mesa model and parallel tutorials

docs/Tutorials/Mesa_model.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Using a MESA model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Using a MESA model entails a few changes in the utilization of STARDIS. Firstly, you must change the model type to 'mesa' under the 'model' section, like this:  \n",
+    "\n",
+    "```\n",
+    "model:\n",
+    "    type: mesa\n",
+    "    fname: end_core_h_burn.mod\n",
+    "```\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Next, you can now specify the outmost depth point for the simulation using the 'truncate_to_shell' parameter. It defaults to -99, which tells the model to use all shells. Place the parameter in the 'model' section, like this: \n",
+    "```\n",
+    "model:\n",
+    "    type: mesa\n",
+    "    fname: end_core_h_burn.mod\n",
+    "    truncate_to_shell: 40\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
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docs/Tutorials/Running_in_Parallel.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Running the Simulation in Parallel"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can change the number of threads that STARDIS uses with the n_threads keyword. \n",
+    "A few things to remember when running STARDIS in parallel:  \n",
+    "  \n",
+    "If no n_threads argument is provided, it defaults to 1 and runs in series.  \n",
+    "  \n",
+    "Set n_threads to 0 to use all available threads.  \n",
+    "  \n",
+    "The n_threads argument must be between the config version and the atom data, like this:  \n",
+    "```\n",
+    "stardis_config_version: 1.0  \n",
+    "n_threads: 4  \n",
+    "atom_data: kurucz_cd23_chianti_H_He.h5\n",
+    "```\n",
+    "\n",
+    "In the [stardis_config_parallel](stardis_config_parallel.yml) file, an n_threads value of 4 is added to the example config. Try running this code yourself to see how n_threads affects STARDIS's efficiency."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "25723fa78e8d43ef8129a7667a39ebf8",
+       "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": "86699bb231414753bfb51786d4a12b7f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Packets:             0/? [00:00<?, ?it/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Atomic Data kurucz_cd23_chianti_H_He already exists in /home/monkhayd/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5. Will not download - override with force_download=True.\n",
+      "WARNING: UnitsWarning: 'erg/cm2/s' contains multiple slashes, which is discouraged by the FITS standard [astropy.units.format.generic]\n",
+      "WARNING:astropy:UnitsWarning: 'erg/cm2/s' contains multiple slashes, which is discouraged by the FITS standard\n",
+      "/home/monkhayd/Software/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide\n",
+      "  (g_lower * n_upper) / (g_upper * n_lower)\n",
+      "/home/monkhayd/Software/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide\n",
+      "  (g_lower * n_upper) / (g_upper * n_lower)\n"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "from tardis.io.atom_data.util import download_atom_data\n",
+    "from stardis.base import run_stardis\n",
+    "from astropy import units as u, constants as const\n",
+    "\n",
+    "download_atom_data('kurucz_cd23_chianti_H_He')\n",
+    "tracing_lambdas = np.mgrid[6540:6590:.01]* u.Angstrom\n",
+    "\n",
+    "sim = run_stardis('Tutorial_data/stardis_config_parallel.yml', tracing_lambdas)"
+   ]
+  }
+ ],
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