n",
       "      <td>-6.173310e-11</td>\n",
       "      <td>-2.632674e-21</td>\n",
       "      <td>-9.488404e-12</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.615789e-16</td>\n",
       "      <td>29.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>8.520992e-11</td>\n",
       "      <td>1.745131e+06</td>\n",
       "      <td>1.632542e+06</td>\n",
       "      <td>0.199765</td>\n",
       "      <td>23.029708</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>29.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>70.550345</td>\n",
       "      <td>1.561732e+10</td>\n",
       "      <td>19196.150147</td>\n",
       "      <td>-0.186404</td>\n",
       "      <td>-1.331461e-06</td>\n",
       "      <td>4.214511e-06</td>\n",
       "      <td>9.140477e-04</td>\n",
       "      <td>1.420212e-05</td>\n",
       "      <td>4.486208e-06</td>\n",
       "      <td>2.200698e-16</td>\n",
       "      <td>7.569884e-07</td>\n",
       "      <td>1.000001</td>\n",
       "      <td>1.800036e-16</td>\n",
       "      <td>15.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>5.609782e-13</td>\n",
       "      <td>9.988074e+03</td>\n",
       "      <td>1.152470e+04</td>\n",
       "      <td>0.001144</td>\n",
       "      <td>0.207770</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>59.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>131.279610</td>\n",
       "      <td>1.834596e+10</td>\n",
       "      <td>16341.063138</td>\n",
       "      <td>0.889373</td>\n",
       "      <td>1.002353e-10</td>\n",
       "      <td>-1.759375e-10</td>\n",
       "      <td>1.254489e-08</td>\n",
       "      <td>3.773530e-08</td>\n",
       "      <td>-1.872797e-10</td>\n",
       "      <td>-1.489269e-20</td>\n",
       "      <td>-4.360820e-11</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>2.353414e-16</td>\n",
       "      <td>17.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>2.896289e-12</td>\n",
       "      <td>3.181092e+04</td>\n",
       "      <td>2.846240e+04</td>\n",
       "      <td>0.006776</td>\n",
       "      <td>52.659800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>9.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>28.011516</td>\n",
       "      <td>1.996738e+10</td>\n",
       "      <td>15014.113923</td>\n",
       "      <td>0.459765</td>\n",
       "      <td>2.753563e-01</td>\n",
       "      <td>-5.095768e-01</td>\n",
       "      <td>1.805005e-03</td>\n",
       "      <td>2.031171e-02</td>\n",
       "      <td>-5.424277e-01</td>\n",
       "      <td>-5.561172e-11</td>\n",
       "      <td>-1.496169e-01</td>\n",
       "      <td>0.874135</td>\n",
       "      <td>2.433650e-16</td>\n",
       "      <td>5.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1.713363e-08</td>\n",
       "      <td>1.459627e+08</td>\n",
       "      <td>1.042591e+08</td>\n",
       "      <td>41.056101</td>\n",
       "      <td>3186.616639</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     iup   ilow         Eup          freq            lam       Tex  \\\n",
       "0   80.0   79.0  175.526266  2.925982e+09  102458.749917 -0.041756   \n",
       "1   15.0   14.0   36.334831  3.387356e+09   88503.380808 -0.078056   \n",
       "2   97.0   96.0  215.895422  7.283364e+09   41161.262570  0.177530   \n",
       "3   31.0   29.0   71.002121  9.400854e+09   31889.917448  0.127315   \n",
       "4   47.0   46.0  109.969910  9.936142e+09   30171.917632 -0.080149   \n",
       "5    6.0    5.0   20.089619  1.217858e+10   24616.364103  0.348475   \n",
       "6  133.0  132.0  291.455583  1.490525e+10   20113.216373  0.292290   \n",
       "7   29.0   28.0   70.550345  1.561732e+10   19196.150147 -0.186404   \n",
       "8   59.0   57.0  131.279610  1.834596e+10   16341.063138  0.889373   \n",
       "9    9.0    8.0   28.011516  1.996738e+10   15014.113923  0.459765   \n",
       "\n",
       "            tau            Tr           fup          flow     flux_Kkms  \\\n",
       "0 -8.661514e-07  2.474329e-06  5.745531e-08  1.791956e-09  2.633842e-06   \n",
       "1 -2.458937e-06  7.058170e-06  6.804199e-03  6.592494e-04  7.513189e-06   \n",
