{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## VALD\n",
    "VALD is a database of atomic and molecular transitions used to create accurate synthetic spectra of many astrophysical systems. More information, as well as linelists can be downloaded from the [VALD website](http://vald.astro.uu.se/~vald/php/vald.ph).\n",
    "\n",
    "In this example, data was downloaded from the [VALD website](http://vald.astro.uu.se/) and extracted to /tmp/vald_sample_linelist.dat"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**_NOTE:_** "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from carsus.io.vald import VALDReader"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "vald_reader = VALDReader(fname='/tmp/vald_sample_linelist.dat')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Table information is parsed to a dataframe which can be accesed via the .vald attribute. The column information is described in https://articles.adsabs.harvard.edu/pdf/1995A%26AS..112..525P and is as follows:\n",
    "\n",
    "Wavelength - either air or vacuum and in nanometers or angstroms: Wavelength of the line\n",
    "\n",
    "log_gf: Log10 of the oscillator strength times the degeneracy of the lower level\n",
    "\n",
    "e_low: Excitation energy of the lower level in ergs\n",
    "\n",
    "j_lo: Principal quantum number of the lower level\n",
    "\n",
    "e_up: Excitation energy of the upper level in ergs\n",
    "\n",
    "j_up: Principal quantum number of the upper level\n",
    "\n",
    "lande_lower: Lande factor of the lower level\n",
    "\n",
    "lande_upper: Lande factor of the upper level\n",
    "\n",
    "lande_mean: Mean lande factor\n",
    "\n",
    "rad: log10 of the radiation damping constant in $(4\\pi s)^{-1}$\n",
    "\n",
    "stark: log10 of the Stark damping constant at 10,000K in $(4\\pi s N_e)^{-1}$\n",
    "\n",
    "waals: log10 of the Van Der Waals damping constant at 10,000K in $(4\\pi s N_H)^{-1}$"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[\u001b[1m        carsus.io.vald.vald\u001b[0m][   \u001b[1;37mINFO\u001b[0m] - Parsing VALD from: /tmp/vald_sample_linelist.dat (\u001b[1mvald.py\u001b[0m:149)\n",
      "[\u001b[1m        carsus.io.vald.vald\u001b[0m][   \u001b[1;37mINFO\u001b[0m] - Found wavelength column header: WL_air(A) (\u001b[1mvald.py\u001b[0m:167)\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>WL_air(A)</th>\n",
       "      <th>log_gf</th>\n",
       "      <th>e_low</th>\n",
       "      <th>j_lo</th>\n",
       "      <th>e_up</th>\n",
       "      <th>j_up</th>\n",
       "      <th>lande_lower</th>\n",
       "      <th>lande_upper</th>\n",
       "      <th>lande_mean</th>\n",
       "      <th>rad</th>\n",
       "      <th>stark</th>\n",
       "      <th>waals</th>\n",
       "      <th>chemical</th>\n",
       "      <th>ion_charge</th>\n",
       "      <th>wavelength</th>\n",
       "      <th>atomic_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>4100.00538</td>\n",
       "      <td>-1.169</td>\n",
       "      <td>8.1293</td>\n",
       "      <td>2.0</td>\n",
       "      <td>11.1524</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.04</td>\n",
       "      <td>1.00</td>\n",
       "      <td>0.96</td>\n",
       "      <td>8.70</td>\n",
       "      <td>-6.47</td>\n",
       "      <td>-7.860</td>\n",
       "      <td>Mn</td>\n",
       "      <td>1</td>\n",
       "      <td>4101.162586</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>4100.04321</td>\n",
       "      <td>-5.992</td>\n",
       "      <td>10.4673</td>\n",
       "      <td>1.5</td>\n",
       "      <td>13.4904</td>\n",
       "      <td>2.5</td>\n",
       "      <td>2.28</td>\n",
       "      <td>1.54</td>\n",
       "      <td>0.99</td>\n",
       "      <td>8.94</td>\n",
       "      <td>-5.86</td>\n",
       "      <td>-7.630</td>\n",
       "      <td>Fe</td>\n",
       "      <td>1</td>\n",
       "      <td>4101.200426</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4100.04405</td>\n",
       "      <td>-0.440</td>\n",
       "      <td>16.8273</td>\n",
       "      <td>2.0</td>\n",
       "      <td>19.8504</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.40</td>\n",
       "      <td>1.48</td>\n",
       "      <td>1.36</td>\n",
       "      <td>9.48</td>\n",
       "      <td>-5.99</td>\n",
       "      <td>-7.710</td>\n",
       "      <td>Ti</td>\n",
       "      <td>2</td>\n",
       "      <td>4101.201266</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4100.04800</td>\n",
       "      <td>-0.725</td>\n",
       "      <td>51.0168</td>\n",
       "      <td>3.5</td>\n",
       "      <td>54.0399</td>\n",
       "      <td>4.5</td>\n",
       "      <td>99.00</td>\n",
       "      <td>99.00</td>\n",
       "      <td>99.00</td>\n",
       "      <td>10.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.000</td>\n",
       "      <td>He</td>\n",
