kurucz_H-Zn_nosql.ipynb

{
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   "source": [
    "# Creating a TARDIS atomic file\n",
    "\n",
    "Import the following classes:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/epassaro/miniconda3/envs/carsus/lib/python3.6/site-packages/tqdm/autonotebook/__init__.py:18: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
      "  \" (e.g. in jupyter console)\", TqdmExperimentalWarning)\n"
     ]
    }
   ],
   "source": [
    "from carsus.io.nist import NISTIonizationEnergies\n",
    "from carsus.io.kurucz import GFALLReader\n",
    "from carsus.io.output import TARDISAtomData"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get ionization energies from NIST and create a `gfall_reader` instance."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloading ionization energies from the NIST Atomic Spectra Database\n"
     ]
    }
   ],
   "source": [
    "ionization_energies = NISTIonizationEnergies('H-Zn')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[\u001b[1mcarsus.io.kurucz.gfall\u001b[0m][\u001b[1;33mWARNING\u001b[0m]  A specific combination to identify unique levels from the gfall data has not been given. Defaulting to [\"energy\", \"j\"]. (\u001b[1mgfall.py\u001b[0m:68)\n"
     ]
    }
   ],
   "source": [
    "gfall_reader = GFALLReader('gfall.dat')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then create a `TARDISAtomData` object passing the `gfall_reader`, `ionization_energies` and the selected ions:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[\u001b[1mcarsus.io.kurucz.gfall\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Parsing GFALL gfall.dat (\u001b[1mgfall.py\u001b[0m:116)\n",
      "[\u001b[1mcarsus.io.kurucz.gfall\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Extracting line data: atomic_number, ion_charge, energy_lower, j_lower, energy_upper, j_upper, wavelength, loggf (\u001b[1mgfall.py\u001b[0m:292)\n",
      "[\u001b[1mpy.warnings         \u001b[0m][\u001b[1;33mWARNING\u001b[0m]  /home/epassaro/Desktop/gsoc/notebooks/carsus/io/output/base.py:132: PerformanceWarning: indexing past lexsort depth may impact performance.\n",
      "  df = gf.lines.loc[ion]\n",
      " (\u001b[1mwarnings.py\u001b[0m:99)\n",
      "[\u001b[1mpy.warnings         \u001b[0m][\u001b[1;33mWARNING\u001b[0m]  /home/epassaro/Desktop/gsoc/notebooks/carsus/io/output/base.py:132: PerformanceWarning: indexing past lexsort depth may impact performance.\n",
      "  df = gf.lines.loc[ion]\n",
      " (\u001b[1mwarnings.py\u001b[0m:99)\n",
      "[\u001b[1mpy.warnings         \u001b[0m][\u001b[1;33mWARNING\u001b[0m]  /home/epassaro/Desktop/gsoc/notebooks/carsus/io/output/base.py:139: PerformanceWarning: indexing past lexsort depth may impact performance.\n",
      "  ['atomic_number', 'ion_number']).loc[ion]\n",
      " (\u001b[1mwarnings.py\u001b[0m:99)\n",
      "[\u001b[1mpy.warnings         \u001b[0m][\u001b[1;33mWARNING\u001b[0m]  /home/epassaro/Desktop/gsoc/notebooks/carsus/io/output/base.py:139: PerformanceWarning: indexing past lexsort depth may impact performance.\n",
      "  ['atomic_number', 'ion_number']).loc[ion]\n",
      " (\u001b[1mwarnings.py\u001b[0m:99)\n",
      "[\u001b[1mpy.warnings         \u001b[0m][\u001b[1;33mWARNING\u001b[0m]  /home/epassaro/miniconda3/envs/carsus/lib/python3.6/site-packages/pandas/core/frame.py:6692: FutureWarning: Sorting because non-concatenation axis is not aligned. A future version\n",
      "of pandas will change to not sort by default.\n",
      "\n",
      "To accept the future behavior, pass 'sort=False'.\n",
      "\n",
      "To retain the current behavior and silence the warning, pass 'sort=True'.\n",
      "\n",
      "  sort=sort)\n",
      " (\u001b[1mwarnings.py\u001b[0m:99)\n",
      "[\u001b[1mpy.warnings         \u001b[0m][\u001b[1;33mWARNING\u001b[0m]  /home/epassaro/miniconda3/envs/carsus/lib/python3.6/site-packages/pandas/core/frame.py:6692: FutureWarning: Sorting because non-concatenation axis is not aligned. A future version\n",
      "of pandas will change to not sort by default.\n",
      "\n",
      "To accept the future behavior, pass 'sort=False'.\n",
      "\n",
      "To retain the current behavior and silence the warning, pass 'sort=True'.\n",
      "\n",
      "  sort=sort)\n",
      " (\u001b[1mwarnings.py\u001b[0m:99)\n"
     ]
    }
   ],
   "source": [
    "atom_data = TARDISAtomData(gfall_reader, ionization_energies, ions='H-Zn')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, dump the object attributes to an HDF5 file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "atom_data.to_hdf('kurucz_H-Zn.h5')"
   ]
  }
 ],
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