update: add atomman whl

other/materials_designer/atomman-mat3ra.ipynb

@@ -0,0 +1,130 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Atomman and Mat3ra integration example\n",
+    "\n",
+    "Installing both packages and related dependencies in JupyterLite/pyodide,\n",
+    "Loading material from environment or Standata\n",
+    "Using Atomman to create a vacancy defect in a material.\n",
+    "Converting back to Mat3ra material and visualizing it."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import Mat3ra related packages\n",
+    "import sys\n",
+    "\n",
+    "if sys.platform == \"emscripten\":\n",
+    "    import micropip\n",
+    "\n",
+    "    # Install and import atomman related packages\n",
+    "    micropip.uninstall(\"packaging\")\n",
+    "    await micropip.install(\"packaging==24.1\")\n",
+    "    await micropip.install(\"https://files.mat3ra.com/uploads/pyyaml-6.0.2-cp311-cp311-emscripten_3_1_45_wasm32.whl\")\n",
+    "    await micropip.install(\"https://files.mat3ra.com/uploads/pymongo-4.15.1-cp311-cp311-emscripten_3_1_45_wasm32.whl\")\n",
+    "    await micropip.install(\"https://files.mat3ra.com/uploads/atomman-1.4.11-cp311-cp311-emscripten_3_1_45_wasm32.whl\",keep_going=True)\n",
+    "\n",
+    "    # Install and import mat3ra related packages\n",
+    "    await micropip.install(\"mat3ra-api-examples\", deps=False)\n",
+    "    await micropip.install('mat3ra-utils')\n",
+    "    await micropip.install('mat3ra-standata', deps=False)\n",
+    "    from mat3ra.utils.jupyterlite.packages import install_packages\n",
+    "    await install_packages(\"\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load material from inputs\n",
+    "from utils.jupyterlite import get_materials\n",
+    "from mat3ra.made.tools.convert import to_poscar\n",
+    "from mat3ra.standata.materials import Materials\n",
+    "from mat3ra.made.material import Material\n",
+    "\n",
+    "materials = get_materials(globals())\n",
+    "material = materials[0] or Material.create(Materials.get_by_name_first_match(\"Si\"))\n",
+    "\n",
+    "poscar = to_poscar(material)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import atomman as am\n",
+    "# Load poscar and pass in prop dictionary\n",
+    "system = am.load('poscar', poscar)\n",
+    "print(system)\n",
+    "system = system.supersize(2,2,1)\n",
+    "system.atoms_df()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Add a vacancy defect\n",
+    "defected_system = am.defect.vacancy(system, ptd_id=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Convert back to Mat3ra material\n",
+    "from mat3ra.made.tools.convert import from_poscar\n",
+    "\n",
+    "defected_system_poscar = defected_system.dump(\"poscar\")\n",
+    "defected_material = Material.create(from_poscar(defected_system_poscar))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from utils.visualize import visualize_materials\n",
+    "\n",
+    "visualize_materials(defected_material)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python (Pyodide)",
+   "language": "python",
+   "name": "python"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "python",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}