From ab7e61d2b1a38387f81ee44b09770cfaf11d5ff8 Mon Sep 17 00:00:00 2001
From: RyanGroneck <GroneckR@msu.edu>
Date: Mon, 18 Nov 2024 11:43:47 -0500
Subject: [PATCH] =?UTF-8?q?new=20Documentation=20for=20setting=20amount=20?=
 =?UTF-8?q?of=20threads=20used=20in=20STARDIS=20simul=E2=80=A6=20(#228)?=
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* new Documentation for setting amount of threads used in STARDIS simulation

* more info added: parallelized stuff and when to use

* direcotry managment and added to index.rst

* name change: Using Stardis in Parallel
---
 docs/index.rst                                |  1 +
 .../stardis_in_parallel.ipynb                 | 61 +++++++++++++++++++
 2 files changed, 62 insertions(+)
 create mode 100644 docs/using_stardis_in_parallel/stardis_in_parallel.ipynb

diff --git a/docs/index.rst b/docs/index.rst
index 3327b50f..7e76e1c4 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -10,6 +10,7 @@ This is the documentation for STARDIS.
    Quickstart <quickstart/quickstart>
    Downloading and Installation <installation>
    Physics of STARDIS <physics/physics_of_stardis>
+   Using STARDIS in Parallel <using_stardis_in_parallel/stardis_in_parallel>
    Example Notebooks <example_notebooks/rotation_broadening>
    Contributing <contributing>
    Bibliography <bibliography>
diff --git a/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb b/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb
new file mode 100644
index 00000000..b2afe6ee
--- /dev/null
+++ b/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb
@@ -0,0 +1,61 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Setting number of threads used in running a STARDIS simulation"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "When you run a STARDIS simulation, the yaml file determines how many threads are used. By default, it will only use 1 thread. The more threads you set a simulation to use, the more computing power the simulation will take advantage of for calculating line opacity and ray tracing steps (as both of these are parallelized in STARDIS). **Setting n_threads to 0 will make the simulation use all available threads.**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here is a what a yaml file that has the STARDIS simulation use 3 threads will look like\n",
+    "\n",
+    "``` yaml\n",
+    "stardis_config_version: 1.0\n",
+    "n_threads: 3 # <-----------  add your 'n_threads: <integer>' here\n",
+    "atom_data: kurucz_cd23_chianti_H_He.h5\n",
+    "model:\n",
+    "    ...\n",
+    "```\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "One reason you may want to consider increasing threads used is when computing spectra with large numbers (i.e. 10,000 or more) of wavelength points."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "stardis",
+   "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": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}