       "      <td>1</td>\n",
       "      <td>4101.205217</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4100.04910</td>\n",
       "      <td>-7.287</td>\n",
       "      <td>15.2375</td>\n",
       "      <td>2.0</td>\n",
       "      <td>18.2606</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.47</td>\n",
       "      <td>3.00</td>\n",
       "      <td>0.71</td>\n",
       "      <td>9.47</td>\n",
       "      <td>-6.35</td>\n",
       "      <td>-7.850</td>\n",
       "      <td>Fe</td>\n",
       "      <td>2</td>\n",
       "      <td>4101.206318</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>990</th>\n",
       "      <td>4109.94851</td>\n",
       "      <td>-5.428</td>\n",
       "      <td>3.8470</td>\n",
       "      <td>2.0</td>\n",
       "      <td>6.8628</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.16</td>\n",
       "      <td>0.95</td>\n",
       "      <td>0.75</td>\n",
       "      <td>8.10</td>\n",
       "      <td>-6.16</td>\n",
       "      <td>-7.750</td>\n",
       "      <td>Cr</td>\n",
       "      <td>0</td>\n",
       "      <td>4111.108321</td>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>991</th>\n",
       "      <td>4109.94900</td>\n",
       "      <td>-1.227</td>\n",
       "      <td>10.6900</td>\n",
       "      <td>1.5</td>\n",
       "      <td>13.7058</td>\n",
       "      <td>2.5</td>\n",
       "      <td>99.00</td>\n",
       "      <td>99.00</td>\n",
       "      <td>99.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>-7.419</td>\n",
       "      <td>N</td>\n",
       "      <td>0</td>\n",
       "      <td>4111.108811</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>992</th>\n",
       "      <td>4109.95324</td>\n",
       "      <td>-2.671</td>\n",
       "      <td>4.6244</td>\n",
       "      <td>2.0</td>\n",
       "      <td>7.6402</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.00</td>\n",
       "      <td>0.83</td>\n",
       "      <td>1.08</td>\n",
       "      <td>7.47</td>\n",
       "      <td>-2.75</td>\n",
       "      <td>-6.710</td>\n",
       "      <td>Ca</td>\n",
       "      <td>0</td>\n",
       "      <td>4111.113052</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>993</th>\n",
       "      <td>4109.96777</td>\n",
       "      <td>-4.848</td>\n",
       "      <td>13.9360</td>\n",
       "      <td>5.0</td>\n",
       "      <td>16.9518</td>\n",
       "      <td>5.0</td>\n",
       "      <td>1.38</td>\n",
       "      <td>1.20</td>\n",
       "      <td>1.29</td>\n",
       "      <td>8.44</td>\n",
       "      <td>-5.18</td>\n",
       "      <td>-7.500</td>\n",
       "      <td>Cu</td>\n",
       "      <td>1</td>\n",
       "      <td>4111.127586</td>\n",
       "      <td>29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>994</th>\n",
       "      <td>4109.98163</td>\n",
       "      <td>-3.441</td>\n",
       "      <td>4.5351</td>\n",
       "      <td>4.0</td>\n",
       "      <td>7.5509</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.07</td>\n",
       "      <td>1.25</td>\n",
       "      <td>0.79</td>\n",
       "      <td>7.61</td>\n",
       "      <td>-4.43</td>\n",
       "      <td>-7.320</td>\n",
       "      <td>Cr</td>\n",
       "      <td>0</td>\n",
       "      <td>4111.141449</td>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>995 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      WL_air(A)  log_gf    e_low  j_lo     e_up  j_up  lande_lower  \\\n",
       "0    4100.00538  -1.169   8.1293   2.0  11.1524   3.0         1.04   \n",
       "1    4100.04321  -5.992  10.4673   1.5  13.4904   2.5         2.28   \n",
       "2    4100.04405  -0.440  16.8273   2.0  19.8504   1.0         1.40   \n",
       "3    4100.04800  -0.725  51.0168   3.5  54.0399   4.5        99.00   \n",
       "4    4100.04910  -7.287  15.2375   2.0  18.2606   1.0         1.47   \n",
       "..          ...     ...      ...   ...      ...   ...          ...   \n",
       "990  4109.94851  -5.428   3.8470   2.0   6.8628   3.0         1.16   \n",
       "991  4109.94900  -1.227  10.6900   1.5  13.7058   2.5        99.00   \n",
       "992  4109.95324  -2.671   4.6244   2.0   7.6402   1.0         1.00   \n",
       "993  4109.96777  -4.848  13.9360   5.0  16.9518   5.0         1.38   \n",
       "994  4109.98163  -3.441   4.5351   4.0   7.5509   3.0         1.07   \n",
       "\n",
       "     lande_upper  lande_mean    rad  stark  waals chemical  ion_charge  \\\n",
       "0           1.00        0.96   8.70  -6.47 -7.860       Mn           1   \n",
       "1           1.54        0.99   8.94  -5.86 -7.630       Fe           1   \n",
       "2           1.48        1.36   9.48  -5.99 -7.710       Ti           2   \n",
       "3          99.00       99.00  10.00   0.00  0.000       He           1   \n",
       "4           3.00        0.71   9.47  -6.35 -7.850       Fe           2   \n",
