{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# TARDIS High Energy (HE) Workflow"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "58317d05a09a46d78b5c97b230d54edf",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Iterations:          0/? [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "86ceeb48e75444e8a3626ba1d99ac9d3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Packets:             0/? [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from tardis.workflows import tardis_he_workflow\n",
    "from tardis.io.configuration import config_reader\n",
    "import astropy.units as u\n",
    "from tardis.io.atom_data import AtomData\n",
    "from tardis.io.atom_data import download_atom_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:tardis.io.atom_data.atom_web_download:Atomic Data kurucz_cd23_chianti_H_He already exists in /home/duttaan2/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5. Will not download - override with force_download=True.\n",
      "INFO:tardis.io.atom_data.util:\n",
      "\tAtom Data kurucz_cd23_chianti_H_He.h5 not found in local path.\n",
      "\tExists in TARDIS Data repo /home/duttaan2/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5\n",
      "INFO:tardis.io.atom_data.util:\n",
      "\tAtom Data kurucz_cd23_chianti_H_He.h5 not found in local path.\n",
      "\tExists in TARDIS Data repo /home/duttaan2/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5\n",
      "INFO:tardis.io.atom_data.base:Reading Atom Data with: UUID = 6f7b09e887a311e7a06b246e96350010 MD5  = 864f1753714343c41f99cb065710cace \n",
      "INFO:tardis.io.atom_data.base:Non provided Atomic Data: synpp_refs, photoionization_data, yg_data, two_photon_data, linelist_atoms, linelist_molecules\n"
     ]
    }
   ],
   "source": [
    "download_atom_data('kurucz_cd23_chianti_H_He_latest')\n",
    "atom_data_file = 'kurucz_cd23_chianti_H_He_latest.h5'\n",
    "atom_data = AtomData.from_hdf(atom_data_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "config = config_reader.Configuration.from_yaml(\"../../tardis/io/configuration/tests/data/tardis_configv1_density_exponential_nebular.yml\")\n",
    "config.supernova.time_explosion = 2.0 * u.day"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:tardis.io.model.parse_density_configuration:Number of density points larger than number of shells. Assuming inner point irrelevant\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 172800.0 seconds\n"
     ]
    }
   ],
   "source": [
    "workflow = tardis_he_workflow.TARDISHEWorkflow(atom_data, config)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "time_start = 2.0\n",
    "time_end = 5.0\n",
    "number_of_packets = 100000\n",
    "time_steps = 10\n",
    "time_space = 'log'\n",
    "seed = 1\n",
    "fp = 0\n",
    "spectrum_bins = 500\n",
    "grey_opacity=-1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:tardis.model.matter.decay:Decaying abundances for 16581.581519365536 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 18172.720672625794 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 19916.542716964905 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 21827.69883181028 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 23922.246097781474 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 26217.782404475234 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 28733.594303762293 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 31490.819050823688 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 34512.6221943585 seconds\n",
      "INFO:tardis.model.matter.decay:Decaying abundances for 37824.3922080323 seconds\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Total energy in gamma-rays is 1.5213954755851723e+48\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Energy per packet is 1.5213954755851722e+43\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Creating packets\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Creating packet list\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Total energy deposited by the positrons is 3.723993921313078e+45\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Entering the main gamma-ray loop\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Total number of packets is 100000\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Total CMF energy is 1.5213954755864064e+48\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Total RF energy is 1.5224907610143594e+48\n",
      "/home/duttaan2/Software/tardis/tardis/energy_input/gamma_packet_loop.py:199: NumbaPerformanceWarning: \u001b[1m\u001b[1m\u001b[1m\u001b[1mnp.dot() is faster on contiguous arrays, called on (Array(float64, 1, 'C', False, aligned=True), Array(float64, 1, 'A', False, aligned=True))\u001b[0m\u001b[0m\u001b[0m\u001b[0m\n",
      "  ) = distance_trace(\n",
      "/home/duttaan2/Software/tardis/tardis/energy_input/gamma_packet_loop.py:235: NumbaPerformanceWarning: \u001b[1m\u001b[1m\u001b[1m\u001b[1m\u001b[1mnp.dot() is faster on contiguous arrays, called on (Array(float64, 1, 'A', False, aligned=True), Array(float64, 1, 'C', False, aligned=True))\u001b[0m\u001b[0m\u001b[0m\u001b[0m\u001b[0m\n",
