Remove deprecated code (#131)

* Fix typo.

* Remove unused file.

* Add jupytext configuration.

* Clean up README.

* Use InverseVolumeRamp

* Reinstate deprecation warnings.

* Execute all notebooks in tests.

* Use InverseVolumeRamp in rigid body tutorial.

* Use InverseVolumeRamp in Barrier tutorial.

* Apply ruff-format to jupyter notebooks.

* pre-commit

* Rewrite Kern-Frenkel tutorial with builtin commands.

* Allow deprecation warnings again.

* Fix small typos.

* Apply suggestions from code review.

* Fix broken link.

.github/workflows/test.yaml

@@ -97,12 +97,7 @@ jobs:
       run: |
         for i in */
         do
-          # Skip CPPPotential examples until they are rewritten.
-          if [[ $i == "07-Modelling-Patchy-Particles"* ]]; then
-              echo "Skipping notebooks in $i"
-          else
-            echo "Running notebooks in: $i" && jupyter nbconvert --execute --inplace $i/*.ipynb || exit 1
-          fi
+          echo "Running notebooks in: $i" && jupyter nbconvert --execute --inplace $i/*.ipynb || exit 1
         done
       working-directory: notebooks
 

.pre-commit-config.yaml

@@ -30,5 +30,6 @@ repos:
     rev: v0.5.0
     hooks:
       - id: ruff-format
+        types_or: [ python, jupyter ]
       - id: ruff
         types_or: [ python, jupyter ]

05-Organizing-and-Executing-Simulations/03-Continuing-Simulations.ipynb

@@ -257,7 +257,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When this **workflow step** is executed, it stores the trial move sizes `a`, `d` and the current timestep in the job document as well as the the state of the simulation in `restart.gsd`.\n",
+    "When this **workflow step** is executed, it stores the trial move sizes `a`, `d` and the current timestep in the job document as well as the state of the simulation in `restart.gsd`.\n",
     "It reads these when starting again to continue from where the previous execution stopped.\n",
     "This is a large code block, see the comments for more details on how this **workflow step** can **continue** from where it stopped.\n",
     "\n",

07-Modelling-Patchy-Particles/00-index.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Modelling Patchy Particles\n",
     "\n",
-    "In this tutorial you will implement the Kern–Frenkel potential as a model for patchy particle interactions. To do so, you will use the `hpmc.pair.user` module, which enables the addition of user-defined, arbitrary, pairwise energetic interactions to a HPMC simulation.\n",
+    "In this tutorial you will implement the Kern–Frenkel potential as a model for patchy particle interactions.\n",
     "\n",
     "**Prerequisites:**\n",
     "\n",
@@ -23,19 +23,23 @@
    "source": [
     "## Outline\n",
     "\n",
-    "1. [Kern–Frenkel Model](01-Kern-Frenkel-Model.ipynb)\n",
-    "1. [Simulating a System of Patchy Particles](02-Simulating-a-System-of-Patchy-Particles.ipynb)"
+    "1. [The Kern–Frenkel Model](01-Kern-Frenkel-Model.ipynb)\n",
+    "1. [Simulating a System of Patchy Particles with HPMC](02-Simulating-a-System-of-Patchy-Particles-with-HPMC.ipynb)"
    ]
   },
   {
    "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."
+    "This tutorial is written with [jupyter](https://jupyter.org/).\n",
+    "You can download the source from the [hoomd-examples](https://github.com/glotzerlab/hoomd-examples) repository."
    ]
   }
  ],
  "metadata": {
+  "jupytext": {
+   "notebook_metadata_filter": "-all"
+  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -46,7 +50,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.4"
   },
   "record_timing": false
  },

