Add Multiparticle Collision Dynamics tutorial (#122)

* Add MPCD tutorial. * Update tutorial to not rely on external gsd file. * Update authors list. * Delete .DS_Store * Update Diffusion in Solution tutorial. * Delete 09-Multiparticle-Collision-Dynamics/.DS_Store * Add semicolons to supress output. * Include MPCD in outline. * Test with `trunk-minor`. * Ruff fixes and update matplotlib imports and usage. * Update pressure driven flow example. * Update diffusion in solution example. * Fix mpcd_particle_sorter in Diffusion in Solution example. * Update to use Frame rather than Snapshot. --------- Co-authored-by: Joshua A. Anderson <[email protected]>
glotzerlab · Jul 8, 2024 · 3faca27 · 3faca27
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diff --git a/09-Multiparticle-Collision-Dynamics/00-index.ipynb b/09-Multiparticle-Collision-Dynamics/00-index.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Introducing Multiparticle Collison Dynamics\n",
+    "\n",
+    "This tutorial introduces how to use the multiparticle collision dynamics (MPCD)\n",
+    "method in HOOMD-blue with examples of pressure-driven flow and diffusion of a\n",
+    "solution of nearly-hard particles.\n",
+    "\n",
+    "**Prerequisites:**\n",
+    "\n",
+    "This tutorial assumes you are familiar with molecular dynamics (MD) (see\n",
+    "[Introducing Molecular Dynamics](../01-Introducing-Molecular-Dynamics/00-index.ipynb))\n",
+    "and have background knowledge on MPCD. To learn more about MPCD, consider\n",
+    "reading one of the following review articles:\n",
+    "\n",
+    "* [Modeling hydrodynamic interactions in soft materials with multiparticle collision dynamics](https://doi.org/10.1016/j.coche.2019.02.007)\n",
+    "* [Multi-Particle Collision Dynamics: A Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids](https://doi.org/10.1007/978-3-540-87706-6_1)\n",
+    "* [Multiparticle Collision Dynamics: Simulation of Complex Systems on Mesoscales](https://doi.org/10.1002/9780470371572.ch2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "nbsphinx-toctree": {
+     "maxdepth": 1
+    }
+   },
+   "source": [
+    "## Outline\n",
+    "\n",
+    "1. [Pressure-Driven Flow Between Parallel Plates](01-Pressure-Driven-Flow.ipynb)\n",
+    "2. [Diffusion of a Solution of Nearly-Hard Spheres](02-Diffusion.ipynb)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This tutorial is written with [jupyter](https://jupyter.org/). You can download the source from the [hoomd-examples](https://github.com/glotzerlab/hoomd-examples) repository."
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  },
+  "record_timing": false
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}