Merge pull request #147 from Exabyte-io/update/SOF-7469

update/SOF 7469

Author: VsevolodX

other/materials_designer/create_point_defect.ipynb

@@ -9,18 +9,11 @@
     "\n",
     "<h2 style=\"color:green\">Usage</h2>\n",
     "\n",
-    "1. Make sure to select Input Materials (in the outer runtime) before running the notebook.\n",
-    "1. Set notebook parameters in cell 1.1. below (or use the default values).\n",
-    "1. Set defects parameters in cell 2.1. (or use default).\n",
+    "1. Make sure to select Input Materials (in the outer runtime) before running the notebook. \n",
+    "1. Set notebook parameters in cell 1.1. below (or use the default values) -- to create multiple defects, fill `DEFECT_CONFIGS` with a list of dictionaries. \n",
     "1. Click “Run” > “Run All” to run all cells. \n",
-    "1. Wait for the run to complete (depending on the parameters can take a few min). \n",
     "1. Scroll down to view results. \n",
     "\n",
-    "## Summary\n",
-    "1. Prepare the Environment: Set up the notebook and install packages, preview the input materials\n",
-    "1. Create the Defect: Add a vacancy defect to the bulk structure\n",
-    "2. Visualize the Defect: Visualize the defect structure\n",
-    "\n",
     "## Notes\n",
     "\n",
     "1. For more information, see [Introduction](Introduction.ipynb)\n",
@@ -35,7 +28,8 @@
    "cell_type": "markdown",
    "source": [
     "## 1. Prepare the Environment\n",
-    "### 1.1. Set up defect parameters "
+    "### 1.1. Set up defects parameters \n",
+    "Defect Configuration parameters are described in [Defect Configuration](https://github.com/Exabyte-io/made/blob/8196b759242551c77d1791bf5bd2f4150763cfef/src/py/mat3ra/made/tools/build/defect/configuration.py#L102)."
    ],
    "metadata": {
     "collapsed": false
@@ -47,10 +41,28 @@
    "outputs": [],
    "source": [
     "DEFECT_TYPE = \"substitution\"  # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
-    "SITE_ID = 0  # Site index of the defect\n",
-    "POSITION = [0, 0.0, 0.0]  # Position of the defect in crystal coordinates\n",
-    "CHEMICAL_ELEMENT = \"Cu\"  # Element to be placed at the site (ignored for vacancy)\n",
-    "SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 3]] "
+    "SITE_ID = None  # Site index of the defect\n",
+    "COORDINATE = None  # Position of the defect in crystal coordinates\n",
+    "APPROXIMATE_COORDINATE = None  # Approximate coordinates of the defect in crystal coordinates\n",
+    "CHEMICAL_ELEMENT = \"C\"  # Element to be placed at the site (ignored for vacancy)\n",
+    "\n",
+    "SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]\n",
+    "\n",
+    "# List of dictionaries with defect parameters\n",
+    "DEFECT_CONFIGS = [\n",
+    "    {\n",
+    "        \"defect_type\": DEFECT_TYPE,\n",
+    "        \"approximate_coordinate\": [0.0, 0.0, 0.0],\n",
+    "        \"chemical_element\": \"C\",\n",
+    "        # \"site_id\": 0,\n",
+    "        # \"coordinate\": None,\n",
+    "    },\n",
+    "    # Uncomment the following to create multiple defects\n",
+    "    # {\n",
+    "    #     \"defect_type\": \"vacancy\",\n",
+    "    #     \"site_id\": 0,\n",
+    "    # },\n",
+    "]"
    ],
    "metadata": {
     "collapsed": false
@@ -77,8 +89,10 @@
     "\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
+    "\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    from utils.jupyterlite import install_packages\n",
+    "\n",
     "    await install_packages(\"create_point_defect.ipynb\", \"../../config.yml\")"
    ],
    "metadata": {
@@ -103,6 +117,7 @@
    "outputs": [],
    "source": [
     "from utils.jupyterlite import get_materials\n",
+    "\n",
     "materials = get_materials(globals())"
    ],
    "metadata": {
@@ -142,7 +157,7 @@
    "cell_type": "markdown",
    "source": [
     "## 2. Create the Defect\n",
-    "### 2.1. Set defect parameters"
+    "### 2.1. Initialize Configuration and Builder parameters"
    ],
    "metadata": {
     "collapsed": false
@@ -156,8 +171,7 @@
     "from mat3ra.made.tools.build.defect import PointDefectConfiguration\n",
     "from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
     "\n",
-    "defect_configuration_with_site_id = PointDefectConfiguration.from_site_id(crystal=supercell, defect_type=DEFECT_TYPE, site_id=SITE_ID, chemical_element=CHEMICAL_ELEMENT)\n",
-    "defect_configuration_with_position = PointDefectConfiguration(crystal=supercell, defect_type=\"interstitial\", position=POSITION, chemical_element=CHEMICAL_ELEMENT)\n",
+    "defect_configurations = [PointDefectConfiguration.from_dict(supercell, defect) for defect in DEFECT_CONFIGS]\n",
     "\n",
     "defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
    ],
@@ -181,10 +195,9 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "from mat3ra.made.tools.build.defect import create_defect\n",
+    "from mat3ra.made.tools.build.defect import create_defects\n",
     "\n",
-    "material_with_defect_at_site_id = create_defect(builder_parameters=defect_builder_parameters, configuration=defect_configuration_with_site_id)\n",
-    "material_with_defect_at_position = create_defect(builder_parameters=defect_builder_parameters, configuration=defect_configuration_with_position)"
+    "material_with_defect = create_defects(builder_parameters=defect_builder_parameters, configurations=defect_configurations)"
    ],
    "metadata": {
     "collapsed": false
@@ -195,7 +208,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## 3. Visualize the Defects"
+    "## 3. Visualize Result(s)"
    ],
    "metadata": {
     "collapsed": false
@@ -209,9 +222,10 @@
     "from utils.visualize import visualize_materials as visualize\n",
     "\n",
     "visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
-    "           {\"material\": material_with_defect_at_site_id, \"title\": f\"Material with defect at site_id={SITE_ID}\"},\n",
-    "           {\"material\": material_with_defect_at_position, \"title\": f\"Material with defect at position={POSITION}\"}],\n",
-    "          rotation=\"-90x\")"
+    "           {\"material\": material_with_defect, \"title\": f\"Material with defect\"}],\n",
+    "          rotation=\"-90x\")\n",
+    "visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
+    "           {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
    ],
    "metadata": {
     "collapsed": false
@@ -235,7 +249,7 @@
    "source": [
     "from utils.jupyterlite import set_materials\n",
     "\n",
-    "set_materials([material_with_defect_at_site_id, material_with_defect_at_position])"
+    "set_materials([material_with_defect])"
    ],
    "metadata": {
     "collapsed": false