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VsevolodXVsevolodX
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Merge pull request #233 from Exabyte-io/feature/SOF-7676
feature/SOF-7676
2 parents 217d20f + c09a222 commit ac9eee3

30 files changed

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lines changed

‎.gitignore

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

‎other/materials_designer/create_adatom_defect.ipynb

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

‎other/materials_designer/create_cluster_custom_shape.ipynb

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@@ -82,8 +82,8 @@
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"source": [
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"RADIUS = 0.3 # in crystal units\n",
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"VACUUM = 10.0 # in Angstroms on each side\n",
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"SUPERCELL_SIZE = 10 # in crystal units\n",
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"Z_ORIENTATION = (0, 0, 1) # Miller indices of the slab orientation along the z-axis for the cluster\n",
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"USE_CARTESIAN_COORDINATES = False\n",
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"NAME = \"Icosahedron\" # Name of the cluster"
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],
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"metadata": {
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"class CustomCoordinateCondition(CoordinateCondition):\n",
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" \"\"\"Creates a regular polyhedron shape using SciPy's ConvexHull\"\"\"\n",
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" radius: float = 1\n",
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" center: List[float] = [0.5, 0.5, 0.5]\n",
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" center_coordinate: List[float] = [0.5, 0.5, 0.5]\n",
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"\n",
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" @property\n",
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" def _hull_planes(self):\n",
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"\n",
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" def condition(self, coordinate: List[float]) -> bool:\n",
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" \"\"\"Returns True if point is inside the polyhedron\"\"\"\n",
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" point = np.array(coordinate) - self.center\n",
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" point = np.array(coordinate) - self.center_coordinate\n",
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" return all(np.dot(plane[:3], point) + plane[3] <= 0\n",
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" for plane in self._hull_planes)\n",
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"\n",
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" \n",
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"condition = CustomCoordinateCondition(radius=RADIUS).condition"
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"condition = CustomCoordinateCondition(radius=RADIUS)"
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],
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"metadata": {
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"collapsed": false
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{
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"cell_type": "code",
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"source": [
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"from mat3ra.made.tools.build.nanoparticle import SlabBasedNanoparticleConfiguration\n",
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"\n",
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"config = SlabBasedNanoparticleConfiguration(\n",
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" material=materials[0],\n",
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" condition_builder=condition,\n",
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" supercell_size=SUPERCELL_SIZE,\n",
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")"
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"from mat3ra.made.tools.build.nanoparticle.helpers import create_nanoparticle_from_material\n",
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"material = materials[0]\n",
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"cluster = create_nanoparticle_from_material(material=material,condition=condition, orientation_z=Z_ORIENTATION, vacuum_padding=VACUUM, use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)"
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],
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"metadata": {
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"collapsed": false
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"outputs": [],
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"#### 2.2. Create the cluster"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "10799f3efede924d"
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},
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{
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"cell_type": "code",
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"source": [
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"from mat3ra.made.tools.build.nanoparticle import create_nanoparticle\n",
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"\n",
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"cluster = create_nanoparticle(config)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a990fa35742d7269",
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"outputs": [],
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 2.2. Set lattice to Cubic"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a01018588e6e55fc"
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},
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{
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"cell_type": "code",
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"source": [
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"from mat3ra.made.lattice import Lattice\n",
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"\n",
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"current_vector_1, current_vector_2, current_vector_3 = cluster.lattice.vectors\n",
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"cubic_vector_1 = [current_vector_1[0], 0, 0]\n",
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"cubic_vector_2 = [0, current_vector_2[1], 0]\n",
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"cubic_vector_3 = [0, 0, current_vector_3[2]]\n",
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"cluster.lattice = Lattice.from_vectors_array([cubic_vector_1, cubic_vector_2, cubic_vector_3], type=\"CUB\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "4f78c4743b370c3b",
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"outputs": [],
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [

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