Merge pull request #205 from Exabyte-io/fix/SOF-7353

fix/SOF 7353

Author: VsevolodX

config.yml

@@ -67,11 +67,6 @@ notebooks:
     packages_pyodide:
       - mat3ra-esse
       - mat3ra-made
-  - name: create_cluster_custom_shape.ipynb
-    packages_common:
-      - icosphere
-    packages_python:
-    packages_pyodide:
   - name: specific_examples
     packages_common:
       - mat3ra-standata

other/materials_designer/create_cluster_custom_shape.ipynb

@@ -48,7 +48,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "import sys\n",
     "\n",
@@ -58,12 +57,13 @@
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    from utils.jupyterlite import install_packages\n",
     "\n",
-    "    await install_packages(\"create_cluster_custom_shape.ipynb\")"
+    "    await install_packages(\"\")"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "d9e6be14343d00a1",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -78,7 +78,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "RADIUS = 0.3  # in crystal units\n",
     "VACUUM = 10.0  # in Angstroms on each side\n",
@@ -90,6 +89,7 @@
     "collapsed": false
    },
    "id": "9d8b1890b34d850a",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -104,41 +104,42 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "import numpy as np\n",
+    "from scipy.spatial import ConvexHull\n",
     "from typing import List\n",
-    "from icosphere import icosphere\n",
     "from mat3ra.made.tools.utils.coordinate import CoordinateCondition\n",
     "\n",
     "\n",
-    "# Example of a custom coordinate condition (icosahedron). Adapt coordinate conditions to your needs.\n",
     "class CustomCoordinateCondition(CoordinateCondition):\n",
-    "    \"\"\"Creates an icosahedron shape using the icosphere module\"\"\"\n",
+    "    \"\"\"Creates a regular polyhedron shape using SciPy's ConvexHull\"\"\"\n",
     "    radius: float = 1\n",
-    "    frequency: int = 1\n",
-    "    vertices: List[List[float]] = icosphere(1)[0]\n",
-    "    faces: List[List[int]] = icosphere(1)[1]\n",
     "    center: List[float] = [0.5, 0.5, 0.5]\n",
     "\n",
+    "    @property\n",
+    "    def _hull_planes(self):\n",
+    "        t = (1 + np.sqrt(5)) / 2\n",
+    "        vertices = np.array([\n",
+    "            [-1, t, 0], [1, t, 0], [-1, -t, 0], [1, -t, 0],\n",
+    "            [0, -1, t], [0, 1, t], [0, -1, -t], [0, 1, -t],\n",
+    "            [t, 0, -1], [t, 0, 1], [-t, 0, -1], [-t, 0, 1]\n",
+    "        ]) * self.radius / np.sqrt(1 + t*t)\n",
+    "        return ConvexHull(vertices).equations\n",
+    "\n",
     "    def condition(self, coordinate: List[float]) -> bool:\n",
-    "        \"\"\"Returns True if point is inside icosahedron\"\"\"\n",
-    "        coordinate = np.array(coordinate) - self.center\n",
-    "        for face in self.faces:\n",
-    "            a, b, c = face\n",
-    "            normal = np.cross(self.vertices[b] - self.vertices[a], self.vertices[c] - self.vertices[a])\n",
-    "            normal = normal / np.linalg.norm(normal)\n",
-    "            if np.dot(normal, coordinate) > self.radius:\n",
-    "                return False\n",
-    "        return True\n",
-    "    \n",
+    "        \"\"\"Returns True if point is inside the polyhedron\"\"\"\n",
+    "        point = np.array(coordinate) - self.center\n",
+    "        return all(np.dot(plane[:3], point) + plane[3] <= 0\n",
+    "                  for plane in self._hull_planes)\n",
+    "\n",
     "    \n",
     "condition = CustomCoordinateCondition(radius=RADIUS).condition"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "8e382d5ab459e2d",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -153,7 +154,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from utils.jupyterlite import get_materials\n",
     "\n",
@@ -163,6 +163,7 @@
     "collapsed": false
    },
    "id": "be38fdda1984c654",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -178,24 +179,21 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
-    "from mat3ra.made.tools.build.nanoparticle import ASEBasedNanoparticleConfiguration\n",
-    "from mat3ra.made.tools.build.nanoparticle.enums import ASENanoparticleShapesEnum\n",
-    "\n",
+    "from mat3ra.made.tools.build.nanoparticle import SlabBasedNanoparticleConfiguration\n",
     "\n",
-    "config = ASEBasedNanoparticleConfiguration(\n",
+    "config = SlabBasedNanoparticleConfiguration(\n",
     "    material=materials[0],\n",
+    "    condition_builder=condition,\n",
     "    supercell_size=SUPERCELL_SIZE,\n",
-    "    vacuum=VACUUM,\n",
-    "    z_orientation=Z_ORIENTATION,\n",
-    "    coordinate_condition=condition\n",
-    ")\n"
+    ")"
    ],
    "metadata": {
     "collapsed": false
    },
-   "id": "8fbe260fa14db47a"
+   "id": "8fbe260fa14db47a",
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -209,14 +207,16 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
-    "from mat3ra.made.tools.build.nanoparticle import ASEBasedNanoparticleBuilder"
+    "from mat3ra.made.tools.build.nanoparticle import create_nanoparticle\n",
+    "\n",
+    "cluster = create_nanoparticle(config)"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "a990fa35742d7269",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -231,7 +231,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from mat3ra.made.lattice import Lattice\n",
     "\n",
@@ -245,6 +244,7 @@
     "collapsed": false
    },
    "id": "4f78c4743b370c3b",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -259,18 +259,16 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
-    "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": cluster, \"title\": f\"Cluster\"}])\n",
-    "\n",
-    "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": cluster, \"title\": f\"Cluster\"}], rotation=\"-90x\")"
+    "from utils.visualize import visualize_materials as visualize\n",
+    "visualize([{\"material\": cluster, \"title\": f\"Cluster\"},\n",
+    "           {\"material\": cluster, \"title\": f\"Cluster\", \"rotation\": \"-90x\"}])"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "509b18661a069e42",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -285,7 +283,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from utils.jupyterlite import set_materials\n",
     "\n",
@@ -296,6 +293,7 @@
     "collapsed": false
    },
    "id": "61daa5afcbc078a9",
+   "outputs": [],
    "execution_count": null
   }
  ],