       "2  4.996841e-08 -1.222974e-07  6.653519e-10  4.353429e-09 -1.301816e-07   \n",
       "3  1.031231e-05 -2.541628e-05  2.278946e-05  9.140477e-04 -2.705479e-05   \n",
       "4 -8.619624e-04  2.548684e-03  5.044697e-05  1.185818e-07  2.712990e-03   \n",
       "5  5.911951e+00 -2.282248e+00  2.923129e-02  2.187644e-01 -2.429378e+00   \n",
       "6  2.522116e-11 -5.799437e-11  9.227090e-12  1.138952e-10 -6.173310e-11   \n",
       "7 -1.331461e-06  4.214511e-06  9.140477e-04  1.420212e-05  4.486208e-06   \n",
       "8  1.002353e-10 -1.759375e-10  1.254489e-08  3.773530e-08 -1.872797e-10   \n",
       "9  2.753563e-01 -5.095768e-01  1.805005e-03  2.031171e-02 -5.424277e-01   \n",
       "\n",
       "       flux_int       flux_Jy      beta           Jnu   gup  glow  \\\n",
       "0  8.497009e-19  1.560018e-08  1.000000  7.131517e-18  23.0  21.0   \n",
       "1  3.760697e-18  5.964070e-08  1.000001  9.464363e-18   9.0   7.0   \n",
       "2 -6.477493e-19 -4.777605e-09  1.000000  4.081381e-17  23.0  21.0   \n",
       "3 -2.894726e-16 -1.654152e-06  0.999995  6.728572e-17  13.0  15.0   \n",
       "4  3.427386e-14  1.853022e-04  1.000431  7.518612e-17  19.0  17.0   \n",
       "5 -5.651281e-11 -2.492788e-01  0.168691  2.371894e-17   5.0   7.0   \n",
       "6 -2.632674e-21 -9.488404e-12  1.000000  1.615789e-16  29.0  31.0   \n",
       "7  2.200698e-16  7.569884e-07  1.000001  1.800036e-16  15.0  13.0   \n",
       "8 -1.489269e-20 -4.360820e-11  1.000000  2.353414e-16  17.0  19.0   \n",
       "9 -5.561172e-11 -1.496169e-01  0.874135  2.433650e-16   5.0   7.0   \n",
       "\n",
       "            Aul           Bul           Blu     n_crit   n_crit_old  \n",
       "0  3.882245e-11  1.051050e+08  1.151150e+08   0.081247    12.132016  \n",
       "1  1.593096e-15  2.779809e+03  3.574040e+03   0.000004     0.000797  \n",
       "2  4.672324e-10  8.201483e+07  8.982576e+07   0.985907   186.892960  \n",
       "3  1.105666e-12  9.025629e+04  7.822212e+04   0.002469     0.480722  \n",
       "4  1.668626e-09  1.153616e+08  1.289335e+08   3.439019   575.636329  \n",
       "5  8.346957e-09  3.133959e+08  2.238542e+08   3.296731   370.541274  \n",
       "6  8.520992e-11  1.745131e+06  1.632542e+06   0.199765    23.029708  \n",
       "7  5.609782e-13  9.988074e+03  1.152470e+04   0.001144     0.207770  \n",
       "8  2.896289e-12  3.181092e+04  2.846240e+04   0.006776    52.659800  \n",
       "9  1.713363e-08  1.459627e+08  1.042591e+08  41.056101  3186.616639  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.run_one_params(\n",
    "    Tkin=30.0, dv_CGS=1e5, Ncol_X_CGS=1e15,\n",
    "    oH2_density_CGS=3e4, pH2_densty_CGS=1e4, solve_method='Newton', geotype='')\n",
    "df = pd.DataFrame(data=a.data_transitions, columns=a.column_names)\n",
    "df.head(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d0bc1e6f-9b59-4f50-92e7-d6385800bdc9",
   "metadata": {},
   "source": [
    "# Try with CO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "98acd6e9-82aa-4dbb-be43-9f2a84bdbfbb",
   "metadata": {},
   "outputs": [],
   "source": [
    "a = myRadex.MyRadexModel(\n",
    "    dir_transition_rates=myRadexPath,\n",
    "    filename_molecule='12C16O_H2.dat')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c4f24f2a-0d97-40ed-8345-694d7e7e2ef8",
   "metadata": {},
   "source": [
    "## Solve with the ODE solver"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9d82b173-de20-4646-9025-6716ef084e82",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>iup</th>\n",
       "      <th>ilow</th>\n",
       "      <th>Eup</th>\n",
       "      <th>freq</th>\n",
       "      <th>lam</th>\n",
       "      <th>Tex</th>\n",
       "      <th>tau</th>\n",
       "      <th>Tr</th>\n",
       "      <th>fup</th>\n",
       "      <th>flow</th>\n",
       "      <th>flux_Kkms</th>\n",
       "      <th>flux_int</th>\n",
       "      <th>flux_Jy</th>\n",
       "      <th>beta</th>\n",
       "      <th>Jnu</th>\n",
       "      <th>gup</th>\n",
       "      <th>glow</th>\n",
       "      <th>Aul</th>\n",
       "      <th>Bul</th>\n",
       "      <th>Blu</th>\n",
