feature/SOF-7676

.gitignore

@@ -83,7 +83,7 @@ celerybeat-schedule
 
 # Environments
 .env
-.venv
+.venv*
 env/
 venv/
 ENV/

other/materials_designer/create_adatom_defect.ipynb

@@ -47,28 +47,32 @@
    "id": "5e43ff288847b784"
   },
   {
+   "metadata": {},
    "cell_type": "code",
    "source": [
+    "from mat3ra.made.tools.build.defect.enums import AdatomPlacementMethodEnum\n",
+    "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
+    "\n",
+    "ELEMENT = \"Si\"  # Chemical element of the adatom\n",
     "DEFECT_CONFIGS = [\n",
     "    {\n",
-    "        \"defect_type\": \"adatom\",\n",
-    "        \"placement_method\": \"equidistant\",\n",
-    "        \"chemical_element\": \"Si\",\n",
-    "        \"position_on_surface\": [0.5, 0.5],\n",
-    "        \"distance_z\": 2.0,\n",
-    "        \"use_cartesian_coordinates\": False\n",
-    "    },\n",
+    "        \"type\": \"adatom\",\n",
+    "        \"coordinate\": [0.5, 0.5], # Crystal coordinates on the surface (x, y)\n",
+    "        \"distance_z\": 1.0,  # Method to place the adatom\n",
+    "        \"element\": ELEMENT,\n",
+    "    }\n",
     "]\n",
+    "PLACEMENT_METHOD = AdatomPlacementMethodEnum.NEW_CRYSTAL_SITE  # Method to place the adatom, e.g., \"NEW_CRYSTAL_SITE\", \"EQUIDISTANT\", \"EXACT_COORDINATE\"\n",
+    "\n",
+    "\n",
     "# Slab parameters\n",
     "MILLER_INDICES = (1, 1, 1)  # Miller indices of the surface\n",
     "SLAB_THICKNESS = 3  # Thickness of the slab in unit cells\n",
-    "VACUUM = 6  # Vacuum thickness in Angstrom\n",
-    "SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 1]]  # Supercell matrix for the slab"
+    "VACUUM = 5.0  # Vacuum thickness in Angstrom\n",
+    "XY_SUPERCELL_MATRIX = [[2, 0], [0, 2]]  # Supercell matrix for the slab\n",
+    "TERMINATION_FORMULA = None  # Stoichiometric formula of the slab termination to be used."
    ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "9d8b1890b34d850a",
+   "id": "b28e2fb6a4ea857f",
    "outputs": [],
    "execution_count": null
   },
@@ -142,24 +146,24 @@
    "cell_type": "code",
    "source": [
     "from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer\n",
-    "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
+    "from mat3ra.made.tools.build.slab.helpers import create_slab, get_slab_terminations\n",
     "from utils.visualize import visualize_materials as visualize\n",
     "\n",
     "material = materials[0]\n",
     "# Create analyzer to get terminations\n",
     "analyzer = CrystalLatticePlanesMaterialAnalyzer(material=material, miller_indices=MILLER_INDICES)\n",
     "slab_terminations = analyzer.terminations\n",
     "# Get termination from analyzer\n",
-    "terminations = analyzer.terminations\n",
-    "termination = terminations[0]  # Use first termination\n",
+    "terminations = get_slab_terminations(material, MILLER_INDICES)\n",
+    "termination = select_slab_termination(terminations, TERMINATION_FORMULA)\n",
     "\n",
     "slab = create_slab(\n",
     "    crystal=material,\n",
     "    termination=termination,\n",
     "    miller_indices=MILLER_INDICES,\n",
-    "    number_of_layers=1,\n",
-    "    vacuum=0,\n",
-    "    xy_supercell_matrix=[[1, 0], [0, 1]],\n",
+    "    number_of_layers=SLAB_THICKNESS,\n",
+    "    vacuum=VACUUM,\n",
+    "    xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
     "    use_orthogonal_c=True,\n",
     "    use_conventional_cell=True\n",
     ")\n",
@@ -172,50 +176,19 @@
   {
    "metadata": {},
    "cell_type": "markdown",
-   "source": [
-    "## 2. Create the Defect\n",
-    "### 2.1. Set adatom parameters"
-   ],
+   "source": "## 2. Create the Defect",
    "id": "b386c06587b2f843"
   },
-  {
-   "metadata": {},
-   "cell_type": "code",
-   "source": [
-    "from mat3ra.made.tools.build.defect import AdatomSlabPointDefectConfiguration\n",
-    "\n",
-    "defect_configurations = [\n",
-    "    AdatomSlabPointDefectConfiguration(\n",
-    "        crystal=slab,\n",
-    "        defect_type=defect[\"defect_type\"],\n",
-    "        placement_method=defect[\"placement_method\"],\n",
-    "        chemical_element=defect[\"chemical_element\"],\n",
-    "        position_on_surface=defect[\"position_on_surface\"],\n",
-    "        distance_z=defect[\"distance_z\"],\n",
-    "        use_cartesian_coordinates=defect[\"use_cartesian_coordinates\"]\n",
-    "    ) for defect in DEFECT_CONFIGS\n",
-    "]"
-   ],
-   "id": "3727ba76ad5101c0",
-   "outputs": [],
-   "execution_count": null
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "### 2.2. Create the adatom"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "489b51f0ee122c48"
-  },
   {
    "cell_type": "code",
    "source": [
-    "from mat3ra.made.tools.build.defect import create_defects\n",
+    "from mat3ra.made.tools.build.defect.adatom.helpers import create_multiple_adatom_defects\n",
     "\n",
-    "slab_with_adatom = create_defects(defect_configurations)"
+    "slab_with_adatom = create_multiple_adatom_defects(\n",
+    "    slab=slab,\n",
+    "    defect_dicts=DEFECT_CONFIGS,\n",
+    "    placement_method=PLACEMENT_METHOD.value,\n",
+    ")"
    ],
    "metadata": {
     "collapsed": false
@@ -226,9 +199,7 @@
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "## 3. Visualize the Slabs with Adatom"
-   ],
+   "source": "## 3. Visualize the Slab with Adatom",
    "metadata": {
     "collapsed": false
    },
@@ -240,10 +211,12 @@
    "source": [
     "from utils.visualize import visualize_materials as visualize\n",
     "\n",
-    "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"}],\n",
-    "          viewer=\"wave\"\n",
-    "          )"
+    "visualize([\n",
+    "    {\"material\": slab, \"title\": \"Original material\"},\n",
+    "    {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"}\n",
+    "],\n",
+    "    viewer=\"wave\"\n",
+    ")"
    ],
    "id": "256b07fb2dd39ae2",
    "outputs": [],

