update: use made 2

Author: VsevolodX

other/materials_designer/import_materials_from_files.ipynb

@@ -37,10 +37,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "9c1f4e9e",
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Upload files to this folder\n",
     "FOLDER_PATH = \"./uploads\"\n",
@@ -51,7 +49,9 @@
     "USE_FILE_NAME_NO_EXTENSION = False\n",
     "# If set to true, the supported formats will be printed below\n",
     "SHOW_SUPPORTED_FORMATS = False"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -63,20 +63,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "ef2b38a5-de7e-419e-b605-110e9e0095f5",
    "metadata": {
     "trusted": true
    },
-   "outputs": [],
    "source": [
     "import sys\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
-    "from utils.jupyterlite import install_packages\n",
-    "await install_packages(\"import_materials_from_files.ipynb\",\"../../config.yml\")"
-   ]
+    "    from utils.jupyterlite import install_packages\n",
+    "    await install_packages(\"import_materials_from_files.ipynb\")"
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -90,13 +90,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "b1ee775d1476f884",
    "metadata": {
     "collapsed": false,
     "trusted": true
    },
-   "outputs": [],
    "source": [
     "import os\n",
     "from pathlib import Path\n",
@@ -118,7 +116,9 @@
     "        print(e)\n",
     "        unreadable_files.append(file_name)\n",
     "        continue"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -130,14 +130,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "0e34472a",
    "metadata": {},
-   "outputs": [],
    "source": [
     "print(f\"Successfully read {len(materials)} files\")\n",
     "print(f\"Unreadable files: {unreadable_files}. \")\n"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -149,10 +149,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "a771a36a",
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Uncomment to see the list of supported formats and their file extensions\n",
     "from ase.io.formats import ioformats\n",
@@ -163,7 +161,9 @@
     "    data = [[frmt.name, frmt.extensions, frmt.description] for frmt in ioformats.values()]\n",
     "    dataframe = pd.DataFrame(data, columns=[\"Format Name\", \"File Extensions\", \"Description\"])\n",
     "    print(dataframe.to_markdown())"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -175,17 +175,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "c41fb68c6d25fe48",
    "metadata": {
     "collapsed": false,
     "trusted": true
    },
-   "outputs": [],
    "source": [
-    "from src.utils import ase_to_poscar\n",
+    "import io\n",
+    "from ase import Atoms\n",
+    "from ase.io import write\n",
     "from express import ExPrESS\n",
     "\n",
+    "def ase_to_poscar(atoms: Atoms):\n",
+    "    \"\"\"\n",
+    "    Converts ase.Atoms object to POSCAR format\n",
+    "\n",
+    "    Args:\n",
+    "        atoms (ase.Atoms): ase.Atoms object\n",
+    "\n",
+    "    Returns:\n",
+    "        str: POSCAR string\n",
+    "    \"\"\"\n",
+    "    output = io.StringIO()\n",
+    "    write(output, atoms, format=\"vasp\")\n",
+    "    content = output.getvalue()\n",
+    "    output.close()\n",
+    "\n",
+    "    return content\n",
+    "\n",
     "def convert_ase_entry_to_esse(ase_entry):\n",
     "    poscar = ase_to_poscar(ase_entry)\n",
     "    kwargs = {\n",
@@ -201,7 +218,9 @@
     "    return esse\n",
     "\n",
     "esse_entries = list(map(convert_ase_entry_to_esse, materials))"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -213,39 +232,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "860b5c1b",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "from src.utils import poscar_to_ase\n",
-    "from ase.visualize import view\n",
-    "from ase.io import write\n",
-    "from ase.build import make_supercell\n",
-    "from IPython.display import Image\n",
+    "from utils.visualize import visualize_materials\n",
+    "from mat3ra.made.material import Material\n",
     "\n",
-    "def visualize_material(material, index: int, number_of_repetitions: int = 3):\n",
-    "    \"\"\"\n",
-    "    Visualize the material using ASE's visualization tool\n",
-    "    Repeat the unit cell to make it easier to see.\n",
+    "materials = [Material(esse_entry) for esse_entry in esse_entries]\n",
     "\n",
-    "    Args:\n",
-    "        material: The material to visualize (Ase.Atoms object)\n",
-    "        index: The index of the material\n",
-    "        number_of_repetitions: The number of unit cell repetitions to visualize\n",
-    "    \"\"\"\n",
-    "    # Set the number of unit cell repetition for the structure to make it easier to see\n",
-    "    n = number_of_repetitions\n",
-    "    material_repeat = make_supercell(material, [[n,0,0],[0,n,0],[0,0,n]])\n",
-    "    filename = f\"material-{index}.png\"\n",
-    "    write(filename, material_repeat)\n",
-    "    img = Image(filename=filename)\n",
-    "    print(filename, \"-\", material.symbols)\n",
-    "    display(img)\n",
-    "\n",
-    "for idx, material in enumerate(materials):\n",
-    "    visualize_material(material, idx)"
-   ]
+    "visualize_materials(materials)"
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -257,16 +255,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "00b187ab",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "from utils.jupyterlite import set_data\n",
+    "from utils.jupyterlite import set_materials\n",
     "\n",
-    "output_materials = esse_entries\n",
-    "set_data(\"materials\", output_materials)"
-   ]
+    "set_materials(materials)"
+   ],
+   "outputs": [],
+   "execution_count": null
   }
  ],
  "metadata": {