       "      <th>n_crit</th>\n",
       "      <th>n_crit_old</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.532139</td>\n",
       "      <td>1.152712e+11</td>\n",
       "      <td>2600.757633</td>\n",
       "      <td>29.999987</td>\n",
       "      <td>21391.136547</td>\n",
       "      <td>26.482411</td>\n",
       "      <td>0.223030</td>\n",
       "      <td>0.089398</td>\n",
       "      <td>28.189653</td>\n",
       "      <td>5.560497e-07</td>\n",
       "      <td>259.136209</td>\n",
       "      <td>0.000016</td>\n",
       "      <td>1.115245e-13</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.203000e-08</td>\n",
       "      <td>3.189381e+06</td>\n",
       "      <td>9.568143e+06</td>\n",
       "      <td>0.007052</td>\n",
       "      <td>0.034462</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>16.596157</td>\n",
       "      <td>2.305380e+11</td>\n",
       "      <td>1300.403656</td>\n",
       "      <td>29.999987</td>\n",
       "      <td>65120.574156</td>\n",
       "      <td>24.612869</td>\n",
       "      <td>0.257065</td>\n",
       "      <td>0.223030</td>\n",
       "      <td>26.199587</td>\n",
       "      <td>4.134124e-06</td>\n",
       "      <td>963.332535</td>\n",
       "      <td>0.000005</td>\n",
       "      <td>4.050751e-13</td>\n",
       "      <td>5.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.910000e-07</td>\n",
       "      <td>3.824775e+06</td>\n",
       "      <td>6.374626e+06</td>\n",
       "      <td>0.019510</td>\n",
       "      <td>0.057813</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>33.191844</td>\n",
       "      <td>3.457960e+11</td>\n",
       "      <td>866.963374</td>\n",
       "      <td>29.999981</td>\n",
       "      <td>93002.412918</td>\n",
       "      <td>22.425294</td>\n",
       "      <td>0.206978</td>\n",
       "      <td>0.257065</td>\n",
       "      <td>23.870986</td>\n",
       "      <td>1.271135e-05</td>\n",
       "      <td>1974.726672</td>\n",
       "      <td>0.000004</td>\n",
       "      <td>8.252421e-13</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.497000e-06</td>\n",
       "      <td>4.095568e+06</td>\n",
       "      <td>5.733795e+06</td>\n",
       "      <td>0.046980</td>\n",
       "      <td>0.133716</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>5.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>55.318268</td>\n",
       "      <td>4.610408e+11</td>\n",
       "      <td>650.251515</td>\n",
       "      <td>29.999964</td>\n",
       "      <td>87407.925122</td>\n",
       "      <td>20.277675</td>\n",
       "      <td>0.127279</td>\n",
       "      <td>0.206978</td>\n",
       "      <td>21.584916</td>\n",
       "      <td>2.724142e-05</td>\n",
       "      <td>3174.137670</td>\n",
       "      <td>0.000004</td>\n",
       "      <td>1.324691e-12</td>\n",
       "      <td>9.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>6.126000e-06</td>\n",
       "      <td>4.239498e+06</td>\n",
       "      <td>5.450783e+06</td>\n",
       "      <td>0.118775</td>\n",
       "      <td>0.335416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>6.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>82.974643</td>\n",
       "      <td>5.762679e+11</td>\n",
       "      <td>520.231028</td>\n",
       "      <td>29.999921</td>\n",
       "      <td>60200.528711</td>\n",
       "      <td>18.265786</td>\n",
       "      <td>0.061878</td>\n",
       "      <td>0.127279</td>\n",
       "      <td>19.443326</td>\n",
       "      <td>4.791874e-05</td>\n",
       "      <td>4467.002615</td>\n",
       "      <td>0.000006</td>\n",
       "      <td>1.863738e-12</td>\n",
       "      <td>11.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>1.221000e-05</td>\n",
       "      <td>4.327108e+06</td>\n",
       "      <td>5.288688e+06</td>\n",
       "      <td>0.332599</td>\n",
       "      <td>0.968171</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>7.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>116.160182</td>\n",
       "      <td>6.914731e+11</td>\n",
       "      <td>433.556227</td>\n",