other/materials_designer/create_cluster_custom_shape.ipynb

@@ -82,8 +82,8 @@
    "source": [
     "RADIUS = 0.3  # in crystal units\n",
     "VACUUM = 10.0  # in Angstroms on each side\n",
-    "SUPERCELL_SIZE = 10  # in crystal units\n",
     "Z_ORIENTATION = (0, 0, 1)  # Miller indices of the slab orientation along the z-axis for the cluster\n",
+    "USE_CARTESIAN_COORDINATES = False\n",
     "NAME = \"Icosahedron\"  # Name of the cluster"
    ],
    "metadata": {
@@ -115,7 +115,7 @@
     "class CustomCoordinateCondition(CoordinateCondition):\n",
     "    \"\"\"Creates a regular polyhedron shape using SciPy's ConvexHull\"\"\"\n",
     "    radius: float = 1\n",
-    "    center: List[float] = [0.5, 0.5, 0.5]\n",
+    "    center_coordinate: List[float] = [0.5, 0.5, 0.5]\n",
     "\n",
     "    @property\n",
     "    def _hull_planes(self):\n",
@@ -129,12 +129,12 @@
     "\n",
     "    def condition(self, coordinate: List[float]) -> bool:\n",
     "        \"\"\"Returns True if point is inside the polyhedron\"\"\"\n",
-    "        point = np.array(coordinate) - self.center\n",
+    "        point = np.array(coordinate) - self.center_coordinate\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"
+    "condition = CustomCoordinateCondition(radius=RADIUS)"
    ],
    "metadata": {
     "collapsed": false
@@ -181,13 +181,9 @@
   {
    "cell_type": "code",
    "source": [
-    "from mat3ra.made.tools.build.nanoparticle import SlabBasedNanoparticleConfiguration\n",
-    "\n",
-    "config = SlabBasedNanoparticleConfiguration(\n",
-    "    material=materials[0],\n",
-    "    condition_builder=condition,\n",
-    "    supercell_size=SUPERCELL_SIZE,\n",
-    ")"
+    "from mat3ra.made.tools.build.nanoparticle.helpers import create_nanoparticle_from_material\n",
+    "material = materials[0]\n",
+    "cluster = create_nanoparticle_from_material(material=material,condition=condition, orientation_z=Z_ORIENTATION, vacuum_padding=VACUUM, use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)"
    ],
    "metadata": {
     "collapsed": false
@@ -196,58 +192,6 @@
    "outputs": [],
    "execution_count": null
   },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "#### 2.2. Create the cluster"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "10799f3efede924d"
-  },
-  {
-   "cell_type": "code",
-   "source": [
-    "from mat3ra.made.tools.build.nanoparticle import create_nanoparticle\n",
-    "\n",
-    "cluster = create_nanoparticle(config)"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "a990fa35742d7269",
-   "outputs": [],
-   "execution_count": null
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "### 2.2. Set lattice to Cubic"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "a01018588e6e55fc"
-  },
-  {
-   "cell_type": "code",
-   "source": [
-    "from mat3ra.made.lattice import Lattice\n",
-    "\n",
-    "current_vector_1, current_vector_2, current_vector_3 = cluster.lattice.vectors\n",
-    "cubic_vector_1 = [current_vector_1[0], 0, 0]\n",
-    "cubic_vector_2 = [0, current_vector_2[1], 0]\n",
-    "cubic_vector_3 = [0, 0, current_vector_3[2]]\n",
-    "cluster.lattice = Lattice.from_vectors_array([cubic_vector_1, cubic_vector_2, cubic_vector_3], type=\"CUB\")"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "4f78c4743b370c3b",
-   "outputs": [],
-   "execution_count": null
-  },
   {
    "cell_type": "markdown",
    "source": [