       "..           ...         ...    ...    ...    ...      ...         ...   \n",
       "990         0.95        0.75   8.10  -6.16 -7.750       Cr           0   \n",
       "991        99.00       99.00   0.00   0.00 -7.419        N           0   \n",
       "992         0.83        1.08   7.47  -2.75 -6.710       Ca           0   \n",
       "993         1.20        1.29   8.44  -5.18 -7.500       Cu           1   \n",
       "994         1.25        0.79   7.61  -4.43 -7.320       Cr           0   \n",
       "\n",
       "      wavelength  atomic_number  \n",
       "0    4101.162586             25  \n",
       "1    4101.200426             26  \n",
       "2    4101.201266             22  \n",
       "3    4101.205217              2  \n",
       "4    4101.206318             26  \n",
       "..           ...            ...  \n",
       "990  4111.108321             24  \n",
       "991  4111.108811              7  \n",
       "992  4111.113052             20  \n",
       "993  4111.127586             29  \n",
       "994  4111.141449             24  \n",
       "\n",
       "[995 rows x 16 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vald_reader.vald"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The specific relevant information is extracted and prepared as a linelist in the .linelist attribute.\n",
    "\n",
    "Note that the wavelengths here are reformated to Angstroms and in vacuum wavelengths."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
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       "      <th>990</th>\n",
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       "      <td>-5.428</td>\n",
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       "      <td>1.5</td>\n",
       "      <td>2.5</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>-7.419</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>992</th>\n",
       "      <td>20</td>\n",
       "      <td>0</td>\n",
       "      <td>4111.113052</td>\n",
       "      <td>-2.671</td>\n",
       "      <td>4.6244</td>\n",
       "      <td>7.6402</td>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.47</td>\n",
       "      <td>-2.75</td>\n",
       "      <td>-6.710</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>993</th>\n",
       "      <td>29</td>\n",
       "      <td>1</td>\n",
       "      <td>4111.127586</td>\n",
       "      <td>-4.848</td>\n",
       "      <td>13.9360</td>\n",
       "      <td>16.9518</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.44</td>\n",
       "      <td>-5.18</td>\n",
       "      <td>-7.500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>994</th>\n",
       "      <td>24</td>\n",
       "      <td>0</td>\n",
       "      <td>4111.141449</td>\n",
       "      <td>-3.441</td>\n",
       "      <td>4.5351</td>\n",
       "      <td>7.5509</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>7.61</td>\n",
       "      <td>-4.43</td>\n",
       "      <td>-7.320</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>995 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     atomic_number  ion_charge   wavelength  log_gf    e_low     e_up  j_lo  \\\n",
       "0               25           1  4101.162586  -1.169   8.1293  11.1524   2.0   \n",
       "1               26           1  4101.200426  -5.992  10.4673  13.4904   1.5   \n",
       "2               22           2  4101.201266  -0.440  16.8273  19.8504   2.0   \n",
       "3                2           1  4101.205217  -0.725  51.0168  54.0399   3.5   \n",
       "4               26           2  4101.206318  -7.287  15.2375  18.2606   2.0   \n",
       "..             ...         ...          ...     ...      ...      ...   ...   \n",
       "990             24           0  4111.108321  -5.428   3.8470   6.8628   2.0   \n",
       "991              7           0  4111.108811  -1.227  10.6900  13.7058   1.5   \n",
       "992             20           0  4111.113052  -2.671   4.6244   7.6402   2.0   \n",
       "993             29           1  4111.127586  -4.848  13.9360  16.9518   5.0   \n",
       "994             24           0  4111.141449  -3.441   4.5351   7.5509   4.0   \n",
       "\n",
       "     j_up    rad  stark  waals  \n",
       "0     3.0   8.70  -6.47 -7.860  \n",
       "1     2.5   8.94  -5.86 -7.630  \n",
       "2     1.0   9.48  -5.99 -7.710  \n",
       "3     4.5  10.00   0.00  0.000  \n",
       "4     1.0   9.47  -6.35 -7.850  \n",
       "..    ...    ...    ...    ...  \n",
       "990   3.0   8.10  -6.16 -7.750  \n",
       "991   2.5   0.00   0.00 -7.419  \n",
       "992   1.0   7.47  -2.75 -6.710  \n",
       "993   5.0   8.44  -5.18 -7.500  \n",
       "994   3.0   7.61  -4.43 -7.320  \n",
       "\n",
       "[995 rows x 11 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vald_reader.linelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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