       "      <td>29.999784</td>\n",
       "      <td>31856.809749</td>\n",
       "      <td>16.405397</td>\n",
       "      <td>0.024192</td>\n",
       "      <td>0.061878</td>\n",
       "      <td>17.463004</td>\n",
       "      <td>7.435432e-05</td>\n",
       "      <td>5776.519401</td>\n",
       "      <td>0.000010</td>\n",
       "      <td>2.409944e-12</td>\n",
       "      <td>13.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>2.137000e-05</td>\n",
       "      <td>4.383633e+06</td>\n",
       "      <td>5.180657e+06</td>\n",
       "      <td>1.054687</td>\n",
       "      <td>3.167206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>8.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>154.873234</td>\n",
       "      <td>8.066518e+11</td>\n",
       "      <td>371.650390</td>\n",
       "      <td>29.999306</td>\n",
       "      <td>13285.772076</td>\n",
       "      <td>14.694732</td>\n",
       "      <td>0.007680</td>\n",
       "      <td>0.024192</td>\n",
       "      <td>15.642058</td>\n",
       "      <td>1.057338e-04</td>\n",
       "      <td>7041.462141</td>\n",
       "      <td>0.000025</td>\n",
       "      <td>2.937634e-12</td>\n",
       "      <td>15.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>3.422000e-05</td>\n",
       "      <td>4.421576e+06</td>\n",
       "      <td>5.101819e+06</td>\n",
       "      <td>3.856867</td>\n",
       "      <td>11.767579</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>9.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>199.112581</td>\n",
       "      <td>9.217997e+11</td>\n",
       "      <td>325.225163</td>\n",
       "      <td>29.997314</td>\n",
       "      <td>4431.237044</td>\n",
       "      <td>13.127159</td>\n",
       "      <td>0.001992</td>\n",
       "      <td>0.007680</td>\n",
       "      <td>13.973428</td>\n",
       "      <td>1.409529e-04</td>\n",
       "      <td>8214.342505</td>\n",
       "      <td>0.000075</td>\n",
       "      <td>3.426761e-12</td>\n",
       "      <td>17.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>5.134000e-05</td>\n",
       "      <td>4.445306e+06</td>\n",
       "      <td>5.038013e+06</td>\n",
       "      <td>16.546452</td>\n",
       "      <td>50.595788</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>10.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>248.876575</td>\n",
       "      <td>1.036912e+12</td>\n",
       "      <td>289.120335</td>\n",
       "      <td>29.987147</td>\n",
       "      <td>1193.669527</td>\n",
       "      <td>11.690664</td>\n",
       "      <td>0.000423</td>\n",
       "      <td>0.001992</td>\n",
       "      <td>12.444326</td>\n",
       "      <td>1.786730e-04</td>\n",
       "      <td>9256.615858</td>\n",
       "      <td>0.000279</td>\n",
       "      <td>3.860757e-12</td>\n",
       "      <td>19.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>7.330000e-05</td>\n",
       "      <td>4.458957e+06</td>\n",
       "      <td>4.983540e+06</td>\n",
       "      <td>83.467666</td>\n",
       "      <td>249.349417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>11.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>304.162988</td>\n",
       "      <td>1.151985e+12</td>\n",
       "      <td>260.239795</td>\n",
       "      <td>29.928406</td>\n",
       "      <td>261.298782</td>\n",
       "      <td>10.348197</td>\n",
       "      <td>0.000074</td>\n",
       "      <td>0.000423</td>\n",
       "      <td>11.015314</td>\n",
       "      <td>2.168699e-04</td>\n",
       "      <td>10113.176883</td>\n",
       "      <td>0.001276</td>\n",
       "      <td>4.213844e-12</td>\n",
       "      <td>21.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>1.006000e-04</td>\n",
       "      <td>4.462852e+06</td>\n",
       "      <td>4.932626e+06</td>\n",
       "      <td>501.970086</td>\n",
       "      <td>1440.167138</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    iup  ilow         Eup          freq          lam        Tex           tau  \\\n",
       "0   2.0   1.0    5.532139  1.152712e+11  2600.757633  29.999987  21391.136547   \n",
