Additional features

README.rst

@@ -1,6 +1,14 @@
 STARDIS Stellar Radiative transfer
 ----------------------------------
 
+Welcome to STARDIS!
+STARDIS is an LTE radiative transfer Python package that utilizes the TARDIS infrastructure 
+to generate synthetic stellar spectra. For more information about STARDIS, 
+including a quickstart notebook, physics walkthrough and installation instructions, go to our `documentation page <https://tardis-sn.github.io/stardis/>`_. 
+Or, try running the `quickstart notebook <docs/quickstart/quickstart.ipynb>`_ yourself!
+
+To learn more about TARDIS, including documentation and collaborator information, go `here <https://tardis-sn.github.io/tardis/>`_.
+
 License
 -------
 

docs/Tutorials/Running_in_Parallel.ipynb

@@ -0,0 +1,114 @@
+{
+ "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)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/Tutorials/Tutorial_data/h_minus_cross_section_wbr.dat

@@ -0,0 +1,74 @@
+180.0,6.700000000000001e-20
+196.0,8.800000000000002e-20
+214.0,1.17e-19
+236.0,1.5500000000000002e-19
+264.0,2.06e-19
+298.0,2.8300000000000005e-19
+343.0,4.14e-19
+404.0,7.03e-19
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+1750.0,7.917999999999999e-18
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docs/Tutorials/Tutorial_data/mesa_model_example.yml

@@ -0,0 +1,24 @@
+stardis_config_version: 1.0
+n_threads: 1
+atom_data: kurucz_cd23_chianti_H_He.h5
+
+model:
+    fname: Tutorial_data/end_core_h_burn.mod
+    type: mesa
+    truncate_to_shell: 40
+    final_atomic_number: 30
+
+opacity:
+    file:
+        Hminus_bf: Tutorial_data/h_minus_cross_section_wbr.dat
+    bf:
+        H_I: {}
+    ff:
+        H_I: {}
+    disable_electron_scattering: False
+    line:
+        disable: False
+        broadening: [radiation, linear_stark, quadratic_stark, van_der_waals]
+        min: 6500 AA
+        max: 6600 AA
+no_of_thetas: 20

docs/Tutorials/Tutorial_data/opacity_example.yml

@@ -0,0 +1,24 @@
+stardis_config_version: 1.0
+n_threads: 1
+atom_data: kurucz_cd23_chianti_H_He.h5
+
+model:
+    fname: Tutorial_data/end_core_h_burn.mod
+    type: mesa
+    truncate_to_shell: 40
+    final_atomic_number: 30
+
+opacity:
+    file:
+        Hminus_bf: ../../stardis/data/h2_plus_bf_S1994.dat
+    bf:
+        H_I: {}
+    ff:
+        H_I: {}
+    disable_electron_scattering: False
+    line:
+        disable: False
+        broadening: [radiation, linear_stark, quadratic_stark, van_der_waals]
+        min: 6500 AA
+        max: 6600 AA
+no_of_thetas: 20

docs/Tutorials/Tutorial_data/stardis_config_parallel.yml

@@ -0,0 +1,22 @@
+stardis_config_version: 1.0
+n_threads: 4
+atom_data: kurucz_cd23_chianti_H_He.h5
+
+model:
+    type: marcs
+    fname: Tutorial_data/sun.mod
+    final_atomic_number: 30
+opacity:
+    file:
+        Hminus_bf: Tutorial_data/h_minus_cross_section_wbr.dat
+    bf:
+        H_I: {}
+    ff:
+        H_I: {}
+    disable_electron_scattering: False
+    line:
+        disable: False
+        broadening: [radiation, linear_stark, quadratic_stark, van_der_waals]
+        min: 6500 AA
+        max: 6600 AA
+no_of_thetas: 20