      "  packet, ejecta_energy_gained = process_packet_path(packet)\n",
      "/home/duttaan2/miniforge3/envs/tardis/lib/python3.11/site-packages/numba/core/ir_utils.py:2149: NumbaPendingDeprecationWarning: \u001b[1m\n",
      "Encountered the use of a type that is scheduled for deprecation: type 'reflected list' found for argument 'packets' of function 'gamma_packet_loop'.\n",
      "\n",
      "For more information visit https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-reflection-for-list-and-set-types\n",
      "\u001b[1m\n",
      "File \"../../tardis/energy_input/gamma_packet_loop.py\", line 33:\u001b[0m\n",
      "\u001b[1m@njit(**njit_dict_no_parallel)\n",
      "\u001b[1mdef gamma_packet_loop(\n",
      "\u001b[0m\u001b[1m^\u001b[0m\u001b[0m\n",
      "\u001b[0m\n",
      "  warnings.warn(NumbaPendingDeprecationWarning(msg, loc=loc))\n",
      "INFO:tardis.energy_input.main_gamma_ray_loop:Total energy deposited by gamma-rays and positrons is 1.4441820535281093e+48\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Entering gamma ray loop for 100000 packets\n",
      "Number of escaped packets: 4822\n",
      "Number of scattered packets: 2242\n"
     ]
    }
   ],
   "source": [
    "tardis_high_energy = workflow.run(time_start, time_end, number_of_packets,\n",
    "            time_steps, time_space, seed, fp, spectrum_bins)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
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     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# escaped energy packets\n",
    "tardis_high_energy.escape_energy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "      <td>1.518037e+43</td>\n",
       "      <td>1.486897e+43</td>\n",
       "      <td>9.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.130305e+19</td>\n",
       "      <td>2.195378e+19</td>\n",
       "      <td>1.501661e+43</td>\n",
       "      <td>1.547531e+43</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.112090e+20</td>\n",
       "      <td>1.073187e+20</td>\n",
       "      <td>1.519772e+43</td>\n",
       "      <td>1.466608e+43</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99995</th>\n",
       "      <td>99995.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.581968e+20</td>\n",
       "      <td>1.558250e+20</td>\n",
       "      <td>1.520342e+43</td>\n",
       "      <td>1.497547e+43</td>\n",
       "      <td>7.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99996</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99997</th>\n",
       "      <td>99997.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.091819e+20</td>\n",
       "      <td>3.041979e+20</td>\n",
       "      <td>1.520698e+43</td>\n",
       "      <td>1.496185e+43</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99998</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99999</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>100000 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       packet_index  status        nu_cmf         nu_rf    energy_cmf  \\\n",
       "0               0.0     0.0  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "1               1.0     3.0  1.483595e+20  1.453161e+20  1.518037e+43   \n",
       "2               0.0     0.0  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "3               3.0     3.0  2.130305e+19  2.195378e+19  1.501661e+43   \n",
       "4               4.0     3.0  1.112090e+20  1.073187e+20  1.519772e+43   \n",
       "...             ...     ...           ...           ...           ...   \n",
       "99995       99995.0     3.0  1.581968e+20  1.558250e+20  1.520342e+43   \n",
       "99996           0.0     0.0  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "99997       99997.0     3.0  3.091819e+20  3.041979e+20  1.520698e+43   \n",
       "99998           0.0     0.0  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "99999           0.0     0.0  0.000000e+00  0.000000e+00  0.000000e+00   \n",
       "\n",
       "          energy_rf  shell_number  \n",
       "0      0.000000e+00           0.0  \n",
       "1      1.486897e+43           9.0  \n",
       "2      0.000000e+00           0.0  \n",
       "3      1.547531e+43           3.0  \n",
       "4      1.466608e+43           0.0  \n",
       "...             ...           ...  \n",
       "99995  1.497547e+43           7.0  \n",
       "99996  0.000000e+00           0.0  \n",
       "99997  1.496185e+43           2.0  \n",
       "99998  0.000000e+00           0.0  \n",
       "99999  0.000000e+00           0.0  \n",
       "\n",
       "[100000 rows x 7 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# packets information\n",
    "\n",
    "tardis_high_energy.packets_escaped"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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