       "1   3.0   2.0   16.596157  2.305380e+11  1300.403656  29.999987  65120.574156   \n",
       "2   4.0   3.0   33.191844  3.457960e+11   866.963374  29.999981  93002.412918   \n",
       "3   5.0   4.0   55.318268  4.610408e+11   650.251515  29.999964  87407.925122   \n",
       "4   6.0   5.0   82.974643  5.762679e+11   520.231028  29.999921  60200.528711   \n",
       "5   7.0   6.0  116.160182  6.914731e+11   433.556227  29.999784  31856.809749   \n",
       "6   8.0   7.0  154.873234  8.066518e+11   371.650390  29.999306  13285.772076   \n",
       "7   9.0   8.0  199.112581  9.217997e+11   325.225163  29.997314   4431.237044   \n",
       "8  10.0   9.0  248.876575  1.036912e+12   289.120335  29.987147   1193.669527   \n",
       "9  11.0  10.0  304.162988  1.151985e+12   260.239795  29.928406    261.298782   \n",
       "\n",
       "          Tr       fup      flow  flux_Kkms      flux_int       flux_Jy  \\\n",
       "0  26.482411  0.223030  0.089398  28.189653  5.560497e-07    259.136209   \n",
       "1  24.612869  0.257065  0.223030  26.199587  4.134124e-06    963.332535   \n",
       "2  22.425294  0.206978  0.257065  23.870986  1.271135e-05   1974.726672   \n",
       "3  20.277675  0.127279  0.206978  21.584916  2.724142e-05   3174.137670   \n",
       "4  18.265786  0.061878  0.127279  19.443326  4.791874e-05   4467.002615   \n",
       "5  16.405397  0.024192  0.061878  17.463004  7.435432e-05   5776.519401   \n",
       "6  14.694732  0.007680  0.024192  15.642058  1.057338e-04   7041.462141   \n",
       "7  13.127159  0.001992  0.007680  13.973428  1.409529e-04   8214.342505   \n",
       "8  11.690664  0.000423  0.001992  12.444326  1.786730e-04   9256.615858   \n",
       "9  10.348197  0.000074  0.000423  11.015314  2.168699e-04  10113.176883   \n",
       "\n",
       "       beta           Jnu   gup  glow           Aul           Bul  \\\n",
       "0  0.000016  1.115245e-13   3.0   1.0  7.203000e-08  3.189381e+06   \n",
       "1  0.000005  4.050751e-13   5.0   3.0  6.910000e-07  3.824775e+06   \n",
       "2  0.000004  8.252421e-13   7.0   5.0  2.497000e-06  4.095568e+06   \n",
       "3  0.000004  1.324691e-12   9.0   7.0  6.126000e-06  4.239498e+06   \n",
       "4  0.000006  1.863738e-12  11.0   9.0  1.221000e-05  4.327108e+06   \n",
       "5  0.000010  2.409944e-12  13.0  11.0  2.137000e-05  4.383633e+06   \n",
       "6  0.000025  2.937634e-12  15.0  13.0  3.422000e-05  4.421576e+06   \n",
       "7  0.000075  3.426761e-12  17.0  15.0  5.134000e-05  4.445306e+06   \n",
       "8  0.000279  3.860757e-12  19.0  17.0  7.330000e-05  4.458957e+06   \n",
       "9  0.001276  4.213844e-12  21.0  19.0  1.006000e-04  4.462852e+06   \n",
       "\n",
       "            Blu      n_crit   n_crit_old  \n",
       "0  9.568143e+06    0.007052     0.034462  \n",
       "1  6.374626e+06    0.019510     0.057813  \n",
       "2  5.733795e+06    0.046980     0.133716  \n",
       "3  5.450783e+06    0.118775     0.335416  \n",
       "4  5.288688e+06    0.332599     0.968171  \n",
       "5  5.180657e+06    1.054687     3.167206  \n",
       "6  5.101819e+06    3.856867    11.767579  \n",
       "7  5.038013e+06   16.546452    50.595788  \n",
       "8  4.983540e+06   83.467666   249.349417  \n",
       "9  4.932626e+06  501.970086  1440.167138  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.run_one_params(\n",
    "    Tkin=30.0, dv_CGS=1e5, Ncol_X_CGS=1e21,\n",
    "    oH2_density_CGS=3e4, pH2_densty_CGS=1e4, solve_method='ODE', geotype='slab')\n",
    "df = pd.DataFrame(data=a.data_transitions, columns=a.column_names)\n",
    "df.head(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a9448a17-b027-4dcc-add8-f717746aaa3a",
   "metadata": {},
   "source": [
    "## Solve with the Newton solver"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ef710762-03a8-4ecf-8598-7720457d65e8",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>iup</th>\n",
       "      <th>ilow</th>\n",
       "      <th>Eup</th>\n",
       "      <th>freq</th>\n",
       "      <th>lam</th>\n",
       "      <th>Tex</th>\n",
       "      <th>tau</th>\n",
       "      <th>Tr</th>\n",
       "      <th>fup</th>\n",
