Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in…

…to 108-JOSS-submission

docs/applications/elastic_constants.ipynb

@@ -0,0 +1,47 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1aad7bd0-ad93-4037-90be-39a90e0609fc",
+   "metadata": {},
+   "source": [
+    "# Elastic Constants\n",
+    "\n",
+    "Solids respond to small external loads through a reversible elastic response. The strength of the response is characterized by the elastic moduli. {py:mod}`matscipy.elasticity` implements functions for computing elastic moduli from small deformation of atomistic systems that consider potential symmetries of the underlying atomic system, in particular for crystals. {py:mod}`matscipy.elasticity` also implements analytic calculation of elastic moduli for some interatomic potentials, described in more detail below. The computation of elastic moduli is a basic prerequisite for multi-scale modelling of materials, as they are the most basic parameters of continuum material models.\n",
+    "\n",
+    "In this tutorial, we will go over different ways that `matscipy` can compute elastic constants of an atomic configuration.\n",
+    "\n",
+    "## Problem setup"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f7edef8b-a391-44fb-8591-2e80db68f9fc",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.11.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/applications/index.rst

@@ -7,4 +7,4 @@ Application domains
 
    elastic_constants
    plasticity
-   fracture_mechanics
+   fracture_mechanics

docs/calculators/manybody.ipynb

@@ -9,24 +9,24 @@
     "\n",
     "`matscipy` implements support for generic manybody potentials. The class `matscipy.calculators.manybody.Manybody` implements the functional form\n",
     "\n",
-    "$$\n",
+    "```{math}\n",
     "  U\n",
     "  =\n",
     "  \\frac{1}{2}\n",
     "  \\sum_{\\substack{ij\\\\ i\\neq j}}\n",
     "  U_2(r^2_{ij}) + U_\\text{m}(r^2_{ij}, \\xi_{ij})\n",
-    "$$\n",
+    "```\n",
     "\n",
     "with\n",
     "\n",
-    "$$\n",
+    "```{math}\n",
     "  \\xi_{ij} \n",
     "  = \n",
     "  \\sum_{\\substack{k\\\\ k\\neq i,j}} \n",
     "  \\Xi(r^2_{ij}, r^2_{ik}, r^2_{jk})\n",
-    "$$\n",
+    "```\n",
     "\n",
-    "as described, e.g. by [Müser et al.](https://doi.org/10.1080/23746149.2022.2093129) and [Grießer et al.](https://doi.org/10.48550/arXiv.2302.08754). On top of energies and forces, the calculator can compute second derivatives (with respect to positions and strain degrees of freedom). Explicit functional forms of $U_2$, $U_\\text{m}$ and $\\Xi$ are implemented for a number of potential."
+    "as described, e.g. by [Müser et al.](https://doi.org/10.1080/23746149.2022.2093129) and [Grießer et al.](https://doi.org/10.48550/arXiv.2302.08754). On top of energies and forces, the calculator can compute second derivatives (with respect to positions and strain degrees of freedom). Explicit functional forms of {math}`U_2`, {math}`U_\\text{m}` and {math}`\\Xi` are implemented for a number of potential."
    ]
   },
   {
@@ -36,7 +36,7 @@
    "source": [
     "## Kumagai potential\n",
     "\n",
-    "The following example compute the elastic constants of a small representation of amorphous silicon using the potential by [Kumagai et al.](https://doi.org/10.1016/j.commatsci.2006.07.013)."
+    "The following example computes the elastic constants of a small representation of amorphous silicon using the potential by [Kumagai et al.](https://doi.org/10.1016/j.commatsci.2006.07.013)."
    ]
   },
   {

docs/conf.py

@@ -42,6 +42,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.autosummary',
+    'sphinx.ext.mathjax',
     'myst_nb'
 ]