other/materials_designer/create_grain_boundary_film.ipynb

@@ -104,7 +104,7 @@
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    from utils.jupyterlite import install_packages\n",
     "\n",
-    "    await install_packages(\"\", \"../../config.yml\")"
+    "    await install_packages(\"\")"
    ],
    "metadata": {
     "collapsed": false

other/materials_designer/custom_transformation.ipynb

@@ -23,17 +23,15 @@
    },
    "outputs": [],
    "source": [
-    "# Install packages for JupyterLite\n",
-    "from mat3ra.utils.jupyterlite.packages import install_packages\n",
     "import sys\n",
     "\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
     "\n",
-    "    # Import the mat3ra api-examples package to allow for relative imports\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
+    "    from utils.jupyterlite import install_packages\n",
     "\n",
-    "await install_packages(\"\")"
+    "    await install_packages(\"\")"
    ]
   },
   {
@@ -58,7 +56,8 @@
    "metadata": {
     "collapsed": false
    },
-   "id": "b2fa69b96b195d30"
+   "id": "b2fa69b96b195d30",
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -75,12 +74,14 @@
    "outputs": [],
    "source": [
     "from utils.jupyterlite import get_materials\n",
+    "\n",
     "materials = get_materials(globals())"
    ],
    "metadata": {
     "collapsed": false
    },
-   "id": "54e68de6c6cc3e03"
+   "id": "54e68de6c6cc3e03",
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -101,7 +102,8 @@
    "metadata": {
     "collapsed": false
    },
-   "id": "91069f5712a65dbb"
+   "id": "91069f5712a65dbb",
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -126,7 +128,8 @@
    "metadata": {
     "collapsed": false
    },
-   "id": "7973f7ee67bdc42a"
+   "id": "7973f7ee67bdc42a",
+   "execution_count": null
   }
  ],
  "metadata": {