       "      <th>flow</th>\n",
       "      <th>flux_Kkms</th>\n",
       "      <th>flux_int</th>\n",
       "      <th>flux_Jy</th>\n",
       "      <th>beta</th>\n",
       "      <th>Jnu</th>\n",
       "      <th>gup</th>\n",
       "      <th>glow</th>\n",
       "      <th>Aul</th>\n",
       "      <th>Bul</th>\n",
       "      <th>Blu</th>\n",
       "      <th>n_crit</th>\n",
       "      <th>n_crit_old</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.532139</td>\n",
       "      <td>1.152712e+11</td>\n",
       "      <td>2600.757633</td>\n",
       "      <td>29.999987</td>\n",
       "      <td>21391.136547</td>\n",
       "      <td>26.482411</td>\n",
       "      <td>0.223030</td>\n",
       "      <td>0.089398</td>\n",
       "      <td>28.189653</td>\n",
       "      <td>5.560497e-07</td>\n",
       "      <td>259.136209</td>\n",
       "      <td>0.000016</td>\n",
       "      <td>1.115245e-13</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.203000e-08</td>\n",
       "      <td>3.189381e+06</td>\n",
       "      <td>9.568143e+06</td>\n",
       "      <td>0.007052</td>\n",
       "      <td>0.034462</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>16.596157</td>\n",
       "      <td>2.305380e+11</td>\n",
       "      <td>1300.403656</td>\n",
       "      <td>29.999987</td>\n",
       "      <td>65120.574156</td>\n",
       "      <td>24.612869</td>\n",
       "      <td>0.257065</td>\n",
       "      <td>0.223030</td>\n",
       "      <td>26.199587</td>\n",
       "      <td>4.134124e-06</td>\n",
       "      <td>963.332535</td>\n",
       "      <td>0.000005</td>\n",
       "      <td>4.050751e-13</td>\n",
       "      <td>5.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.910000e-07</td>\n",
       "      <td>3.824775e+06</td>\n",
       "      <td>6.374626e+06</td>\n",
       "      <td>0.019510</td>\n",
       "      <td>0.057813</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>33.191844</td>\n",
       "      <td>3.457960e+11</td>\n",
       "      <td>866.963374</td>\n",
       "      <td>29.999981</td>\n",
       "      <td>93002.412918</td>\n",
       "      <td>22.425294</td>\n",
       "      <td>0.206978</td>\n",
       "      <td>0.257065</td>\n",
       "      <td>23.870986</td>\n",
       "      <td>1.271135e-05</td>\n",
       "      <td>1974.726672</td>\n",
       "      <td>0.000004</td>\n",
       "      <td>8.252421e-13</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>2.497000e-06</td>\n",
       "      <td>4.095568e+06</td>\n",
       "      <td>5.733795e+06</td>\n",
       "      <td>0.046980</td>\n",
       "      <td>0.133716</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>5.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>55.318268</td>\n",
       "      <td>4.610408e+11</td>\n",
       "      <td>650.251515</td>\n",
       "      <td>29.999964</td>\n",
       "      <td>87407.925122</td>\n",
       "      <td>20.277675</td>\n",
       "      <td>0.127279</td>\n",
       "      <td>0.206978</td>\n",
       "      <td>21.584916</td>\n",
       "      <td>2.724142e-05</td>\n",
       "      <td>3174.137670</td>\n",
       "      <td>0.000004</td>\n",
       "      <td>1.324691e-12</td>\n",
       "      <td>9.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>6.126000e-06</td>\n",
       "      <td>4.239498e+06</td>\n",
       "      <td>5.450783e+06</td>\n",
       "      <td>0.118775</td>\n",
       "      <td>0.335416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>6.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>82.974643</td>\n",
       "      <td>5.762679e+11</td>\n",
       "      <td>520.231028</td>\n",
       "      <td>29.999921</td>\n",
       "      <td>60200.528711</td>\n",
       "      <td>18.265786</td>\n",
       "      <td>0.061878</td>\n",
       "      <td>0.127279</td>\n",
       "      <td>19.443326</td>\n",
       "      <td>4.791874e-05</td>\n",
       "      <td>4467.002615</td>\n",
       "      <td>0.000006</td>\n",
       "      <td>1.863738e-12</td>\n",
       "      <td>11.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>1.221000e-05</td>\n",