07-Modelling-Patchy-Particles/01-Kern-Frenkel-Model.ipynb

@@ -5,7 +5,7 @@
    "id": "0",
    "metadata": {},
    "source": [
-    "# Kern–Frenkel Model\n",
+    "# The Kern–Frenkel Model\n",
     "\n",
     "## Overview\n",
     "\n",
@@ -25,44 +25,46 @@
    "source": [
     "## Patchy Particles\n",
     "In the [Introducing Molecular Dynamics](../01-Introducing-Molecular-Dynamics/00-index.ipynb) tutorial, you simulated a system of particles interacting through the Lennard-Jones pair potential.\n",
-    "The Lennard-Jones pair potential is spherically symmetric, that is, the pair potential does not depend on the relative orientation of the interacting particles.\n",
-    "\n",
-    "Some systems are better represented by anisotropic pair potentials, where there is a dependence on the relative orientation of particles.\n",
-    "The hard octahedra you simulated in [Intoducing HOOMD-blue](../00-Introducing-HOOMD-blue/00-index.ipynb) interacted through a purely repulsive anisotropic pair potential.\n",
-    "Particles that interact with anisotropic pair potentials where some relative orientations are more attractive than others are known as **patchy particles**, since we can imagine that there are attractive **patches** on the surface of the particles.\n",
+    "The Lennard-Jones pair potential is spherically symmetric.\n",
+    "In other words, the pair potential does not depend on the relative orientation of the interacting particles.\n",
     "\n",
+    "Some systems are better represented by anisotropic pair potentials that depend on relative particle orientations. \n",
+    "For example, **patchy particles** interact via anisotropic pair potentials where some relative orientations are more attractive than others.\n",
     "\n",
     "## The Kern–Frenkel Model\n",
     "\n",
-    "One of the simplest patchy particle models is the Kern–Frenkel model, which was introduced in a [2003 Journal of Chemical Physics paper](https://doi.org/10.1063/1.1569473).\n",
-    "The Kern–Frenkel model contains directional pairwise energetic interactions in addition to hard sphere-like volume exclusion.\n",
-    "The pair potential $u_{ij}(r_{ij}, \\Omega_i, \\Omega_j)$ between particles $i$ and $j$ at a center-to-center distance $r_{ij}$ and orientations $\\Omega_i$ and $\\Omega_j$ is of the form\n",
+    "The Kern–Frenkel model, introduced in a [2003 Journal of Chemical Physics paper](https://doi.org/10.1063/1.1569473), models particles with a single patch.\n",
+    "It consists of a directional pairwise energetic interaction in addition to hard sphere volume exclusion.\n",
+    "The pair potential $U_{ij}(\\vec{r}_{ij}, \\mathbf{q}_i, \\mathbf{q}_j)$ between particles $i$ and $j$ at a center-to-center separation $\\vec{r}_{ij}$ and orientations $\\mathbf{q}_i$ and $\\mathbf{q}_j$ is of the form\n",
     "$$\n",
-    "\\beta u_{ij} = \n",
+    "U_{ij} = \n",
     "\\begin{cases}\n",
     "\\infty & r_{ij} < \\sigma_{ij} \\\\\n",
-    "-\\beta\\varepsilon\\cdot f(\\Omega_1, \\Omega_2) & \\sigma_{ij} \\leq r_{ij} < \\lambda_{ij}\\sigma_{ij} \\\\\n",
+    "-\\varepsilon\\cdot f(\\vec{r}_{ij}, \\mathbf{q}_i, \\mathbf{q}_j) & \\sigma_{ij} \\leq r_{ij} < \\lambda_{ij}\\sigma_{ij} \\\\\n",
     "0 & r_{ij} \\geq \\lambda_{ij}\\sigma_{ij}\n",
     "\\end{cases}\n",
     "$$\n",
-    "where $\\beta = 1/k_BT$, $\\varepsilon$ is the strength of the patchy interaction, $\\sigma_{ij}$ is sum of the radii of particles $i$ and $j$, $\\lambda$ is the range of the square well attraction, and $f(\\Omega_i, \\Omega_j)$ is an orientational masking function given by\n",
+    "where $\\varepsilon$ is the strength of the patchy interaction, $\\sigma_{ij}$ is sum of the radii of particles $i$ and $j$, $\\lambda_{ij}$ is the range of the square well attraction, and $f$ is an orientational masking function given by\n",
     "$$\n",
-    "f(\\Omega_1, \\Omega_2) = \n",
+    "f(\\vec{r}_{ij}, \\mathbf{q}_i, \\mathbf{q}_j) = \n",
     "\\begin{cases}\n",
-    "1 & \\hat{e}_i \\cdot \\hat{r}_{ij} > \\cos \\delta \\mathrm{~~and~~} \\hat{e}_j \\cdot \\hat{r}_{ji} > \\cos \\delta \\\\\n",
+    "1 & \\hat{e}_i \\cdot \\hat{r}_{ij} \\ge \\cos \\delta \\land \\hat{e}_j \\cdot \\hat{r}_{ji} \\ge \\cos \\delta \\\\\n",
     "0 & \\mathrm{otherwise}\n",
     "\\end{cases}\n",
     "$$\n",
     "where $\\hat{e}_i$ is the **director** of the patch on particle $i$ and $\\delta$ is the half-opening angle of the patch.\n",
     "\n",
-    "Graphically, this pair potential corresponds to the following criterion: two particles interact with energy $\\infty$ if the gray shaded regions on the two particles overlap at all, $-\\varepsilon$ if the blue shaded regions on the two particles overlap, and zero otherwise.\n",
+    "Graphically, this pair potential corresponds to the following: two particles interact with energy $\\infty$ if the gray shaded regions on the two particles overlap at all, $-\\varepsilon$ if the blue shaded regions on the two particles overlap, and zero otherwise.\n",
     "\n",
     "![Kern–Frenkel](kern-frenkel-schematic.svg)"
    ]
   }
  ],
  "metadata": {
   "celltoolbar": "Raw Cell Format",
+  "jupytext": {
+   "notebook_metadata_filter": "-all"
+  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -73,7 +75,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,