       "      <td>4.327108e+06</td>\n",
       "      <td>5.288688e+06</td>\n",
       "      <td>0.332599</td>\n",
       "      <td>0.968171</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>7.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>116.160182</td>\n",
       "      <td>6.914731e+11</td>\n",
       "      <td>433.556227</td>\n",
       "      <td>29.999784</td>\n",
       "      <td>31856.809749</td>\n",
       "      <td>16.405397</td>\n",
       "      <td>0.024192</td>\n",
       "      <td>0.061878</td>\n",
       "      <td>17.463004</td>\n",
       "      <td>7.435432e-05</td>\n",
       "      <td>5776.519401</td>\n",
       "      <td>0.000010</td>\n",
       "      <td>2.409944e-12</td>\n",
       "      <td>13.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>2.137000e-05</td>\n",
       "      <td>4.383633e+06</td>\n",
       "      <td>5.180657e+06</td>\n",
       "      <td>1.054687</td>\n",
       "      <td>3.167206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>8.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>154.873234</td>\n",
       "      <td>8.066518e+11</td>\n",
       "      <td>371.650390</td>\n",
       "      <td>29.999306</td>\n",
       "      <td>13285.772076</td>\n",
       "      <td>14.694732</td>\n",
       "      <td>0.007680</td>\n",
       "      <td>0.024192</td>\n",
       "      <td>15.642058</td>\n",
       "      <td>1.057338e-04</td>\n",
       "      <td>7041.462141</td>\n",
       "      <td>0.000025</td>\n",
       "      <td>2.937634e-12</td>\n",
       "      <td>15.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>3.422000e-05</td>\n",
       "      <td>4.421576e+06</td>\n",
       "      <td>5.101819e+06</td>\n",
       "      <td>3.856867</td>\n",
       "      <td>11.767579</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>9.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>199.112581</td>\n",
       "      <td>9.217997e+11</td>\n",
       "      <td>325.225163</td>\n",
       "      <td>29.997314</td>\n",
       "      <td>4431.237044</td>\n",
       "      <td>13.127159</td>\n",
       "      <td>0.001992</td>\n",
       "      <td>0.007680</td>\n",
       "      <td>13.973428</td>\n",
       "      <td>1.409529e-04</td>\n",
       "      <td>8214.342505</td>\n",
       "      <td>0.000075</td>\n",
       "      <td>3.426761e-12</td>\n",
       "      <td>17.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>5.134000e-05</td>\n",
       "      <td>4.445306e+06</td>\n",
       "      <td>5.038013e+06</td>\n",
       "      <td>16.546452</td>\n",
       "      <td>50.595788</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>10.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>248.876575</td>\n",
       "      <td>1.036912e+12</td>\n",
       "      <td>289.120335</td>\n",
       "      <td>29.987147</td>\n",
       "      <td>1193.669527</td>\n",
       "      <td>11.690664</td>\n",
       "      <td>0.000423</td>\n",
       "      <td>0.001992</td>\n",
       "      <td>12.444326</td>\n",
       "      <td>1.786730e-04</td>\n",
       "      <td>9256.615858</td>\n",
       "      <td>0.000279</td>\n",
       "      <td>3.860757e-12</td>\n",
       "      <td>19.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>7.330000e-05</td>\n",
       "      <td>4.458957e+06</td>\n",
       "      <td>4.983540e+06</td>\n",
       "      <td>83.467666</td>\n",
       "      <td>249.349417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>11.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>304.162988</td>\n",
       "      <td>1.151985e+12</td>\n",
       "      <td>260.239795</td>\n",
       "      <td>29.928406</td>\n",
       "      <td>261.298782</td>\n",
       "      <td>10.348197</td>\n",
       "      <td>0.000074</td>\n",
       "      <td>0.000423</td>\n",
       "      <td>11.015314</td>\n",
       "      <td>2.168699e-04</td>\n",
       "      <td>10113.176883</td>\n",
       "      <td>0.001276</td>\n",
       "      <td>4.213844e-12</td>\n",
       "      <td>21.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>1.006000e-04</td>\n",
       "      <td>4.462852e+06</td>\n",
       "      <td>4.932626e+06</td>\n",
       "      <td>501.970086</td>\n",
       "      <td>1440.167138</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    iup  ilow         Eup          freq          lam        Tex           tau  \\\n",
       "0   2.0   1.0    5.532139  1.152712e+11  2600.757633  29.999987  21391.136547   \n",
       "1   3.0   2.0   16.596157  2.305380e+11  1300.403656  29.999987  65120.574156   \n",
       "2   4.0   3.0   33.191844  3.457960e+11   866.963374  29.999981  93002.412918   \n",
       "3   5.0   4.0   55.318268  4.610408e+11   650.251515  29.999964  87407.925122   \n",
       "4   6.0   5.0   82.974643  5.762679e+11   520.231028  29.999921  60200.528711   \n",
       "5   7.0   6.0  116.160182  6.914731e+11   433.556227  29.999784  31856.809749   \n",
       "6   8.0   7.0  154.873234  8.066518e+11   371.650390  29.999306  13285.772076   \n",
       "7   9.0   8.0  199.112581  9.217997e+11   325.225163  29.997314   4431.237044   \n",
       "8  10.0   9.0  248.876575  1.036912e+12   289.120335  29.987147   1193.669527   \n",
       "9  11.0  10.0  304.162988  1.151985e+12   260.239795  29.928406    261.298782   \n",
       "\n",
       "          Tr       fup      flow  flux_Kkms      flux_int       flux_Jy  \\\n",
       "0  26.482411  0.223030  0.089398  28.189653  5.560497e-07    259.136209   \n",
       "1  24.612869  0.257065  0.223030  26.199587  4.134124e-06    963.332535   \n",
       "2  22.425294  0.206978  0.257065  23.870986  1.271135e-05   1974.726672   \n",
       "3  20.277675  0.127279  0.206978  21.584916  2.724142e-05   3174.137670   \n",
       "4  18.265786  0.061878  0.127279  19.443326  4.791874e-05   4467.002615   \n",
       "5  16.405397  0.024192  0.061878  17.463004  7.435432e-05   5776.519401   \n",
       "6  14.694732  0.007680  0.024192  15.642058  1.057338e-04   7041.462141   \n",
       "7  13.127159  0.001992  0.007680  13.973428  1.409529e-04   8214.342505   \n",
       "8  11.690664  0.000423  0.001992  12.444326  1.786730e-04   9256.615858   \n",
       "9  10.348197  0.000074  0.000423  11.015314  2.168699e-04  10113.176883   \n",
       "\n",
       "       beta           Jnu   gup  glow           Aul           Bul  \\\n",
       "0  0.000016  1.115245e-13   3.0   1.0  7.203000e-08  3.189381e+06   \n",
       "1  0.000005  4.050751e-13   5.0   3.0  6.910000e-07  3.824775e+06   \n",
       "2  0.000004  8.252421e-13   7.0   5.0  2.497000e-06  4.095568e+06   \n",
       "3  0.000004  1.324691e-12   9.0   7.0  6.126000e-06  4.239498e+06   \n",
       "4  0.000006  1.863738e-12  11.0   9.0  1.221000e-05  4.327108e+06   \n",
       "5  0.000010  2.409944e-12  13.0  11.0  2.137000e-05  4.383633e+06   \n",
       "6  0.000025  2.937634e-12  15.0  13.0  3.422000e-05  4.421576e+06   \n",
       "7  0.000075  3.426761e-12  17.0  15.0  5.134000e-05  4.445306e+06   \n",
       "8  0.000279  3.860757e-12  19.0  17.0  7.330000e-05  4.458957e+06   \n",
       "9  0.001276  4.213844e-12  21.0  19.0  1.006000e-04  4.462852e+06   \n",
       "\n",
       "            Blu      n_crit   n_crit_old  \n",
       "0  9.568143e+06    0.007052     0.034462  \n",
       "1  6.374626e+06    0.019510     0.057813  \n",
       "2  5.733795e+06    0.046980     0.133716  \n",
       "3  5.450783e+06    0.118775     0.335416  \n",
       "4  5.288688e+06    0.332599     0.968171  \n",
       "5  5.180657e+06    1.054687     3.167206  \n",
       "6  5.101819e+06    3.856867    11.767579  \n",
       "7  5.038013e+06   16.546452    50.595788  \n",
       "8  4.983540e+06   83.467666   249.349417  \n",
       "9  4.932626e+06  501.970086  1440.167138  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.run_one_params(\n",
    "    Tkin=30.0, dv_CGS=1e5, Ncol_X_CGS=1e21,\n",
    "    oH2_density_CGS=3e4, pH2_densty_CGS=1e4, solve_method='Newton', geotype='slab')\n",
    "df = pd.DataFrame(data=a.data_transitions, columns=a.column_names)\n",
    "df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9ad6638b-1c09-41a4-98a3-00ea44323707",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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